- a() - Static method in class org.biojava.bio.seq.DNATools
-
- a() - Static method in class org.biojava.bio.seq.NucleotideTools
-
- a() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Alanine
- a() - Static method in class org.biojava.bio.seq.RNATools
-
- A_THALIANA - Static variable in interface org.biojava.bio.program.homologene.Taxon
-
- AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
AA indicates that a sequence contains AA (amino
acid) symbols.
- AAindex - Class in org.biojava.bio.proteomics.aaindex
-
Symbol property table based on the Amino Acid Index Database.
- AAindex(String) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindex
-
Initializes the AAindex symbol property table.
- AAindexStreamReader - Class in org.biojava.bio.proteomics.aaindex
-
Iterator over
AAindex objects that
are stored in a stream in the AAindex1 file format.
- AAindexStreamReader(Reader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
-
Initializes the iterator.
- AAindexStreamReader(BufferedReader) - Constructor for class org.biojava.bio.proteomics.aaindex.AAindexStreamReader
-
Initializes the iterator.
- ABBREV_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- abbreviation - Variable in class org.biojava.bibliography.BiblioJournal
-
An abbreviation of the journal title.
- ABI_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
-
The magic number for ABIF files.
- ABIFChromatogram - Class in org.biojava.bio.program.abi
-
An implementation of
Chromatogram to
encapulsulate chromatogram data extracted from the files produced by ABI
sequencers, such as the the 377 and the 3700.
- ABIFChromatogram() - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram
-
- ABIFChromatogram.Parser - Class in org.biojava.bio.program.abi
-
An extension of
ABIFParser that reads the particular fields from
the ABIF that contain the chromatogram data and initializes the fields
in its enclosing
ABIFChromatogram instance.
- ABIFChromatogram.Parser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
-
- ABIFChromatogram.Parser(File) - Constructor for class org.biojava.bio.program.abi.ABIFChromatogram.Parser
-
- ABIFParser - Class in org.biojava.bio.program.abi
-
A general base parser for files produced by ABI software.
- ABIFParser(File) - Constructor for class org.biojava.bio.program.abi.ABIFParser
-
Creates a new ABIFParser for a file.
- ABIFParser(InputStream) - Constructor for class org.biojava.bio.program.abi.ABIFParser
-
Creates a new ABIFParser for an input stream.
- ABIFParser(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser
-
- ABIFParser.DataAccess - Interface in org.biojava.bio.program.abi
-
Concatenation of the
Seekable and
DataInput interfaces.
- ABIFParser.TaggedDataRecord - Class in org.biojava.bio.program.abi
-
An aggregate immutable type for an ABIF tagged data record.
- ABIFParser.TaggedDataRecord(ABIFParser.DataAccess) - Constructor for class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
-
Creates a new TaggedDataRecord from the next 28 bytes of
din.
- ABITools - Class in org.biojava.bio.program.abi
-
Useful functionality for working with fasta files where the quality of the
DNA is encoded as upper and lower case DNA characters.
- ABITools() - Constructor for class org.biojava.bio.program.abi.ABITools
-
- ABITrace - Class in org.biojava.bio.program.abi
-
Title: ABITrace
ABITrace is a class for managing ABI file information,
it is capable of opening an ABI file and storing
the most important fields, which can be recalled as simple java types.
- ABITrace(File) - Constructor for class org.biojava.bio.program.abi.ABITrace
-
The File constructor opens a local ABI file and parses the content.
- ABITrace(URL) - Constructor for class org.biojava.bio.program.abi.ABITrace
-
The URL constructor opens an ABI file from any URL.
- ABITrace(byte[]) - Constructor for class org.biojava.bio.program.abi.ABITrace
-
The byte[] constructor parses an ABI file represented as a byte array.
- AbiTraceRenderer - Class in org.biojava.bio.gui.sequence
-
Renders an ABI trace file as a chromatogram graph.
- AbiTraceRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- ABORT_PARSING - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
-
- AbstractAlignmentStyler - Class in org.biojava.bio.program.blast2html
-
Abstract implementation of AlignmentStyler, contains
utility methods for generating a set of HTML styles from a list of
RGB colours.
- AbstractAlignmentStyler() - Constructor for class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
- AbstractAlphabet - Class in org.biojava.bio.symbol
-
An abstract implementation of Alphabet.
- AbstractAlphabet() - Constructor for class org.biojava.bio.symbol.AbstractAlphabet
-
- AbstractAnnotation - Class in org.biojava.bio
-
A utility class to ease the problem of implementing an Annotation to that of
providing an apropreate implementation of Map.
- AbstractAnnotation() - Constructor for class org.biojava.bio.AbstractAnnotation
-
Protected no-args constructor intended for sub-classes.
- AbstractAnnotation(Annotation) - Constructor for class org.biojava.bio.AbstractAnnotation
-
Copy-constructor.
- AbstractAnnotation(Map) - Constructor for class org.biojava.bio.AbstractAnnotation
-
Create a new Annotation by copying the key-value pairs from a map.
- AbstractBeadRenderer - Class in org.biojava.bio.gui.sequence
-
AbstractBeadRenderer is a an abstract base class
for the creation of FeatureRenderers which use a
'string of beads' metaphor for displaying features.
- AbstractBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Creates a new AbstractBeadRenderer with no
delegates.
- AbstractBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Creates a new AbstractBeadRenderer object.
- AbstractBean - Class in org.biojava.bio.structure.io.mmcif.model
-
a generic class that implements the toString method for a bean
- AbstractBean() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AbstractBean
-
- AbstractBioEntryDB - Class in org.biojavax.bio.db
-
An abstract implementation of BioEntryDB that provides the getBioEntryIterator
method.
- AbstractBioEntryDB() - Constructor for class org.biojavax.bio.db.AbstractBioEntryDB
-
- AbstractChangeable - Class in org.biojava.utils
-
Useful base-class for objects implementing Changeable
- AbstractChangeable() - Constructor for class org.biojava.utils.AbstractChangeable
-
- AbstractChromatogram - Class in org.biojava.bio.chromatogram
-
- AbstractChromatogram() - Constructor for class org.biojava.bio.chromatogram.AbstractChromatogram
-
Create a new AbstractChromatogram.
- AbstractCrossOverFunction - Class in org.biojavax.ga.functions
-
Abstract implementation of CrossOverFunction.
- AbstractCrossOverFunction() - Constructor for class org.biojavax.ga.functions.AbstractCrossOverFunction
-
- AbstractDistribution - Class in org.biojava.bio.dist
-
An abstract implementation of Distribution.
- AbstractDistribution() - Constructor for class org.biojava.bio.dist.AbstractDistribution
-
- AbstractFeatureHolder - Class in org.biojava.bio.seq
-
An abstract implementation of FeatureHolder.
- AbstractFeatureHolder() - Constructor for class org.biojava.bio.seq.AbstractFeatureHolder
-
- AbstractGeneticAlgorithm - Class in org.biojavax.ga.impl
-
Base class from which most implementations of GeneticAlgorithm will inherit.
- AbstractGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- AbstractLocation - Class in org.biojava.bio.symbol
-
An abstract implementation of Location.
- AbstractLocation() - Constructor for class org.biojava.bio.symbol.AbstractLocation
-
- AbstractLocationDecorator - Class in org.biojava.bio.symbol
-
Abstract Location decorator (wrapper).
- AbstractLocationDecorator(Location) - Constructor for class org.biojava.bio.symbol.AbstractLocationDecorator
-
Construct a new decorator wrapping the specified Location.
- AbstractManyToOneTranslationTable - Class in org.biojava.bio.symbol
-
an abstract class implementing basic functionality
of a translation table that translates Symbols from
one Alphabet to another.
- AbstractManyToOneTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
-
- AbstractMatrixPairDPCursor - Class in org.biojava.bio.dp.twohead
-
- AbstractMatrixPairDPCursor(SymbolList, SymbolList, int, int, int, int, PairDPMatrix, EmissionCache) - Constructor for class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
-
- AbstractMutationFunction - Class in org.biojavax.ga.functions
-
Abstract implementation of MutationFunction all custom
implementations should inherit from here.
- AbstractMutationFunction() - Constructor for class org.biojavax.ga.functions.AbstractMutationFunction
-
- AbstractOrderNDistribution - Class in org.biojava.bio.dist
-
Simple base class for OrderNDistributions.
- AbstractOrderNDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.AbstractOrderNDistribution
-
Construct a new NthOrderDistribution.
- AbstractOrganism - Class in org.biojavax.ga.impl
-
Abstract implementation of Organism.
- AbstractOrganism() - Constructor for class org.biojavax.ga.impl.AbstractOrganism
-
- AbstractOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.AbstractOrganism
-
- AbstractOrthologueSet - Class in org.biojava.bio.program.homologene
-
- AbstractOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthologueSet
-
- AbstractOrthoPairCollection - Class in org.biojava.bio.program.homologene
-
An abstract implementation of the OrthoPairCollection
interface.
- AbstractOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
-
- AbstractOrthoPairSet - Class in org.biojava.bio.program.homologene
-
represents the Homologene Group.
- AbstractOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.AbstractOrthoPairSet
-
- AbstractPeptideDigestRenderer - Class in org.biojava.bio.gui.sequence
-
A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that
they do not overlap in the display.
- AbstractPeptideDigestRenderer() - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- AbstractPeptideDigestRenderer(FeatureSource) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- AbstractPeptideDigestRenderer(FeatureSource, FeatureFilter, int) - Constructor for class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- AbstractPopulation - Class in org.biojavax.ga.impl
-
Most Population implementations will want to inherit from here.
- AbstractPopulation() - Constructor for class org.biojavax.ga.impl.AbstractPopulation
-
- AbstractPopulation(String) - Constructor for class org.biojavax.ga.impl.AbstractPopulation
-
- AbstractRangeLocation - Class in org.biojava.bio.symbol
-
Base class for simple contiguous Location implementations.
- AbstractRangeLocation() - Constructor for class org.biojava.bio.symbol.AbstractRangeLocation
-
- AbstractReversibleTranslationTable - Class in org.biojava.bio.symbol
-
an abstract class implementing basic functionality
of a translation table that translates Symbols from
one Alphabet to another.
- AbstractReversibleTranslationTable() - Constructor for class org.biojava.bio.symbol.AbstractReversibleTranslationTable
-
- AbstractRichSequenceDB - Class in org.biojavax.bio.db
-
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator
method.
- AbstractRichSequenceDB() - Constructor for class org.biojavax.bio.db.AbstractRichSequenceDB
-
- AbstractSequenceDB - Class in org.biojava.bio.seq.db
-
An abstract implementation of SequenceDB that provides the sequenceIterator
method.
- AbstractSequenceDB() - Constructor for class org.biojava.bio.seq.db.AbstractSequenceDB
-
- AbstractSVMClassifierModel - Class in org.biojava.stats.svm
-
Abstract implementation of SVMClassifierModel.
- AbstractSVMClassifierModel() - Constructor for class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- AbstractSVMTarget - Class in org.biojava.stats.svm
-
An abstract implementation of an SVMModel.
- AbstractSVMTarget() - Constructor for class org.biojava.stats.svm.AbstractSVMTarget
-
- AbstractSymbol - Class in org.biojava.bio.symbol
-
The base-class for Symbol implementations.
- AbstractSymbol() - Constructor for class org.biojava.bio.symbol.AbstractSymbol
-
- AbstractSymbolList - Class in org.biojava.bio.symbol
-
Abstract helper implementation of the SymbolList core interface.
- AbstractSymbolList() - Constructor for class org.biojava.bio.symbol.AbstractSymbolList
-
- AbstractSymbolList.EditScreener - Class in org.biojava.bio.symbol
-
This adapter screens all edit events to see if they overlap with a window
of interest.
- AbstractSymbolList.EditScreener(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
-
- AbstractSymbolList.EditTranslater - Class in org.biojava.bio.symbol
-
This translates edit events that fall within a window into window co-ordinates.
- AbstractSymbolList.EditTranslater(Object, ChangeSupport, int, int) - Constructor for class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
-
- AbstractTaxon - Class in org.biojava.bio.taxa
-
- AbstractTaxon() - Constructor for class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- AbstractTaxon(String, String) - Constructor for class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- AbstractTerm - Class in org.biojava.ontology
-
Abstract implementation of term
This provides basic change-forwarding functionality from
the annotation and ontology properties.
- AbstractTerm() - Constructor for class org.biojava.ontology.AbstractTerm
-
- AbstractTrainer - Class in org.biojava.bio.dp
-
An abstract implementation of TrainingAlgorithm that provides a framework
for plugging in per-cycle code for parameter optimization.
- AbstractTrainer(DP) - Constructor for class org.biojava.bio.dp.AbstractTrainer
-
- AbstractTrainer() - Constructor for class org.biojava.bio.dp.AbstractTrainer
-
- abstractType - Variable in class org.biojava.bibliography.BiblioDescription
-
- AbstractULAlignment - Class in org.biojava.bio.alignment
-
- AbstractULAlignment() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment
-
- AbstractULAlignment.LeftRightLocationComparator - Class in org.biojava.bio.alignment
-
Orders by location left to right.
- AbstractULAlignment.LeftRightLocationComparator() - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
-
- AbstractULAlignment.SubULAlignment - Class in org.biojava.bio.alignment
-
- AbstractULAlignment.SubULAlignment(Set, Location) - Constructor for class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- AbstractWrapper - Class in org.biojava.bio.program.tagvalue
-
An abstract TagValueWrapper that does nothing!
- AbstractWrapper() - Constructor for class org.biojava.bio.program.tagvalue.AbstractWrapper
-
- ACC_VERSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- accept(Object) - Method in interface org.biojava.bio.CollectionConstraint
-
accept returns true if the value fulfills the
constraint.
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
-
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.And
-
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Contains
-
- accept(Object) - Method in class org.biojava.bio.CollectionConstraint.Or
-
- accept(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFRecordFilter
-
Return whether or not to accept record.
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
-
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
- accept(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- accept(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueFilter
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.AcceptAll
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.And
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByAccession
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByHomologeneID
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByLocusID
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxon
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTaxonID
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.ByTitle
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Not
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Or
-
- accept(Orthologue) - Method in class org.biojava.bio.program.homologene.OrthologueFilter.Xor
-
- accept(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairFilter
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.AcceptAll
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.And
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMaxIdentity
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByMinIdentity
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.ByRef
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.BySimilarityType
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Not
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Or
-
- accept(OrthoPair) - Method in class org.biojava.bio.program.homologene.OrthoPairFilter.Xor
-
- accept(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairSetFilter
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AcceptAll
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.AllPairsInCollection
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.And
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByMinIdentity
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.ByTaxon
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Not
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Or
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.SomePairsInCollection
-
- accept(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.OrthoPairSetFilter.Xor
-
- accept(Object) - Method in interface org.biojava.bio.PropertyConstraint
-
accept returns true if the value fulfills the
constraint.
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.And
-
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
-
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ByClass
-
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
-
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
-
- accept(Object) - Method in class org.biojava.bio.PropertyConstraint.Or
-
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
-
- accept() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
-
returns a TriState indicating the current outcome
of evaluating this filter.
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.And
-
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Not
-
- accept() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.Or
-
- accept(Object) - Method in interface org.biojava.bio.search.FilterTest
-
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.Equals
-
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.FindRegex
-
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.GreaterThan
-
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.LessThan
-
- accept(Object) - Method in class org.biojava.bio.search.FilterTest.MatchRegex
-
- accept(Feature) - Method in interface org.biojava.bio.seq.FeatureFilter
-
This method determines whether a feature is to be accepted.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.And
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
-
Accept a Feature if it is an instance of
SimilarityPairFeature and its score is <= filter's minimum
score and >= filter's maximum score.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.BySource
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ByType
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
-
Returns true if the feature is within this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
-
Accept the Feature if it is an instance of FramedFeature and matches
the value of getFrame().
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Not
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.Or
-
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
-
Returns true if the feature overlaps this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
-
Returns true if the feature is within this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
-
Returns true if the feature overlaps this filter's location.
- accept(Feature) - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
-
Accept the Feature if it is an instance of StrandedFeature and matches
the value of getStrand().
- accept(PDBHeader) - Method in interface org.biojava.bio.structure.server.PDBFilter
-
return true if this PDBHeader is passing this filter.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
-
Returns true if the feature has a matching source property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
Returns true if the feature has a matching source property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
Returns true if the feature overlaps this filter's location.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
Returns true if the feature has a matching type property.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
Returns true if the feature is within this filter's location.
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
-
- accept(Feature) - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
Returns true if the feature overlaps this filter's location.
- ACCEPT_ALL - Static variable in interface org.biojava.bio.program.gff.GFFRecordFilter
-
A GFFRecordFilter that accepts everything.
- ACCESSION - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
- ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- accessionNumber() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the accession number of the AAindex entry.
- AcnumHitReader - Class in org.biojava.bio.seq.db.emblcd
-
AcnumHitReader reads the "acnum.hit" file of an EMBL
CD-ROM format binary index.
- AcnumHitReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumHitReader
-
Creates a new AcnumHitReader.
- AcnumTrgReader - Class in org.biojava.bio.seq.db.emblcd
-
AcnumTrgReader reads the "acnum.trg" file of an EMBL
CD-ROM format binary index.
- AcnumTrgReader(InputStream) - Constructor for class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
-
Creates a new AcnumTrgReader.
- ACRONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
Use this to define acronyms for things.
- ACRONYM - Static variable in interface org.biojavax.Namespace
-
- actionPerformed(ActionEvent) - Method in class org.biojava.bio.structure.gui.RasmolCommandListener
-
- activityFailed(Object, Exception) - Method in interface org.biojava.utils.ActivityListener
-
Notification of errors behind the scenes.
- ActivityListener - Interface in org.biojava.utils
-
Interface for object which monitor long-running activities.
- activityProgress(Object, int, int) - Static method in class org.biojava.bio.program.das.DAS
-
- activityProgress(Object, int, int) - Method in interface org.biojava.utils.ActivityListener
-
Estimated progress of an activity.
- adapter - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
-
- add(String) - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Add a comment to the end of this set.
- add(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Add a GFFRecord to the end of this set.
- add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
-
- add(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
-
- add(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
-
- add(int, int, int, int) - Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- add(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
add two atoms ( a + b).
- add(Object) - Method in class org.biojava.utils.FileAsList
-
- add(Object) - Method in class org.biojava.utils.MergingSet
-
- add(Object) - Method in class org.biojava.utils.SmallSet
-
- add(Object) - Method in class org.biojavax.ga.util.WeightedSet
-
Adds a new Object with a weight of zero.
- ADD_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
-
- addActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
-
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- addAlignmentPositionListener(AlignmentPositionListener) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
-
- addAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
-
- addAllFeatures(Sequence, FeatureHolder) - Static method in class org.biojava.bio.seq.SequenceTools
-
Add features to a sequence that contain the same information as all
those in a feature holder.
- addAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
-
Add a new Annotation to to the end of the list to be merged.
- addAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
Add a DB to be merged in this view.
- addAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
-
- addAtom(Atom) - Method in interface org.biojava.bio.structure.Group
-
add an atom to this group.
- addAtom(Atom) - Method in class org.biojava.bio.structure.HetatomImpl
-
add an atom to this group.
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
-
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- addBioEntry(BioEntry) - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Adds a sequence to the database.
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- addBioEntry(BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
Add a BioEntry, the name of the BioEntry will be used as the ID
- addBioEntry(String, BioEntry) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
- addBlock(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
Add a "Block" Annotation.
- addBottomConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
-
Add a configuration as the most default place to look.
- addChain(Chain) - Method in class org.biojava.bio.structure.Compound
-
- addChain(Chain) - Method in interface org.biojava.bio.structure.Structure
-
add a new chain.
- addChain(Chain, int) - Method in interface org.biojava.bio.structure.Structure
-
add a new chain, if several models are available.
- addChain(Chain) - Method in class org.biojava.bio.structure.StructureImpl
-
add a new chain.
- addChain(Chain, int) - Method in class org.biojava.bio.structure.StructureImpl
-
add a new chain, if several models are available.
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addChangeListener adds a listener for all types of
change.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addChangeListener adds a listener for specific
types of change.
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addChangeListener adds a listener for all types of
change.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addChangeListener adds a listener for specific
types of change.
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
-
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- addChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- addChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Add a ChangeListener to a projected feature.
- addChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- addChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
-
- addChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
-
Deprecated.
use addChangeListener(cl, ChangeType.UNKNOWN)
- addChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
-
Add a listener that will be informed of changes of a given type.
- addChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
-
Add a listener that will be informed of all changes.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
-
Add a listener that will be informed of changes of a given type (and it's subtypes)
- addChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
-
- addChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Add a listener that will be informed of all changes.
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Add a listener that will be informed of changes of a given type.
- addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- addChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- addChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- addChemComp(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
add a new component to the dictionary
- addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- addChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.
Add a taxon as a child to a parent.
- addChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- addCluster(UnigeneCluster) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
-
Add a cluster to a database.
- addComment(Comment) - Method in interface org.biojavax.bio.BioEntry
-
Adds a comment instance to this bioentry.
- addComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a comment instance to this bioentry.
- addComponentSequence(ComponentFeature.Template) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
-
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainer
-
Registers that sym was counted in this state.
- addCount(Distribution, Symbol, double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Registers that sym was counted in this state.
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
-
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
-
- addCount(DistributionTrainerContext, AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
-
Deprecated.
- addCount(Distribution, Symbol, double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- addCount(State, State, double) - Method in interface org.biojava.bio.dp.TransitionTrainer
-
Add 'count' to the transition from->to.
- addDasURL(URL) - Method in class org.biojava.bio.program.das.DAS
-
- addDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
Add a distributed data source.
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
-
- addDbId(AGAVEDbId) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdCallbackItf
-
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
-
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
-
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
-
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
-
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
-
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
add @param id
- addDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
-
- addDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
-
Adds a descriptor.
- addDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Adds a descriptor.
- addDetailHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Extend this FeatureSetHandler to delegate certain detail elements
to the specified handler type.
- addDigestFeatures() - Method in class org.biojava.bio.proteomics.Digest
-
Adds peptides as features to the Sequence in this class.
- addElementId(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEEvidenceCallbackItf
-
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
-
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
-
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
-
- addElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
-
- addEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
-
addEnzyme adds an enzyme to be searched for in the
Sequence.
- addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
-
Add a silent optimisable transition to instance.
- addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
-
- addEpsilonTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
-
- addExtension(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- addExtension(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
define supported file extensions
compressed extensions .Z,.gz do not need to be specified
they are dealt with automatically.
- addExtension(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
add a known File extension.
- addFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
Add a feature to the featureholder
- addFeatureHandler(ElementRecognizer, XFFPartHandlerFactory) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Extend this FeatureSetHandler to delegate certain feature elements
to the specified handler type.
- addFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
-
Add an extra FeatureHolder to the set of FeatureHolders which
are merged.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- addFeatureProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of a feature property.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
Add an annotation-bundle entry to the feature.
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- addFeatureProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Null implementation
- addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- addFeatureProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of a feature property.
- addFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
-
Adds a relationship to this feature holder.
- addFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Adds a relationship to this feature holder.
- addFeatureToSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- addFile(File) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
Add sequences from a file to the sequence database.
- addFile(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- addFilterAndGlyph(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- addForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
-
- addGapInSource(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add a gap at pos within the source coordinates.
- addGapInSource(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- addGapInView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add a single gap at pos within the view coordintates.
- addGapInView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- addGapsInSource(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add length gaps at pos within the source coordinates.
- addGapsInSource(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- addGapsInView(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Add length gaps at pos within the view coordinates.
- addGapsInView(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- addGroup(Group) - Method in interface org.biojava.bio.structure.Chain
-
add a group to the list of ATOM record group of this chain.
- addGroup(Group) - Method in class org.biojava.bio.structure.ChainImpl
-
add a group to the list of ATOM record group of this chain.
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
-
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
-
- addHandler(ElementRecognizer, StAXHandlerFactory) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
-
Adds a feature to the Handler attribute of the StAXFeatureHandler object
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- addHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
-
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
-
- addHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
-
The addHitProperty method adds a key/value pair
containing some property of a particular hit.
- addHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- addHotSpot(ImageMap.HotSpot) - Method in interface org.biojava.bio.gui.sequence.ImageMap
-
addHotSpot adds a hotspot to the map.
- addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ClientSide
-
- addHotSpot(ImageMap.HotSpot) - Method in class org.biojava.bio.gui.sequence.ImageMap.ServerSide
-
- addIdAlias(AGAVEIdAlias) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
-
- addIdAlias(AGAVEIdAlias) - Method in interface org.biojava.bio.seq.io.agave.AGAVEIdAliasCallbackItf
-
- addImplementation(Class, Class) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
-
Install a new mapping from a class of Feature.Template to
a class of Feature implementations.
- addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- addItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
-
- addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- addItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- addItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- addItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
-
- addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- addItemAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- addItemAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- addItemTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
-
- addItemTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- addItemTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
-
- addKey(String, int) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
addKey adds a new identifier namespace.
- addKeyPath(String, Object[]) - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
Add a key and a path to that key in the tag-value hierachy.
- addLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Add a piece of text to this renderer's label
- addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
-
Add a silent persistent transition to instance.
- addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in interface org.biojava.utils.automata.NfaBuilder
-
- addLambdaTransition(FiniteAutomaton.Node, FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.NfaSubModel
-
- addListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
-
add a ChangeListener associated with given key.
- addListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
-
- addMapPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
-
- addMatrix(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
add Annotation of DAS alignment "matrix" type.
- addMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
-
Add a MMcifConsumer that listens to even being triggered by the parser and processes the data into a backend provided by the Consumer.
- addMMcifConsumer(MMcifConsumer) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- addModel(List<Chain>) - Method in interface org.biojava.bio.structure.Structure
-
add a new model.
- addModel(List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
-
add a new model.
- addName(Connection, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Adds a new name of the given nameClass to the taxon.
- addName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Adds the name to this taxon in the given name class.
- addName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Adds the name to this taxon in the given name class.
- addNeg(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
-
- addNode(boolean) - Method in class org.biojava.utils.automata.FiniteAutomaton
-
Add a node to the FA.
- addNode(boolean) - Method in interface org.biojava.utils.automata.NfaBuilder
-
- addNode(boolean) - Method in class org.biojava.utils.automata.NfaSubModel
-
- addNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
-
Adds a note to this annotation.
- addNote(Note) - Method in interface org.biojavax.RichAnnotation
-
Adds a note to this annotation.
- addNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
-
Adds a note to this annotation.
- addObject(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
add Annotation of DAS alignment "object" type.
- addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.ontology.obo.OboFileParser
-
- addOntology(Ontology) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- addOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- addOrganism(Organism) - Method in interface org.biojavax.ga.Population
-
Adds an Organism to the Population
- addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- addOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
-
- addOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- addOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- addOrganisms(Population) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- addOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
-
Adds several organisms to the population
- addOrganisms(Set) - Method in interface org.biojavax.ga.Population
-
Adds several organisms to the population
- addOrganisms(Population) - Method in interface org.biojavax.ga.Population
-
Adds the residents of one population to this one
- addOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
-
Add an orthologue to the set.
- addOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
-
- addOrthologueProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
add a property to the current Orthologue
- addOrthologueProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- addOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
adds a specified OrthoPair relationship
to this group.
- addOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- addOrthoPairProperty(String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
add a property to the current OrthoPair
- addOrthoPairProperty(String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
-
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
-
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
- addParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
-
Adds a parse error listener to the list of listeners.
- addPattern(String) - Method in class org.biojava.utils.automata.PatternBlitz
-
add the specified regex to the patterns
used for searching.
- addPattern(String, boolean) - Method in class org.biojava.utils.regex.Search
-
add a search pattern to the searches to be conducted
by this object.
- addPattern(String, String, boolean) - Method in class org.biojava.utils.regex.Search
-
add a search pattern to the searches to be conducted
by this object.
- addPDBFilter(PDBFilter) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- addPDBFilter(PDBFilter) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- addPDBFilter(PDBFilter) - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
add a filter for PDB files.
- addPos(Object) - Method in class org.biojava.stats.svm.DiagonalAddKernel
-
- addPosition(AGAVEMapPosition) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- addProp(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- addProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
-
Add a value to the specified property slot.
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
-
- addProperty(AGAVEProperty) - Method in interface org.biojava.bio.seq.io.agave.AGAVEDbIdPropCallbackItf
-
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
-
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
-
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
-
- addProperty(AGAVEProperty) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
-
- addProperty(Annotation, Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
-
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
-
Deprecated.
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
-
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
-
- addPropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
-
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
-
- addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Adds a ranked cross reference to the existing set.
- addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a ranked cross reference to the existing set.
- addRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Adds a ranked cross reference to the existing set.
- addRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
-
Adds a ranked cross reference to the existing set.
- addRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
-
Adds a ranked docref instance to this bioentry.
- addRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a ranked docref instance to this bioentry.
- addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
-
- addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
-
- addRelatedAnnot(AGAVERelatedAnnot) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
-
- addRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
-
Adds a relation instance to this bioentry.
- addRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
-
Adds a relation instance to this bioentry.
- addRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
-
- addRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
addRenderer adds a renderer as a new track.
- addRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
addRenderer adds a renderer.
- addRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
-
- addRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
-
Add a repository to FeatureTypes.
- addRequest(Runnable) - Method in class org.biojava.utils.SimpleThreadPool
-
- addRequest(Runnable) - Method in interface org.biojava.utils.ThreadPool
-
addRequest requests that a Runnable
be scheduled to be run by one of the threads in the pool.
- addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- addRichSequence(RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
Add a sequence.
- addRichSequence(String, RichSequence) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- addRichSequence(RichSequence) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
-
Adds a sequence to the database.
- addScore(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
adds a "Score" Annotation.
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
-
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
-
- addSearchProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
-
The addSearchProperty method adds a key/value pair
containing some property of the overall search result.
- addSearchProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- addSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
-
Add a secondary key.
- addSequence(AlignmentElement) - Method in interface org.biojava.bio.alignment.ARAlignment
-
- addSequence(AlignmentElement) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
add a new a alignment usings a location to the reference sequence.
- addSequence(Sequence) - Method in class org.biojava.bio.program.das.DASSequenceDB
-
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
-
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
addSequence always throws a
ChangeVetoException as this implementation is
immutable.
- addSequence(String, Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
Add a sequence under a particular id.
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- addSequence(Sequence) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
-
Adds a sequence to the database.
- addSequence(Sequence) - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
Not supported, You can't add sequences to a WebDB!
- addSequence(Sequence) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- addSequence(String, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
Add a sequence into the tree.
- addSequence(Sequence) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
-
As this is a dummy implementation adding a sequenceDB doesn't do anything
- addSequenceDB(SequenceDBLite, Set) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
-
addSequenceDB adds a new SequenceDB
under its own identifier which will additionally be recognised
by the set of other identifiers.
- addSequenceDB(String, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
This method creates a new (and empty) HashSequenceDB with the
given name that will be accessible through this sequence db
installation through this name and all given other identifiers.
- addSequenceDB(SequenceDBLite, Set) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
addSequenceDB adds a new SequenceDB which will be
accessible via the name returned by its getName() method and
via all other given identifiers.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.EmblProcessor
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.FastaDescriptionLineParser
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.OrganismParser
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- addSequenceProperty(Object, Object) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of a sequence-wide property.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
Add an annotation-bundle entry to the sequence.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Notify the listener of a sequence-wide property.
- addSequenceProperty(Object, Object) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.
- addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- addSequenceProperty(Object, Object) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of a sequence-wide property.
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addSequenceViewerListener adds a listener for
mouse click SequenceViewerEvents.
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
-
- addSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addSequenceViewerListener adds a listener for
mouse click SequenceViewerEvents.
- addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addSequenceViewerMotionListener adds a listener for
mouse motion SequenceViewerEvents.
- addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
-
- addSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addSequenceViewerMotionListener adds a listener for
mouse motion SequenceViewerEvents.
- addSet(Set) - Method in class org.biojava.utils.MergingSet
-
- addSSBond(SSBond) - Method in interface org.biojava.bio.structure.Structure
-
add a single SSBond to this structure
- addSSBond(SSBond) - Method in class org.biojava.bio.structure.StructureImpl
-
add a single SSBond to this structure
- addState(State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Adds a state to the model.
- addState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- addState(State) - Method in class org.biojava.bio.dp.WMAsMM
-
- addStructureListener(StructureListener) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- addStructureListener(StructureListener) - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
- addStructureListener(StructureListener) - Method in interface org.biojava.bio.structure.server.StructureServer
-
- addStyle(String, String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
Add a colour style to this Styler.
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentAdapter
-
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentFilter
-
- addSubHitProperty(Object, Object) - Method in interface org.biojava.bio.search.SearchContentHandler
-
The addSubHitProperty method adds a key/value pair
containing some property of a particular subhit.
- addSubHitProperty(Object, Object) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- addSymbol(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- addSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
-
Adds a symbol to this alphabet.
- addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
Add a new Symbol to the end of this list.
- addSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
SoftMaskedAlphabets cannot add new Symbols.
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- addSymbolImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- addSymbolList(SymbolList, String, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ChunkedSymbolListFactory
-
tool to construct the SymbolList by adding Symbols.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
-
Deprecated.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of symbol data.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
-
does nothing for now.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleAssemblyBuilder
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SimpleSequenceBuilder
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SmartSequenceBuilder
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Prints out the sequences properties in order.
- addSymbols(SymbolList, int) - Method in class org.biojava.bio.symbol.SuffixTree
-
Add a count for all motifs with length of up to window
to this tree.
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- addSymbols(Alphabet, Symbol[], int, int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of symbol data.
- addSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- addSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- addSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- addSynonym(Object) - Method in interface org.biojava.ontology.Term
-
Add a synonym for this term.
- addSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
-
- addSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
-
- addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Add a synonym for this term.
- addSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Add a synonym for this term.
- addTable(SymbolPropertyTable) - Method in class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
-
Adds a symbol property table to the database.
- addTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
Add a tag to retain.
- addTitle(int, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
add title information to an Orthologue
(this is not in enclosed in the Orthologue element
because it comes completely separate in the Homologene
data files.
- addTitle(int, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- addToEnvironment(String, Object) - Method in class org.biojava.naming.ObdaContext
-
- addTopConfig(RegistryConfiguration) - Method in class org.biojava.directory.RegistryConfiguration.Composite
-
Add a configuration as the most authoritative place to look.
- addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
-
- addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in interface org.biojava.utils.automata.NfaBuilder
-
- addTransition(FiniteAutomaton.Node, FiniteAutomaton.Node, Symbol) - Method in class org.biojava.utils.automata.NfaSubModel
-
- addTypeWithParent(Class) - Method in class org.biojava.utils.walker.WalkerFactory
-
Register a type as being a 'container' class.
- addVariableModification(char, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
-
Add Variable modifications.
- addVariableModification(Symbol, double[]) - Method in class org.biojava.bio.proteomics.MassCalc
-
Add Variable modifications.
- addVector(Annotation) - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
add Annotation of DAS alignment "vector" type.
- addVector(Object, double, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- addVector(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- addXMLCollectionConstraintWriter(Class, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for the specified class of collection constraint
- addXMLCollectionConstraintWriter(CollectionConstraint, XMLAnnotationTypeWriter.XMLCollectionConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for a singleton property constraint.
- addXMLFilterWriter(Class, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
-
Add a writer for the specified class of filters
- addXMLFilterWriter(FeatureFilter, XMLFilterWriter.FilterWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
-
Add a writer for a singleton filter.
- addXMLPropertyConstraintWriter(Class, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for the specified class of property constraint
- addXMLPropertyConstraintWriter(PropertyConstraint, XMLAnnotationTypeWriter.XMLPropertyConstraintWriter) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Register a writer for a singleton property constraint.
- addXref(AGAVEXref) - Method in interface org.biojava.bio.seq.io.agave.AGAVEXrefCallbackItf
-
- addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
add @param xref
- addXref(AGAVEXref) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
-
- ADVANCE - Static variable in interface org.biojava.bio.dp.EmissionState
-
This signals that the advance array has been altered.
- advance() - Method in interface org.biojava.bio.dp.MarkovModel
-
The maximum advance for this model.
- advance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
Advance.
- advance() - Method in class org.biojava.bio.dp.onehead.SmallCursor
-
- advance() - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- advance() - Method in class org.biojava.bio.dp.WMAsMM
-
- affiliation - Variable in class org.biojava.bibliography.BiblioPerson
-
Their affiliation.
- Agave2AgaveAnnotFilter - Class in org.biojava.bio.seq.io.agave
-
Dumping the data from biojava with source of agave into agave format
- AGAVE_AGAVE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- AGAVE_ALT_IDS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAltIdsPropHandler
-
- AGAVE_ANNOTATIONS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAnnotationsHandler
-
- AGAVE_ASSEMBLY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEAssemblyHandler
-
- AGAVE_BIO_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
-
- AGAVE_BIO_SEQUENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
-
- AGAVE_CDS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
-
- AGAVE_CHROMOSOME_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
-
- AGAVE_CLASSIFICATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
-
- AGAVE_COMP_RESULT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
-
- AGAVE_COMPUTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
-
- AGAVE_CONTIG_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
-
- AGAVE_DBID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
-
- AGAVE_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
-
- AGAVE_ELEMENT_ID_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
-
- AGAVE_EVIDENCE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEEvidenceHandler
-
- AGAVE_EXONS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEExonsPropHandler
-
- AGAVE_FRAGMENT_ORDER_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
-
- AGAVE_FRAGMENT_ORIENTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
-
- AGAVE_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
-
- AGAVE_ID_ALIAS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
-
- AGAVE_KEYWORD_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
-
- AGAVE_MAP_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
-
- AGAVE_MAP_POSITION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
-
- AGAVE_MATCH_ALIGN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
-
- AGAVE_MATCH_DESC_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
-
- AGAVE_MATCH_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
-
- AGAVE_MRNA_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
-
- AGAVE_NOTE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
-
- AGAVE_PREDICTED_PROTEIN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
-
- AGAVE_QUALIFIER_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
-
- AGAVE_QUERY_REGION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
-
- AGAVE_RELATED_ANNOT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
-
- AGAVE_RESULT_GROUP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
-
- AGAVE_RESULT_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
-
- AGAVE_SCI_PROPERTY_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
-
- AGAVE_SEQ_FEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
-
- AGAVE_SEQ_LOCATION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
-
- AGAVE_SEQ_MAP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
-
- AGAVE_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
-
- AGAVE_TRANSCRIPT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
-
- AGAVE_UNORDERED_FRAGMENTS_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEUnorderedFragmentsHandler
-
- AGAVE_VIEW_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
-
- AGAVE_XREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropHandler
-
- AGAVE_XREF_PROP_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
-
- AGAVE_XREFS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEXrefsPropHandler
-
- AGAVEAltIdsPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with alternate sequence IDs
- AGAVEAnnotationsHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEAnnotFilter - Interface in org.biojava.bio.seq.io.agave
-
This interface defines mapping from BioJava into AGAVE format.
- AGAVEAnnotFilterFactory - Interface in org.biojava.bio.seq.io.agave
-
- AGAVEAssemblyHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEBioSeqCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- AGAVEBioSeqHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <bio_sequence> element
- AGAVEBioSequenceHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <bio_sequence> element
- AGAVECallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- AGAVECdsHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <cds> element
- AGAVEChromosomeCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- AGAVEChromosomeHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <chromosome> element
- AGAVEClassificationHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVECompResultHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEComputationHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEContigCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- AGAVEContigHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <contig> element
- AGAVEDbId - Class in org.biojava.bio.seq.io.agave
-
- AGAVEDbId() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- AGAVEDbIdCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
this is the interface implemented by several classes
- AGAVEDbIdPropCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
- AGAVEDbIdPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with database crossreferences
- AGAVEDescPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with database crossreferences
- AGAVEElementIdPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEEvidenceCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
- AGAVEEvidenceHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEExonsPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- AGAVEFragmentOrderHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEFragmentOrientationHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEGeneHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the root AGAVE element
modified for agave format
- AGAVEHandler() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEHandler
-
- AGAVEIdAlias - Class in org.biojava.bio.seq.io.agave
-
- AGAVEIdAliasCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
- AGAVEIdAliasPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEKeywordPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with AGAVE keywords
- AGAVEMapLocation - Class in org.biojava.bio.seq.io.agave
-
- AGAVEMapLocation() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- AGAVEMapLocationPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEMapPosition - Class in org.biojava.bio.seq.io.agave
-
- AGAVEMapPosition() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMapPosition
-
- AGAVEMapPositionPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEMatchAlignPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with match_align
- AGAVEMatchDescPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with match_desc
- AGAVEMatchRegion - Class in org.biojava.bio.seq.io.agave
-
match_region
- AGAVEMatchRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- AGAVEMatchRegionPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with match_region
- AGAVEMrnaHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <mrna> element
- AGAVENotePropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with note
- AGAVEPredictedProteinHandler - Class in org.biojava.bio.seq.io.agave
-
Handles the AGAVE <predicted_protein> element
- AGAVEProperty - Class in org.biojava.bio.seq.io.agave
-
- AGAVEProperty(String, String, String, String) - Constructor for class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- AGAVEQualifierPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEQueryRegion - Class in org.biojava.bio.seq.io.agave
-
- AGAVEQueryRegion() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- AGAVEQueryRegionPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVERelatedAnnot - Class in org.biojava.bio.seq.io.agave
-
- AGAVERelatedAnnot() - Constructor for class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
construct..
- AGAVERelatedAnnotPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEResultGroupHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVEResultPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
-
- AGAVESciPropertyPropHandler - Class in org.biojava.bio.seq.io.agave
-
sci_property
- AGAVESeqFeatureHandler - Class in org.biojava.bio.seq.io.agave
-
seq_feature
- AGAVESeqLocationPropHandler - Class in org.biojava.bio.seq.io.agave
-
seq_location
- AGAVESeqMapHandler - Class in org.biojava.bio.seq.io.agave
-
sequence_map
- AGAVESeqPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with sequence code
- AGAVETranscriptHandler - Class in org.biojava.bio.seq.io.agave
-
transcript
- AGAVEUnorderedFragmentsHandler - Class in org.biojava.bio.seq.io.agave
-
unordered_fragments
- AGAVEViewPropHandler - Class in org.biojava.bio.seq.io.agave
-
Moves view attributes into annotation properties.
- AgaveWriter - Class in org.biojava.bio.seq.io.agave
-
Writes Sequence into AGAVE XML document.
- AgaveWriter() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
-
Default constructor uses generic annotation to attribute mapping.
- AgaveWriter(AGAVEAnnotFilter) - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter
-
Construct with data source specific annotation to attribute
mapping.
- AgaveWriter.Indent - Class in org.biojava.bio.seq.io.agave
-
Implements indenting for elements.
- AgaveWriter.Indent() - Constructor for class org.biojava.bio.seq.io.agave.AgaveWriter.Indent
-
- AGAVEXref - Class in org.biojava.bio.seq.io.agave
-
xref
- AGAVEXref() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXref
-
- AGAVEXrefCallbackItf - Interface in org.biojava.bio.seq.io.agave
-
- AGAVEXrefPropHandler - Class in org.biojava.bio.seq.io.agave
-
handle AGAVE xref
- AGAVEXrefPropPropHandler - Class in org.biojava.bio.seq.io.agave
-
xref_property
- AGAVEXrefs - Class in org.biojava.bio.seq.io.agave
-
xrefs
- AGAVEXrefs() - Constructor for class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
- AGAVEXrefsPropHandler - Class in org.biojava.bio.seq.io.agave
-
Deals with database crossreferences (xrefs)
- Aggregator - Class in org.biojava.bio.program.tagvalue
-
Joins multipel values into single values.
- Aggregator(TagValueListener, BoundaryFinder, String) - Constructor for class org.biojava.bio.program.tagvalue.Aggregator
-
- ala() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid Alanine
(A)
- ALIGFACTOR - Static variable in class org.biojava.bio.structure.align.pairwise.Gotoh
-
- AligMatEl - Class in org.biojava.bio.structure.align.helper
-
- AligMatEl() - Constructor for class org.biojava.bio.structure.align.helper.AligMatEl
-
- align(Structure, Structure) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
calculate the alignment between the two full structures with default parameters
- align(Structure, Structure, StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
calculate the alignment between the two full structures with user provided parameters
- align(Atom[], Atom[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
calculate the protein structure superimposition, between two sets of atoms.
- align(Structure, List<Chain>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- align(List<Group>, List<Group>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
aligns two chains of groups, where the first chain is representing the
list of amino acids as obtained from the SEQRES records, and the second chain
represents the groups obtained from the ATOM records (and containing the actual ATOM information).
- align_NPE(Matrix, StrucAligParameters) - Static method in class org.biojava.bio.structure.align.pairwise.AligNPE
-
Align w/o penalizing endpags.
- Alignable - Interface in org.biojava.bio.structure.align.pairwise
-
- alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
- alignAll(SequenceIterator, SequenceDB) - Method in class org.biojava.bio.alignment.SequenceAlignment
-
- AlignedPosition - Class in org.biojava.bio.structure.gui.util
-
- AlignedPosition() - Constructor for class org.biojava.bio.structure.gui.util.AlignedPosition
-
- AlignIOConstants - Class in org.biojava.bio.seq.io
-
AlignIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments.
- AlignIOConstants() - Constructor for class org.biojava.bio.seq.io.AlignIOConstants
-
- alignment - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
-
The result of a successful alignment as a simple String.
- Alignment - Class in org.biojava.bio.program.das.dasalignment
-
Alignment object to contain/manage a DAS alignment.
- Alignment() - Constructor for class org.biojava.bio.program.das.dasalignment.Alignment
-
Construct a new empty Alignment object.
- ALIGNMENT - Static variable in interface org.biojava.bio.seq.homol.Homology
-
Signals that the alignment describing the homologous sequences
has changed.
- alignment - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
-
alignment Alignment field.
- Alignment - Interface in org.biojava.bio.symbol
-
An alignment containing multiple SymbolLists.
- alignment(Map) - Static method in class org.biojava.bio.symbol.SymbolListViews
-
Construct an alignment of the SymbolLists contained in the values collection
of labelToSymList.
- alignment(List, SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
-
View a SymbolList over a cross-product Alphabet as an Alignment.
- Alignment.SymbolListIterator - Class in org.biojava.bio.symbol
-
Iterator implementation looping over symbol lists in an alignment using
the labels.
- Alignment.SymbolListIterator(Alignment) - Constructor for class org.biojava.bio.symbol.Alignment.SymbolListIterator
-
- ALIGNMENT_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.ssbind.AlignmentStAXHandler
-
- AlignmentCalc - Class in org.biojava.bio.structure.gui.util
-
A class that obtains two structures via DAS and aligns them
This is done in a separate thread.
- AlignmentCalc(AlignmentGui, Structure, Structure) - Constructor for class org.biojava.bio.structure.gui.util.AlignmentCalc
-
requests an alignment of pdb1 vs pdb 2.
- AlignmentElement - Interface in org.biojava.bio.alignment
-
AlignmentElement is a class which represents a SymbolList and its
location within an Alignment This is for use in
UnequalLengthAlignments and ARAlignments.
- AlignmentFormat - Interface in org.biojava.bio.seq.io
-
- AlignmentGui - Class in org.biojava.bio.structure.gui
-
A JFrame that allows to trigger a pairwise structure alignment,
either from files in a directory,
or after manual upload.
- AlignmentGui() - Constructor for class org.biojava.bio.structure.gui.AlignmentGui
-
- AlignmentMarker - Class in org.biojava.bio.program.blast2html
-
Class to do simple HTML colouring of sequence alignments.
- AlignmentMarker(ColourCommand, AlignmentStyler) - Constructor for class org.biojava.bio.program.blast2html.AlignmentMarker
-
Creates a new AlignmentMarker instance.
- AlignmentPositionListener - Interface in org.biojava.bio.structure.gui.events
-
- alignmentRange - Variable in class org.biojava.bio.alignment.FlexibleAlignment
-
- AlignmentRenderer - Class in org.biojava.bio.gui.sequence
-
- AlignmentRenderer() - Constructor for class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- AlignmentStAXHandler - Class in org.biojava.bio.program.ssbind
-
AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML.
- AligNPE - Class in org.biojava.bio.structure.align.pairwise
-
- AligNPE() - Constructor for class org.biojava.bio.structure.align.pairwise.AligNPE
-
- AlignTools - Class in org.biojava.bio.structure.align.helper
-
- AlignTools() - Constructor for class org.biojava.bio.structure.align.helper.AlignTools
-
- ALL - Static variable in interface org.biojava.bio.program.xff.ElementRecognizer
-
- all - Static variable in interface org.biojava.bio.seq.FeatureFilter
-
All features are selected by this filter.
- all() - Static method in class org.biojava.bio.seq.FilterUtils
-
Return a filter which matches all features.
- ALL - Static variable in interface org.biojava.bio.seq.io.agave.ElementRecognizer
-
- ALL - Static variable in interface org.biojava.bio.seq.io.game.ElementRecognizer
-
- all - Static variable in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
-
All features are selected by this filter.
- ALL_POLYMER_TYPES - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
-
Convenience Set of all polymer types.
- allEntryPointsDB() - Method in class org.biojava.bio.program.das.DASSequenceDB
-
- allGaps(SymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
make sure that all Symbols in this range are gaps
- allIn(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
-
Destructive down-cast an annotation to a type.
- allOut(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
-
allOut returns a new Annotation
containing only those values in the Annotation
argument which are not of a type specified by
the AnnotationType.
- alph - Variable in class org.biojava.bio.program.hmmer.HmmerProfileParser
-
- alphabet - Variable in class org.biojava.bio.alignment.AbstractULAlignment
-
- alphabet - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
-
- Alphabet - Interface in org.biojava.bio.symbol
-
The set of AtomicSymbols which can be concatenated together to make a
SymbolList.
- alphabetForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Retrieve the alphabet for a specific name.
- AlphabetIndex - Interface in org.biojava.bio.symbol
-
Map between Symbols and index numbers.
- AlphabetManager - Class in org.biojava.bio.symbol
-
Utility methods for working with Alphabets.
- AlphabetManager() - Constructor for class org.biojava.bio.symbol.AlphabetManager
-
- AlphabetResolver - Class in org.biojava.bio.program.ssbind
-
AlphabetResolvers are helpers which determine which
type of sequence Alphabet to expect from a search
result.
- AlphabetResolver() - Constructor for class org.biojava.bio.program.ssbind.AlphabetResolver
-
- alphabets() - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Get an iterator over all alphabets known.
- AlphaCTools - Class in org.biojava.bio.structure
-
AlphaCTools is a collection of static convenience methods for dealing with
Alpha Carbon Backbone Phi / Psi angles.
- AlphaCTools() - Constructor for class org.biojava.bio.structure.AlphaCTools
-
- alphaIndex(Symbol) - Method in class org.biojava.utils.automata.FiniteAutomaton
-
- alphaIndex(Symbol) - Method in class org.biojava.utils.automata.Nfa
-
- AlreadyExistsException - Exception in org.biojava.ontology
-
Thrown to indicate that a term or triple can't be added to an ontology
because it is already present.
- AlreadyExistsException() - Constructor for exception org.biojava.ontology.AlreadyExistsException
-
- AlreadyExistsException(String) - Constructor for exception org.biojava.ontology.AlreadyExistsException
-
- ALT_ID - Static variable in class org.biojava.ontology.obo.OboFileHandler
-
- ALT_YEAST_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the alternative yeast nuclear
genetic code.
- AltAligComparator - Class in org.biojava.bio.structure.align.pairwise
-
a comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.
- AltAligComparator() - Constructor for class org.biojava.bio.structure.align.pairwise.AltAligComparator
-
- AlternateTokenization - Class in org.biojava.bio.seq.io
-
Implementation of SymbolTokenization which binds symbols to
strings of characters.
- AlternateTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.AlternateTokenization
-
- ALTERNATIVE_PRODUCTS - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
-
A name for a comment type.
- AlternativeAlignment - Class in org.biojava.bio.structure.align.pairwise
-
Implements a class which handles one possible (alternative) solution.
- AlternativeAlignment() - Constructor for class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- AlternativeAlignmentFrame - Class in org.biojava.bio.structure.gui.util
-
a frame showing the alternative alignments, which are the result of a structure superimposition
- AlternativeAlignmentFrame(Structure, Structure) - Constructor for class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
-
- ALWAYS_VETO - Static variable in interface org.biojava.utils.ChangeListener
-
Convenience implementation which vetoes every change of which it is
notified.
- AMBIGUOUS - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
AMBIGUOUS indicates that a sequence contains
ambiguity symbols.
- AminoAcid - Interface in org.biojava.bio.structure
-
A
Group that represents an AminoAcid.
- AMINOACID - Static variable in class org.biojava.bio.structure.GroupType
-
the type for amino acids
- AminoAcidImpl - Class in org.biojava.bio.structure
-
AminoAcid inherits most from Hetatom.
- AminoAcidImpl() - Constructor for class org.biojava.bio.structure.AminoAcidImpl
-
- aminoAcids - Static variable in class org.biojavax.bio.seq.io.FastaFormat
-
- amount(Atom) - Static method in class org.biojava.bio.structure.Calc
-
amount.
- and(FeatureFilter.And, FeatureFilter, FeatureFilter) - Method in class org.biojava.bio.seq.filter.FilterTransformer
-
- and(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a new filter which matches the intersection of two other
filters.
- and(FeatureFilter[]) - Static method in class org.biojava.bio.seq.FilterUtils
-
Constructs a new filter which matches the intersection of a set of filters.
- and - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
-
- angle(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
angle.
- annot - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- Annotatable - Interface in org.biojava.bio
-
Indicates that an object has an associated annotation.
- Annotatable.AnnotationForwarder - Class in org.biojava.bio
-
Deprecated.
use
new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
instead
- Annotatable.AnnotationForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.Annotatable.AnnotationForwarder
-
Deprecated.
Create a new AnnotationForwarder that will forward events for a source
using a change support.
- annotate(Sequence) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
-
- annotate(Sequence) - Method in class org.biojava.bio.molbio.RestrictionMapper
-
annotate adds Features which
represent restriction sites.
- annotate(Sequence) - Method in interface org.biojava.bio.seq.SequenceAnnotator
-
Return an annotated version of a sequence.
- ANNOTATE_EXISTING - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
-
- AnnotatedSequenceDB - Class in org.biojava.bio.seq.db
-
SequenceDB implementation which lazily applies a SequenceAnnotator
to sequences retrieved from a SequenceDB.
- AnnotatedSequenceDB(SequenceDB, SequenceAnnotator) - Constructor for class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
- annotateSequence(Sequence, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Annotates a sequence with the features from a GFF entry set with sequence
name matching this sequence.
- annotateSequence(Sequence, GFFEntrySet, boolean) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Annotates a sequence with the features from a GFF entry set.
- annotateSequences(SequenceDB, GFFEntrySet) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Annotates all sequences in a sequence DB with features from a GFF entry set.
- annotateXFF(File, Sequence) - Static method in class org.biojava.bio.program.xff.XFFTools
-
- annotateXFF(File, Sequence, Annotation) - Static method in class org.biojava.bio.program.xff.XFFTools
-
- ANNOTATION - Static variable in interface org.biojava.bio.Annotatable
-
Signals that the associated Annotation has altered in some way.
- Annotation - Interface in org.biojava.bio
-
Arbitrary annotation associated with one or more objects.
- annotation - Variable in class org.biojava.bio.seq.Feature.Template
-
- annotation - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- ANNOTATION_ADD - Static variable in class org.biojava.bio.MergeAnnotation
-
ChangeType of ChangeEvent fired before and after an annotation is added
to MergeAnnotation.
- ANNOTATION_CHANGED - Static variable in class org.biojava.bio.MergeAnnotation
-
ChangeType of ChangeEvent fired before and after an annotation is added
to MergeAnnotation.
- ANNOTATION_REMOVE - Static variable in class org.biojava.bio.MergeAnnotation
-
ChangeType of ChangeEvent fired before and after an annotation is added
to MergeAnnotation.
- AnnotationBuilder - Class in org.biojava.bio.program.tagvalue
-
Builds an Annotation tree from TagValue events using an AnnotationType to
work out which fields are of what type.
- AnnotationBuilder(AnnotationType) - Constructor for class org.biojava.bio.program.tagvalue.AnnotationBuilder
-
Make a new AnnotationBuilder that will build Annotation instances of a
given type.
- AnnotationChanger - Class in org.biojava.bio
-
AnnotationChanger remaps the values of an
Annotation to new values specified by a
ValueChanger.
- AnnotationChanger(Annotation, ChangeTable) - Constructor for class org.biojava.bio.AnnotationChanger
-
Creates a new AnnotationChanger using the
specified ValueChanger to remap its values.
- AnnotationDB - Interface in org.biojava.bio.annodb
-
A database of Annotation instances.
- AnnotationFactory - Class in org.biojava.bio.program.ssbind
-
AnnotationFactory is a utility class for making
Annotations from Maps.
- AnnotationFactory() - Constructor for class org.biojava.bio.program.ssbind.AnnotationFactory
-
- annotationForwarder - Variable in class org.biojava.bio.dp.SimpleEmissionState
-
- annotationForwarder - Variable in class org.biojava.bio.program.das.DASSequence
-
- annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- annotationForwarder - Variable in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- annotationForwarder - Variable in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- annotationForwarder - Variable in class org.biojava.bio.seq.impl.SubSequence
-
- annotationForwarder - Variable in class org.biojava.bio.seq.NewSimpleAssembly
-
- annotationForwarder - Variable in class org.biojava.bio.seq.SimpleAssembly
-
- annotationForwarder - Variable in class org.biojava.bio.symbol.AbstractSymbol
-
- annotationForwarder - Variable in class org.biojava.bio.symbol.SimpleAlphabet
-
- AnnotationRenamer - Class in org.biojava.bio
-
AnnotationRenamer remaps the keys of an
Annotation to new keys specified by a
TagMapper.
- AnnotationRenamer(Annotation, PropertyChanger) - Constructor for class org.biojava.bio.AnnotationRenamer
-
Creates a new AnnotationRenamer using the
specified TagMapper to remap its keys.
- ANNOTATIONS - Static variable in class org.biojava.bio.program.das.DASSequence
-
Change type which indicates that the set of annotation servers used
by this DASSequence has been changed.
- AnnotationTools - Class in org.biojava.bio
-
AnnotationTools is a set of static utility methods for
manipulating Annotations and AnnotationTypes.
- AnnotationTools() - Constructor for class org.biojava.bio.AnnotationTools
-
- AnnotationType - Interface in org.biojava.bio
-
A set of constraints on the data contained in an Annotation.
- AnnotationType.Abstract - Class in org.biojava.bio
-
An abstract base class useful for implementing AnnotationType
instances.
- AnnotationType.Abstract() - Constructor for class org.biojava.bio.AnnotationType.Abstract
-
- AnnotationType.Impl - Class in org.biojava.bio
-
An implementation of AnnotationType.
- AnnotationType.Impl() - Constructor for class org.biojava.bio.AnnotationType.Impl
-
Create a new Impl with no constraints.
- AnnotationType.Impl(PropertyConstraint, Location) - Constructor for class org.biojava.bio.AnnotationType.Impl
-
Create a new Impl with a default property and cardinality constraint.
- AnnotationType.Impl(CollectionConstraint) - Constructor for class org.biojava.bio.AnnotationType.Impl
-
Create a new Impl with a default collection constraint.
- ANNOTATOR - Static variable in class org.biojava.bio.program.das.ReferenceServer
-
- ANY - Static variable in interface org.biojava.bio.AnnotationType
-
The type that accepts all annotations and is the supertype of all
other annotations.
- ANY - Static variable in class org.biojava.bio.CardinalityConstraint
-
The property can have any number of values, including none.
- ANY - Static variable in interface org.biojava.bio.CollectionConstraint
-
ANY is a constraint which accepts a property for
addition under all conditions.
- ANY - Static variable in interface org.biojava.bio.PropertyConstraint
-
ANY is a constraint which accepts a property for
addition under all conditions.
- ANY - Static variable in class org.biojava.ontology.OntoTools
-
- apairs_from_idxlst(JointFragments) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
Set apairs according to a list of (i,j) tuples.
- apairs_from_seed(int, int, int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
Set apairs according to a seed position.
- AppBeanRunner - Class in org.biojava.utils.xml
-
Create a bean from an XML file, then attempt to enter it.
- AppBeanRunner() - Constructor for class org.biojava.utils.xml.AppBeanRunner
-
- append(T, Fastq...) - Method in interface org.biojava.bio.program.fastq.FastqWriter
-
Append the specified FASTQ formatted sequences to the specified appendable.
- append(T, Iterable<Fastq>) - Method in interface org.biojava.bio.program.fastq.FastqWriter
-
Append the specified FASTQ formatted sequences to the specified appendable.
- append(NfaSubModel) - Method in class org.biojava.utils.automata.NfaSubModel
-
- appendQuality(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Return this FASTQ formatted sequence builder configured with the specified quality scores
appended to its current quality scores.
- appendSequence(String) - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Return this FASTQ formatted sequence builder configured with the specified sequence
appended to its current sequence.
- AppEntry - Interface in org.biojava.utils.xml
-
- AppException - Exception in org.biojava.utils.xml
-
- AppException(String) - Constructor for exception org.biojava.utils.xml.AppException
-
- applicants - Variable in class org.biojava.bibliography.BiblioPatent
-
Array of applicants.
- applyFilters() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- approach_ap3(Atom[], Atom[], FragmentPair[], StrucAligParameters) - Method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
- ARAlignment - Interface in org.biojava.bio.alignment
-
ARAlignment is an interface that defines methods for adding and
removing seqeunces from an Alignment.
- arcHeight - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
- ARCHITECTURE - Static variable in interface org.biojava.bio.dp.MarkovModel
-
Signals that the architecture of the model is changing.
- arcWidth - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
- areDisjoint(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Determines if two queries can be proven to be disjoint.
- areEmissionSpectraEqual(Distribution, Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
-
Compares the emission spectra of two distributions.
- areEmissionSpectraEqual(Distribution[], Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
-
Compares the emission spectra of two distribution arrays.
- areEqual(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Decide if two feature filters accept exactly the same set of features.
- areEqual(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return whether two locations are equal.
- areProperSubset(FeatureFilter, FeatureFilter) - Static method in class org.biojava.bio.seq.FilterUtils
-
Determines if the set of features matched by sub can be proven to be a
proper subset of the features matched by sup.
- arg() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Arginine (R)
- ARG_C - Static variable in class org.biojava.bio.proteomics.Protease
-
- ARG_C - Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- arrayLeftDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element left division, C = A.\B
- arrayLeftDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element left division in place, A = A.\B
- arrayRightDivide(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element right division, C = A./B
- arrayRightDivideEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element right division in place, A = A./B
- ArrayStateMachineToolkit - Class in org.biojava.utils.automata
-
- arrayTimes(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element multiplication, C = A.*B
- arrayTimesEquals(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Element-by-element multiplication in place, A = A.*B
- ArrowedFeatureRenderer - Class in org.biojava.bio.gui.sequence
-
A Feature Renderer that paints the Feature as a right facing arrow Based heavily on
BasicFeatureRenderer
- ArrowedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- ArrowGlyph - Class in org.biojava.bio.gui.glyph
-
A Glyph that paints an arrow shape within the bounds.
- ArrowGlyph() - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
Creates a new ArrowGlyph, which is filled with the color
blue by default.
- ArrowGlyph(Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
Creates a new ArrowGlyph, which is filled with the given
color.
- ArrowGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
This constructs an arrow in the given bounds, which is colored blue.
- ArrowGlyph(Rectangle2D.Float, Paint, Paint) - Constructor for class org.biojava.bio.gui.glyph.ArrowGlyph
-
Constructor which sets both the size of this arrow and its color.
- ASCID_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the ascidian mitochondrial genetic
code.
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
-
- asCriterion() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
-
This method returns a Hibernate Criterion object that can be used to
query the database.
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
-
- asCriterion() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
- asMap() - Method in class org.biojava.bio.AbstractAnnotation
-
- asMap() - Method in interface org.biojava.bio.Annotation
-
Return a map that contains the same key/values as this Annotation.
- asMap() - Method in class org.biojava.bio.MergeAnnotation
-
- asMap() - Method in class org.biojava.bio.OverlayAnnotation
-
Return a Map view onto this annotation.
- asMap() - Method in class org.biojavax.EmptyRichAnnotation
-
Return a map that contains the same key/values as this Annotation.
- asMap() - Method in class org.biojavax.ga.util.WeightedSet
-
Converts the Set to a map from key Objects to Double
weights.
- asMap() - Method in class org.biojavax.SimpleRichAnnotation
-
Return a map that contains the same key/values as this Annotation.
- asn() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Asparagine (N)
- asp() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Aspartic Acid (D)
- ASP_N - Static variable in class org.biojava.bio.proteomics.Protease
-
- ASP_N - Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- AssembledSymbolList - Class in org.biojava.bio.seq.impl
-
Support class for applications which need to patch together sections
of sequence into a single SymbolList.
- AssembledSymbolList() - Constructor for class org.biojava.bio.seq.impl.AssembledSymbolList
-
- AssertionFailure - Error in org.biojava.utils
-
An unchecked exception representing an Assertion failure.
- AssertionFailure(String) - Constructor for error org.biojava.utils.AssertionFailure
-
- AssertionFailure(Throwable) - Constructor for error org.biojava.utils.AssertionFailure
-
- AssertionFailure(String, Throwable) - Constructor for error org.biojava.utils.AssertionFailure
-
- Atom - Interface in org.biojava.bio.structure
-
A simple interface for an Atom.
- ATOM_CA_THRESHOLD - Static variable in class org.biojava.bio.structure.io.PDBFileParser
-
the maximum number of atoms that will be parsed before the parser switches to a CA-only
representation of the PDB file.
- AtomicSymbol - Interface in org.biojava.bio.symbol
-
A symbol that is not ambiguous.
- AtomImpl - Class in org.biojava.bio.structure
-
Implementation of an Atom of a PDB file.
- AtomImpl() - Constructor for class org.biojava.bio.structure.AtomImpl
-
- AtomIterator - Class in org.biojava.bio.structure
-
an iterator over all atoms of a structure / group.
- AtomIterator(Structure) - Constructor for class org.biojava.bio.structure.AtomIterator
-
Constructs an AtomIterator object.
- AtomIterator(Group) - Constructor for class org.biojava.bio.structure.AtomIterator
-
Constructs an AtomIterator object.
- ATOMRECORD - Static variable in interface org.biojava.bio.structure.AminoAcid
-
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
- AtomSite - Class in org.biojava.bio.structure.io.mmcif.model
-
- AtomSite() - Constructor for class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- attemptClose(Statement) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Attempt to close the Statement.
- attemptClose(ResultSet) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Attempt to close the ResultSet.
- ATTR_FORMAT - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name, or a part of a vocabulary name.
- ATTR_PROPERTIES - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A part of a vocabulary name.
- ATTR_SCOPE - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name, or a part of a vocabulary name.
- attribute(String, String) - Method in class org.biojava.utils.xml.FastXMLWriter
-
- attribute(String, String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
-
- attribute(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
-
- attribute(String, String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Add an attribute to an element.
- attribute(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Add an un-qualified attribute to an element.
- Author - Class in org.biojava.bio.structure
-
Describes author attributes for author information in a PDB file.
- Author() - Constructor for class org.biojava.bio.structure.Author
-
- AUTHOR_LIST_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- AUTHOR_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- AUTHORITY - Static variable in interface org.biojavax.Namespace
-
- authors - Variable in class org.biojava.bibliography.BibRef
-
The authors and contributors are responsible for creating the contents of the cited resource.
- AUTHORS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- AUTHORS_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- AUTHORS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- automaticUpdate(Connection, DBHelper, TaxonFactory, File, File) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
This method tries to perform a complete update according to the given
TaxonFactory, which already contains the newes taxa and the files
available at the NCBI-FTP-Site.
- AutomatonException - Exception in org.biojava.utils.automata
-
An exception thrown by classes of this package.
- AutomatonException(String) - Constructor for exception org.biojava.utils.automata.AutomatonException
-
- AutomatonException(Throwable) - Constructor for exception org.biojava.utils.automata.AutomatonException
-
- AutomatonException(Throwable, String) - Constructor for exception org.biojava.utils.automata.AutomatonException
-
- available() - Method in class org.biojava.utils.io.UncompressInputStream
-
- average(Distribution[]) - Static method in class org.biojava.bio.dist.DistributionTools
-
Averages two or more distributions.
- AVG_MASS - Static variable in interface org.biojava.bio.symbol.SymbolPropertyTable
-
- c() - Static method in class org.biojava.bio.seq.DNATools
-
- c() - Static method in class org.biojava.bio.seq.NucleotideTools
-
- c() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Cysteine
- c() - Static method in class org.biojava.bio.seq.RNATools
-
- C_ELEGANS - Static variable in interface org.biojava.bio.program.homologene.Taxon
-
- caAtomName - Static variable in class org.biojava.bio.structure.StructureTools
-
The Atom name of C-alpha atoms.
- Cache - Interface in org.biojava.utils.cache
-
Interface for managing caches of objects.
- cache - Variable in class org.biojava.utils.io.CachingInputStream
-
The byte cache itself.
- cachedOutcome - Variable in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
-
- CacheMap - Interface in org.biojava.utils.cache
-
Interface for managing caches of objects fetchable by key.
- CacheReference - Interface in org.biojava.utils.cache
-
Interface for a reference to an object, analogous to
java.lang.ref.Referencce, but more flexible.
- CachingInputStream - Class in org.biojava.utils.io
-
A wrapper around InputStream that provides in-memory
caching of the input data.
- CachingInputStream(InputStream) - Constructor for class org.biojava.utils.io.CachingInputStream
-
- CachingKernel - Class in org.biojava.stats.svm
-
Caches the results of a nested kernel so that k(a, b) need only be calculated
once.
- CachingKernel() - Constructor for class org.biojava.stats.svm.CachingKernel
-
- CachingKernel(SVMKernel) - Constructor for class org.biojava.stats.svm.CachingKernel
-
- CachingSequenceDB - Class in org.biojava.bio.seq.db
-
SequenceDB implementation that caches the results of another SequenceDB.
- CachingSequenceDB(SequenceDB) - Constructor for class org.biojava.bio.seq.db.CachingSequenceDB
-
Create a new CachingSequenceDB that caches the sequences in parent.
- CAConverter - Class in org.biojava.bio.structure.io
-
Converts full atom representations to Calpha only ones.
- CAConverter() - Constructor for class org.biojava.bio.structure.io.CAConverter
-
- Calc - Class in org.biojava.bio.structure
-
utility operations on Atoms, AminoAcids, etc.
- Calc() - Constructor for class org.biojava.bio.structure.Calc
-
- calcCell(Cell[][]) - Method in interface org.biojava.bio.dp.twohead.CellCalculator
-
Calculate the 'scores' array in the cell at cells[0][0].
- calcDist() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByName
-
- calcID(Sequence) - Method in class org.biojava.bio.seq.db.IDMaker.ByURN
-
- calcID(Sequence) - Method in interface org.biojava.bio.seq.db.IDMaker
-
Calculate the id for a sequence.
- calcKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- calcLineExtent(MouseEvent) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- calcScale(int) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
a value of 100 means that the whole sequence should be displayed in the current visible window
a factor of 1 means that one amino acid shoud be drawn as big as possible
- calcScores(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
calculates scores for this alignment ( %id )
- calculatePrimRecLen(int) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
calculatePrimRecLen calculates the byte length of
primary namespace records.
- calculateScore(Distribution, Symbol) - Method in interface org.biojava.bio.dp.ScoreType
-
Calculates the score associated with a distribution and a symbol.
- calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.NullModel
-
- calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Odds
-
- calculateScore(Distribution, Symbol) - Method in class org.biojava.bio.dp.ScoreType.Probability
-
- calculateSecRecLen(int, String, Map) - Static method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
calculateSecRecLen calculates the byte length of
secondary namespace records.
- calculateSuperpositionByIdx(Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- callbackStack - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
this is the stack of handler objects for the current feature.
- callbackStack - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
this is the stack of handler objects for the current feature.
- callboxesValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Flag for call boxes.
- canAccept(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
-
Accepts all URLs that are of the file protocol.
- canAccept(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
-
Accepts all URLs that are of the jdbc protocol.
- canAccept(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
-
- canAdvance() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
Can we advance?
- CANDIES_NOT_SORTED - Static variable in interface org.biojava.utils.candy.CandyVocabulary
-
A property name.
- CandyEntry - Class in org.biojava.utils.candy
-
This is a basic container for a vocabulary entry.
- CandyEntry() - Constructor for class org.biojava.utils.candy.CandyEntry
-
An empty constructor.
- CandyEntry(String) - Constructor for class org.biojava.utils.candy.CandyEntry
-
It creates an entry instance with given name and empty value.
- CandyEntry(String, String) - Constructor for class org.biojava.utils.candy.CandyEntry
-
It creates an entry instance with given name and value.
- CandyEntry(String, String, Hashtable) - Constructor for class org.biojava.utils.candy.CandyEntry
-
It creates an entry instance with given name, value and
additional properties.
- CandyException - Exception in org.biojava.utils.candy
-
- CandyException(String) - Constructor for exception org.biojava.utils.candy.CandyException
-
- CandyException(Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
-
- CandyException(String, Throwable) - Constructor for exception org.biojava.utils.candy.CandyException
-
- CandyFinder - Interface in org.biojava.utils.candy
-
This interface is a main entry point to a set of controlled
vocabularies.
- CandyVocabulary - Interface in org.biojava.utils.candy
-
This interface defines functionality of a controlled vocabulary.
- canMerge(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Determines whether the locations are touching or not (if they could be
merged in a single Location.
- canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Check to see if a given file is in our format.
- canRead(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
Check to see if a given stream is in our format.
- canRead(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Check to see if a given file is in our format.
- canRead(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Check to see if a given stream is in our format.
- CardinalityConstraint - Class in org.biojava.bio
-
A constraint on the number of values a property can have.
- Cavg - Static variable in class org.biojava.bio.proteomics.MassCalc
-
Constant value of Carbon average mass
- Cell - Class in org.biojava.bio.dp.twohead
-
A single cell in the DP matrix.
- Cell() - Constructor for class org.biojava.bio.dp.twohead.Cell
-
- CellCalculator - Interface in org.biojava.bio.dp.twohead
-
The interface for all functions that can calculate the 'scores' array for
a given cell.
- CellCalculatorFactory - Interface in org.biojava.bio.dp.twohead
-
- CellCalculatorFactoryMaker - Interface in org.biojava.bio.dp.twohead
-
The interface for all functions that can calculate the 'scores' array for
a given cell.
- centerAtoms(Atom[]) - Static method in class org.biojava.bio.structure.Calc
-
Center the atoms at the Centroid.
- CEREVISIAE_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
-
Saccharomyces cerevisiae codon preferences
- Chain - Interface in org.biojava.bio.structure
-
Defines the interface for a Chain.
- ChainImpl - Class in org.biojava.bio.structure
-
A Chain in a PDB file.
- ChainImpl() - Constructor for class org.biojava.bio.structure.ChainImpl
-
Constructs a ChainImpl object.
- change(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
-
- change(Object, Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
-
- change(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Changer
-
Produce a modified value from an old value.
- change(Object) - Method in class org.biojava.bio.program.tagvalue.RegexChanger
-
- CHANGE_COMMON_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
Change type to indicate that the common name of this Taxon is
changing.
- CHANGE_SCIENTIFIC_NAME - Static variable in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
Change type to indicate that the scientific name of this Taxon is
changing.
- Changeable - Interface in org.biojava.utils
-
This is a flag interface that defines the common add/remove listener methods
for classes and interfaces that wish to indicate that they are sources of
ChangeEvents.
- ChangeableCache - Class in org.biojava.utils.cache
-
A cache that clears values as the keys fire ChangeEvents of a given type.
- ChangeableCache(ChangeType) - Constructor for class org.biojava.utils.cache.ChangeableCache
-
- ChangeAdapter - Class in org.biojava.utils
-
This is a ChangeListener that ignores everything.
- ChangeAdapter() - Constructor for class org.biojava.utils.ChangeAdapter
-
- ChangeEvent - Class in org.biojava.utils
-
Event which encapsulates a change in any mutable BioJava object.
- ChangeEvent(Object, ChangeType) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent with no change details.
- ChangeEvent(Object, ChangeType, Object) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent specifying a new value for
a property, or an object to be added to a collection.
- ChangeEvent(Object, ChangeType, Object, Object) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent specifying a new value for
a property, and giving the previous value.
- ChangeEvent(Object, ChangeType, Object, Object, ChangeEvent) - Constructor for class org.biojava.utils.ChangeEvent
-
Construct a ChangeEvent to be fired because another ChangeEvent has
been received from a property object.
- ChangeForwarder - Class in org.biojava.utils
-
This is a ChangeListener that is designed to adapt events of one type from
one source to events of another type emitted by another source.
- ChangeForwarder(Object, ChangeSupport) - Constructor for class org.biojava.utils.ChangeForwarder
-
Create a new ChangeForwarder for forwarding events.
- ChangeForwarder.Retyper - Class in org.biojava.utils
-
A ChangeForwarder that systematically uses a given type and wraps the old
event.
- ChangeForwarder.Retyper(Object, ChangeSupport, ChangeType) - Constructor for class org.biojava.utils.ChangeForwarder.Retyper
-
Create a new Retyper for forwarding events.
- ChangeHub - Interface in org.biojava.utils
-
Interface implemented by ChangeHubs, i.e.
- ChangeListener - Interface in org.biojava.utils
-
Interface for objects which listen to ChangeEvents.
- ChangeListener.AlwaysVetoListener - Class in org.biojava.utils
-
An implementation that always vetoes everything.
- ChangeListener.AlwaysVetoListener() - Constructor for class org.biojava.utils.ChangeListener.AlwaysVetoListener
-
Private constructor.
- ChangeListener.ChangeEventRecorder - Class in org.biojava.utils
-
A listener that remembers the ChangeEvent of the last change.
- ChangeListener.ChangeEventRecorder() - Constructor for class org.biojava.utils.ChangeListener.ChangeEventRecorder
-
- ChangeListener.LoggingListener - Class in org.biojava.utils
-
A listener that writes information about the event stream to a PrintStream.
- ChangeListener.LoggingListener(PrintStream) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
-
Create a LoggingListener that will log all events to 'out'.
- ChangeListener.LoggingListener(PrintStream, String) - Constructor for class org.biojava.utils.ChangeListener.LoggingListener
-
Create a LoggingListener that will log all events to 'out' with a prefix.
- changeSupport() - Method in class org.biojava.utils.ChangeForwarder
-
Return the underlying ChangeSupport instance that can be used to
fire ChangeEvents and mannage listeners.
- ChangeSupport - Class in org.biojava.utils
-
A utility class to provide management for informing ChangeListeners of
ChangeEvents.
- ChangeSupport() - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance.
- ChangeSupport(int) - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance which has room for initialSize
listeners before it needs to grow any resources.
- ChangeSupport(int, int) - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance which has room for initialSize
listeners before it needs to grow any resources, and which will grow by
delta each time.
- ChangeSupport(Set) - Constructor for class org.biojava.utils.ChangeSupport
-
- ChangeSupport(Set, int, int) - Constructor for class org.biojava.utils.ChangeSupport
-
Generate a new ChangeSupport instance which has room for initialSize
listeners before it needs to grow any resources, and which will grow by
delta each time.
- ChangeTable - Class in org.biojava.bio.program.tagvalue
-
A mapping between keys and actions to turn old values into new values.
- ChangeTable() - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable
-
- ChangeTable.ChainedChanger - Class in org.biojava.bio.program.tagvalue
-
An implementation of Changer that applies a list of Changer instances to
the value in turn.
- ChangeTable.ChainedChanger(ChangeTable.Changer[]) - Constructor for class org.biojava.bio.program.tagvalue.ChangeTable.ChainedChanger
-
- ChangeTable.Changer - Interface in org.biojava.bio.program.tagvalue
-
Callback used to produce a new value from an old one.
- ChangeTable.Splitter - Interface in org.biojava.bio.program.tagvalue
-
Callback used to produce a list of values from a single old one.
- ChangeType - Class in org.biojava.utils
-
Class for all constants which are used to indicate change
types.
- ChangeType(String, Field, ChangeType) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType.
- ChangeType(String, Field) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType with superType UNKNOWN.
- ChangeType(String, Class, String) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType with supertype UNKNOWN.
- ChangeType(String, Class, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
-
Construct a new ChangeType.
- ChangeType(String, String, String, ChangeType) - Constructor for class org.biojava.utils.ChangeType
-
- ChangeType(String, String, String) - Constructor for class org.biojava.utils.ChangeType
-
- ChangeVetoException - Exception in org.biojava.utils
-
Exception which is thrown when a ChangeListener does not
wish a change to take place.
- ChangeVetoException() - Constructor for exception org.biojava.utils.ChangeVetoException
-
- ChangeVetoException(ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Construct an exception to veto a change without explanation.
- ChangeVetoException(String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Create an exception with a detail message
- ChangeVetoException(ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Construct an exception to veto a change for a specified reason.
- ChangeVetoException(Throwable, ChangeEvent) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Propogate an exception without (additional) explanation.
- ChangeVetoException(Throwable, String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Deprecated.
use new ChangeVetoException(reason, ex);
- ChangeVetoException(String, Throwable) - Constructor for exception org.biojava.utils.ChangeVetoException
-
- ChangeVetoException(Throwable, ChangeEvent, String) - Constructor for exception org.biojava.utils.ChangeVetoException
-
Propogate an exception, giving a detail message
- CHARACTER - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
-
- characters(char[], int, int) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
-
Describe characters method here.
- characters(char[], int, int) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
-
- characters(char[], int, int) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
-
- characters(char[], int, int) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- characters(char[], int, int) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEDescPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEKeywordPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchAlignPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchDescPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVENotePropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
- characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
-
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
Signal a span of character data in the XML input.
- characters(char[], int, int) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
-
- characters(char[], int, int) - Method in interface org.biojava.bio.seq.io.StreamParser
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.CharElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.LongElementHandlerBase
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
-
- characters(char[], int, int) - Method in interface org.biojava.utils.stax.StAXContentHandler
-
- characters(char[], int, int) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
Signal a span of character data in the XML input.
- characters(char[], int, int) - Method in class org.biojava.utils.stax.StringElementHandlerBase
-
- CharacterTokenization - Class in org.biojava.bio.seq.io
-
Implementation of SymbolTokenization which binds symbols to
single unicode characters.
- CharacterTokenization(Alphabet, boolean) - Constructor for class org.biojava.bio.seq.io.CharacterTokenization
-
- charAt(int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
-
- charAt(int) - Method in class org.biojava.utils.RepeatedCharSequence
-
- CharElementHandlerBase - Class in org.biojava.utils.stax
-
StAX handler for any element which just contains a string representation of
a char.
- CharElementHandlerBase() - Constructor for class org.biojava.utils.stax.CharElementHandlerBase
-
- charValue(Symbol) - Method in class org.biojava.utils.regex.PatternFactory
-
Returns the character that represents the specified Symbol in
the Alphabet that this PatternFactory was defined for.
- charValue(Symbol) - Method in class org.biojava.utils.regex.Search
-
- checkException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- checkException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- checkIOException() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- checkIOException() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- checkIOException() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- chem_comp_type - Variable in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
-
String value of the type
- ChemComp - Class in org.biojava.bio.structure.io.mmcif.model
-
- ChemComp() - Constructor for class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- ChemCompConsumer - Class in org.biojava.bio.structure.io.mmcif
-
- ChemCompConsumer() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
-
- ChemCompTools - Class in org.biojava.bio.structure.io.mmcif.chem
-
Some tools for working with chemical compounds.
- ChemCompTools() - Constructor for class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- ChemicalComponentDictionary - Class in org.biojava.bio.structure.io.mmcif
-
A representation of the Chemical Component Dictionary.
- ChemicalComponentDictionary() - Constructor for class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
- children - Variable in class org.biojava.bio.taxa.SimpleTaxon
-
Deprecated.
- CHLORO_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the chlorophycean mitochondrial genetic
code.
- chol() - Method in class org.biojava.bio.structure.jama.Matrix
-
Cholesky Decomposition
- CholeskyDecomposition - Class in org.biojava.bio.structure.jama
-
Cholesky Decomposition.
- CholeskyDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.CholeskyDecomposition
-
Cholesky algorithm for symmetric and positive definite matrix.
- Chromatogram - Interface in org.biojava.bio.chromatogram
-
Encapsulates the basic information you would want from a chromatogram.
- ChromatogramFactory - Class in org.biojava.bio.chromatogram
-
A factory that creates
Chromatogram objects from files or streams.
- ChromatogramFactory() - Constructor for class org.biojava.bio.chromatogram.ChromatogramFactory
-
- ChromatogramGraphic - Class in org.biojava.bio.chromatogram.graphic
-
Encapsulates a configurable method for drawing a
Chromatogram
into a graphics context.
- ChromatogramGraphic() - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Default constructor with no Chromatogram.
- ChromatogramGraphic(Chromatogram) - Constructor for class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Creates a new ChromatogramGraphic, initially displaying
the given chromatogram.
- ChromatogramGraphic.Option - Class in org.biojava.bio.chromatogram.graphic
-
A typesafe enumeration of the options available for configuring
the behavior of a
ChromatogramGraphic instance.
- ChromatogramNonlinearScaler - Interface in org.biojava.bio.chromatogram.graphic
-
Provides the mechanism whereby a ChromatogramGraphic can display
a Chromatogram with a non-linear horizontal scale.
- ChromatogramNonlinearScaler.Identity - Class in org.biojava.bio.chromatogram.graphic
-
The default scaler that displays the chromatogram 1:1.
- ChromatogramTools - Class in org.biojava.bio.chromatogram
-
- chromosomes - Variable in class org.biojavax.ga.impl.AbstractOrganism
-
- CHROMOSOMES - Static variable in interface org.biojavax.ga.Organism
-
- ChunkedSymbolList - Class in org.biojava.bio.symbol
-
SymbolList implementation using constant-size chunks.
- ChunkedSymbolList(SymbolList[], int, int, Alphabet) - Constructor for class org.biojava.bio.symbol.ChunkedSymbolList
-
- ChunkedSymbolListFactory - Class in org.biojava.bio.seq.io
-
class that makes ChunkedSymbolLists with the chunks
implemented as SymbolLists themselves.
- ChunkedSymbolListFactory(SymbolListFactory) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
-
- ChunkedSymbolListFactory(SymbolListFactory, int) - Constructor for class org.biojava.bio.seq.io.ChunkedSymbolListFactory
-
- CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.Protease
-
- CHYMOTRYP - Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- CILIATE_NUC - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the ciliate nuclear genetic code.
- CIRCLE - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
-
CIRCLE indicates a circular image map hotspot.
- CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichLocation
-
- CIRCULAR - Static variable in interface org.biojavax.bio.seq.RichSequence
-
- CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- CIRCULAR_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- CircularFeatureFilteringRenderer - Class in org.biojava.bio.gui.sequence
-
- CircularFeatureFilteringRenderer(CircularRenderer, FeatureFilter, boolean) - Constructor for class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
-
- CircularFeatureRenderer - Interface in org.biojava.bio.gui.sequence
-
- CircularFeaturesRenderer - Class in org.biojava.bio.gui.sequence
-
- CircularFeaturesRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
-
- CircularFeaturesRenderer(CircularFeatureRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
-
- circularLength - Variable in class org.biojavax.bio.seq.SimpleRichLocation
-
- CircularLocation - Class in org.biojava.bio.symbol
-
Circular view onto an underlying Location instance.
- CircularLocation(Location, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
-
Constructs a CircularLocation by wrapping another Location
It is preferable to use LocationTools to make CircularLocations
- CircularLocation(Location, int, int) - Constructor for class org.biojava.bio.symbol.CircularLocation
-
Makes a CircularLocation where the 5' end of the Location is specified.
- CircularMLR - Class in org.biojava.bio.gui.sequence
-
Renders multiple renderers, each in their own concentric rings.
- CircularMLR() - Constructor for class org.biojava.bio.gui.sequence.CircularMLR
-
- CircularPaddedRenderer - Class in org.biojava.bio.gui.sequence
-
- CircularPaddedRenderer() - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
-
- CircularPaddedRenderer(CircularRenderer) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
-
- CircularPaddedRenderer(double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
-
- CircularPaddedRenderer(CircularRenderer, double, double) - Constructor for class org.biojava.bio.gui.sequence.CircularPaddedRenderer
-
- CircularReferenceException - Exception in org.biojava.bio.taxa
-
- CircularReferenceException() - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularReferenceException(Throwable) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularReferenceException(String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularReferenceException(Throwable, String) - Constructor for exception org.biojava.bio.taxa.CircularReferenceException
-
Deprecated.
- CircularRenderer - Interface in org.biojava.bio.gui.sequence
-
Render information from a CircularRendererContext onto a graphics context.
- CircularRendererContext - Interface in org.biojava.bio.gui.sequence
-
A context providing information for rendering sequences into circular coordinate systems.
- CircularRendererPanel - Class in org.biojava.bio.gui.sequence
-
Renders a sequence as a circle using a CircularRenderer.
- CircularRendererPanel() - Constructor for class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- CircularView - Class in org.biojava.bio.seq
-
A circular view onto another Sequence object.
- CircularView(Sequence, FeatureRealizer) - Constructor for class org.biojava.bio.seq.CircularView
-
- CircularView(Sequence) - Constructor for class org.biojava.bio.seq.CircularView
-
- CITATION_DATE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_FIRST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_ID_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_INSTITUTE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_ISSUE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_LAST_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_NAME_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_PATENT_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_PUB_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- CITATION_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_VOL_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CITATION_YEAR_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- ClassifierExample - Class in org.biojava.stats.svm.tools
-
A simple toy example that allows you to put points on a canvas, and find a
polynomial hyperplane to seperate them.
- ClassifierExample() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample
-
- ClassifierExample.PointClassifier - Class in org.biojava.stats.svm.tools
-
An extention of JComponent that contains the points & encapsulates the
classifier.
- ClassifierExample.PointClassifier() - Constructor for class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Make a new PointClassifier.
- classify(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- classify(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- classify(Object) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- classify() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Learn a model from the current points.
- Classify - Class in org.biojava.stats.svm.tools
-
- Classify() - Constructor for class org.biojava.stats.svm.tools.Classify
-
- ClassTools - Class in org.biojava.utils
-
Utility methods for manipulating class objects and resources.
- cleanUp() - Method in class org.biojava.bio.structure.gui.AlignmentGui
-
- cleanup() - Method in class org.biojava.bio.structure.gui.util.AlignmentCalc
-
- clear() - Method in class org.biojava.bio.dp.twohead.EmissionCache
-
- clear() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- clear() - Method in class org.biojava.stats.svm.AbstractSVMTarget
-
- clear() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- clear() - Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- clear() - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- clear() - Method in interface org.biojava.stats.svm.SVMTarget
-
- clear() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Remove all points from the canvas, and discard any model.
- clear() - Method in interface org.biojava.utils.cache.CacheReference
-
- clear() - Method in class org.biojava.utils.FileAsList
-
- clear() - Method in class org.biojavax.EmptyRichAnnotation
-
Removes all notes from this annotation object.
- clear() - Method in class org.biojavax.ga.util.WeightedSet
-
- clear() - Method in interface org.biojavax.RichAnnotation
-
Removes all notes from this annotation object.
- clear() - Method in class org.biojavax.SimpleRichAnnotation
-
Removes all notes from this annotation object.
- clearAtoms() - Method in interface org.biojava.bio.structure.Group
-
Remove all atoms from this group.
- clearAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
-
remove all atoms
- clearConsumers() - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
-
Remove all consumers from the parser.
- clearConsumers() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- clearCounts(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.DistributionTrainer
-
Clears all of the counts to zero.
- clearCounts() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Clears all of the counts to zero.
- clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
-
- clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
-
- clearCounts(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
-
Deprecated.
- clearCounts() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- clearCounts() - Method in interface org.biojava.bio.dp.TransitionTrainer
-
Clears all of the counts to zero.
- clearEnzymes() - Method in class org.biojava.bio.molbio.RestrictionMapper
-
clearEnzymes removes all enzymes from those to be
searched for in the Sequence.
- clearExtensions() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- clearExtensions() - Method in class org.biojava.bio.structure.io.PDBFileReader
-
clear the supported file extensions
- clearExtensions() - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
clear all file extensions
- clearFilters() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- clearFilters() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- clearFilters() - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
remove all filters, next time getAll is called, it will return all available PDBs
- clearListeners() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- clearListeners() - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
-
- clearListeners() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
- clearLRUCache() - Static method in class org.biojavax.RichObjectFactory
-
Removes all objects from the LRU cache.
- clearLRUCache(Class) - Static method in class org.biojavax.RichObjectFactory
-
Removes all objects of the specified class from the LRU cache.
- clearPatterns() - Method in class org.biojava.utils.regex.Search
-
remove all patterns from the pattern cache.
- clearRenderers() - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
clearRenderers removes all renderers from this
renderer.
- clearRenderers() - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
clearRenderers removes all the renderers.
- clearStructureListeners() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- clearStructureListeners() - Method in interface org.biojava.bio.structure.server.StructureServer
-
- clearTraces() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Sets the trace data structures to null.
- clearTraceValues() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
-
Sets all the traces to null.
- clobToString(Connection, ResultSet, int) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- clone() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Performs a partial deep copy and invalidates regenerable structures.
- clone() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
- clone() - Method in class org.biojava.bio.seq.Feature.Template
-
- clone() - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
clone() should make a complete copy of the Sequence with all features (and children) and return
a SimpleSequence that is unconnected from the original sequence.
- clone() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- clone() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
returns and identical copy of this Group object .
- clone() - Method in interface org.biojava.bio.structure.Atom
-
returns and identical copy of this object .
- clone() - Method in class org.biojava.bio.structure.AtomImpl
-
returns and identical copy of this object .
- clone() - Method in interface org.biojava.bio.structure.Chain
-
returns an identical copy of this Chain.
- clone() - Method in class org.biojava.bio.structure.ChainImpl
-
Returns an identical copy of this Chain .
- clone() - Method in class org.biojava.bio.structure.Compound
-
- clone() - Method in interface org.biojava.bio.structure.Group
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.bio.structure.GroupIterator
-
Creates and returns a copy of this object.
- clone() - Method in class org.biojava.bio.structure.HetatomImpl
-
returns and identical copy of this Group object .
- clone() - Method in class org.biojava.bio.structure.jama.Matrix
-
Clone the Matrix object.
- clone() - Method in class org.biojava.bio.structure.NucleotideImpl
-
- clone() - Method in class org.biojava.bio.structure.SSBond
-
- clone() - Method in interface org.biojava.bio.structure.Structure
-
returns an identical copy of this Structure object
- clone() - Method in class org.biojava.bio.structure.StructureImpl
-
returns an identical copy of this structure .
- clone() - Method in class org.biojava.utils.ExecRunner
-
We override the clone method here to prevent cloning of our class.
- clone() - Method in class org.biojava.utils.TypedProperties
-
- close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
close closes the underlying
InputStream.
- close() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
close closes the underlying
RandomAccessFile.
- close() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
close closes the underlying
EntryNamRandomAccess which in turn closes the
lower level RandomAccessFile.
- close() - Method in interface org.biojava.bio.seq.io.StreamParser
-
- close() - Method in class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
-
- close() - Method in class org.biojava.naming.ObdaContext
-
- close() - Method in class org.biojava.utils.io.CountedBufferedReader
-
- close() - Method in class org.biojava.utils.io.RandomAccessReader
-
close closes the underlying
RandomAccessFile.
- close() - Method in class org.biojava.utils.xml.PrettyXMLWriter
-
- close() - Method in interface org.biojava.utils.xml.XMLWriter
-
Close this XMLWriter, and it's underlying stream.
- closeTag(String) - Method in class org.biojava.utils.xml.FastXMLWriter
-
- closeTag(String, String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
-
- closeTag(String) - Method in class org.biojava.utils.xml.PrettyXMLWriter
-
- closeTag(String, String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Closes an element
- closeTag(String) - Method in interface org.biojava.utils.xml.XMLWriter
-
Closes an un-qualified element.
- CLUSTAL - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL indicates that the alignment format is
Clustal.
- CLUSTAL_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL_AA premade CLUSTAL | AA;
- CLUSTAL_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL_DNA premade CLUSTAL | DNA;
- CLUSTAL_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
CLUSTAL_RNA premade CLUSTAL | RNA;
- ClustalWAlignmentSAXParser - Class in org.biojava.bio.program.sax
-
A SAX2 parser for dealing with a multiple sequence
alignment as produced by ClustalW outputing .aln format.
- ClustalWAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.ClustalWAlignmentSAXParser
-
Initialises internal state
Sets namespace prefix to "biojava"
- cluster(AlternativeAlignment[]) - Static method in class org.biojava.bio.structure.align.ClusterAltAligs
-
- cluster(AlternativeAlignment[], int) - Static method in class org.biojava.bio.structure.align.ClusterAltAligs
-
- ClusterAltAligs - Class in org.biojava.bio.structure.align
-
A class that clusters alternative alignments according to their
similarity.
- ClusterAltAligs() - Constructor for class org.biojava.bio.structure.align.ClusterAltAligs
-
- Cmono - Static variable in class org.biojava.bio.proteomics.MassCalc
-
Constant value of Carbon monoisotopic mass
- CNBr - Static variable in class org.biojava.bio.proteomics.Protease
-
- CNBr - Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- codes - Variable in class org.biojava.bibliography.BiblioSubject
-
Classification code (call number) is usually either Dewey decimal or
Congress classification.
- CodonPref - Interface in org.biojava.bio.symbol
-
- CodonPrefFilter - Interface in org.biojava.bio.symbol
-
- CodonPrefFilter.AcceptAll - Class in org.biojava.bio.symbol
-
- CodonPrefFilter.AcceptAll() - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
-
- CodonPrefFilter.ByName - Class in org.biojava.bio.symbol
-
- CodonPrefFilter.ByName(String) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.ByName
-
- CodonPrefFilter.EverythingToXML - Class in org.biojava.bio.symbol
-
- CodonPrefFilter.EverythingToXML(PrintWriter) - Constructor for class org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML
-
- CodonPrefTools - Class in org.biojava.bio.symbol
-
An utility class for codon preferences
- CodonPrefTools() - Constructor for class org.biojava.bio.symbol.CodonPrefTools
-
- CollectionConstraint - Interface in org.biojava.bio
-
Used by AnnotationType to represent the constraint on
the collection of values in a property-slot.
- CollectionConstraint.AllValuesIn - Class in org.biojava.bio
-
CollectionConstraint which validates all members of a Collection.
- CollectionConstraint.AllValuesIn(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.AllValuesIn
-
Create an AllValuesIn based upon a PropertyConstraint and a
cardinality.
- CollectionConstraint.And - Class in org.biojava.bio
-
A collection constraint that accpepts collections iff they are accepted by both
child constraints.
- CollectionConstraint.And(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.And
-
Create a new And from two child constraints.
- CollectionConstraint.Contains - Class in org.biojava.bio
-
CollectionConstraint which validates a portion of a Collection.
- CollectionConstraint.Contains(PropertyConstraint, Location) - Constructor for class org.biojava.bio.CollectionConstraint.Contains
-
Create a Contains based upon a PropertyConstraint and a
cardinality.
- CollectionConstraint.Or - Class in org.biojava.bio
-
A collection constraint that accepts items iff they are accepted by either
child constraints.
- CollectionConstraint.Or(CollectionConstraint, CollectionConstraint) - Constructor for class org.biojava.bio.CollectionConstraint.Or
-
Create a new Or from two child constraints.
- colors - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
The map containing the colors for drawing traces.
- ColourCommand - Interface in org.biojava.bio.program.blast2html
-
Interface for specifying whether a particular pair
of residues/bases should be coloured.
- colSymbols - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
-
- columns() - Method in class org.biojava.bio.dp.ProfileHMM
-
Retrieve the number of columns in the model.
- columns() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
-
- columns - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
-
- columns() - Method in interface org.biojava.bio.dp.WeightMatrix
-
The number of columns modeled by the weight matrix.
- COMMENT - Static variable in class org.biojava.ontology.obo.OboFileHandler
-
- COMMENT - Static variable in interface org.biojavax.bio.BioEntry
-
- Comment - Interface in org.biojavax
-
A simple ranked comment designed to be used for BioEntry comments
in BioSQL.
- COMMENT_ABS_MAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_ABSORPTION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_ERROR_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_EVENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_EXPERIMENTS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_INTERACT_INTACT_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_INTERACT_LABEL_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_INTERACTANT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_ISOFORM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_KIN_KM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_KIN_VMAX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_KINETICS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_LINK_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_LINK_URI_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_LOCTYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_METHOD_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_ORGANISMS_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_PH_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_REDOX_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- COMMENT_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- COMMENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- COMMENT_TEMPERATURE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- commentLine(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
-
A comment line has been encountered.
- commentLine(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
-
- commentLine(String) - Method in class org.biojava.bio.program.gff.GFFWriter
-
Prints the comment directly to the PrintWriter
after adding a leading '#'.
- commentLine(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
-
A comment line has been encountered.
- commit() - Method in class org.biojava.bio.program.indexdb.BioStore
-
commit writes an index to disk.
- commit() - Method in class org.biojava.bio.seq.db.BioIndex
-
- commit() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
commit commits changes.
- commit() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Commit the stored indices to permanent storage.
- commit() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- commit() - Method in interface org.biojava.utils.Commitable
-
commit commits pending changes.
- commit() - Method in class org.biojava.utils.FileAsList
-
- Commitable - Interface in org.biojava.utils
-
Implementations of Commitable support atomic changes
from one known state to another via commit/rollback semantics.
- CommitFailure - Exception in org.biojava.utils
-
- CommitFailure(String) - Constructor for exception org.biojava.utils.CommitFailure
-
- CommitFailure(Throwable) - Constructor for exception org.biojava.utils.CommitFailure
-
- CommitFailure(String, Throwable) - Constructor for exception org.biojava.utils.CommitFailure
-
- commitStore() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- COMMON - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
Use this to define common names for things.
- COMMON_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- COMNAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CompactedDataStore - Class in org.biojava.bio.program.ssaha
-
An implementation of DataStore that will map onto a file using the NIO
constructs.
- CompactedDataStoreFactory - Class in org.biojava.bio.program.ssaha
-
Builder for a data store that is backed by a java.nio.MappedByteBuffer.
- CompactedDataStoreFactory() - Constructor for class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
-
- ComparableOntology - Interface in org.biojavax.ontology
-
An Ontology that can be compared to another.
- ComparableTerm - Interface in org.biojavax.ontology
-
Makes Term objects comparable properly and adds some extra features to them.
- ComparableTriple - Interface in org.biojavax.ontology
-
Comparable triples, obviously.
- comparator() - Static method in class org.biojava.bio.seq.ByLocationMinMaxComparator
-
- COMPARATOR - Static variable in class org.biojava.ontology.Synonym
-
- compare(Object, Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.seq.ByLocationMinMaxFeatureComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.seq.Feature.ByLocationComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.seq.io.EmblReferenceComparator
-
- compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblFeatureComparator
-
Deprecated.
- compare(Object, Object) - Method in class org.biojava.bio.seq.io.GenEmblPropertyComparator
-
Deprecated.
- compare(AlternativeAlignment, AlternativeAlignment) - Method in class org.biojava.bio.structure.align.pairwise.AltAligComparator
-
- compareTo(Synonym) - Method in class org.biojava.ontology.Synonym
-
- compareTo(Object) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Locations are sorted first by rank, then crossref, then
strand, then term, then min, then max.
- compareTo(Object) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Empty Rich Locations return 0 when compared to other Empty ones,
or -1 otherwise.
- compareTo(Object) - Method in class org.biojavax.bio.seq.RichLocation.Strand
-
Strands are compared first by symbol, then by number.
- compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Features are sorted first by rank, then parent, type, and source.
- compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Relations are compared first by rank, then object, subject, then finally term.
- compareTo(Object) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Locations are sorted first by rank, then crossref, then
strand, then term, then min, then max.
- compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntry
-
Bioentries are ordered first by namespace, then name, accession, and
finally version.
- compareTo(Object) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
A relationship is compared first by rank, then object, subject, and term.
- compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
NCBITaxon objects are compared only by their NCBITaxID fields.
- compareTo(Object) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Taxon names are sorted by class first, then name.
- compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Ontologies are compared only by name.
- compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Terms are sorted by ontology first, then name.
- compareTo(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Triples are sorted in order of ontology, subject, object, and finally
predicate.
- compareTo(Object) - Method in class org.biojavax.SimpleComment
-
Comments are ordered first by their rank, then by a string
comparison of their text values.
- compareTo(Object) - Method in class org.biojavax.SimpleCrossRef
-
Compares cross references first by database name, then by accession,
then by version.
- compareTo(Object) - Method in class org.biojavax.SimpleDocRef
-
Document references are compared first by author, then by location, then
by title.
- compareTo(Object) - Method in class org.biojavax.SimpleDocRefAuthor
-
Document authors are compared first by name, then consortium status, then editor status.
- compareTo(Object) - Method in class org.biojavax.SimpleNamespace
-
Namespaces are compared only by name.
- compareTo(Object) - Method in class org.biojavax.SimpleNote
-
Notes are compared first by rank, then by the term.
- compareTo(Object) - Method in class org.biojavax.SimpleRankedCrossRef
-
Ranked cross references are sorted first by rank, then by cross reference.
- compareTo(Object) - Method in class org.biojavax.SimpleRankedDocRef
-
Ranked document references are sorted first by rank then location
then by actual document reference.
- compile(String) - Method in class org.biojava.utils.regex.PatternFactory
-
Returns a Pattern object that applies the specified regex
against SymbolLists in the Alphabet that this PatternFactory
was defined against.
- compile(String, String) - Method in class org.biojava.utils.regex.PatternFactory
-
Returns a Pattern object that applies the specified regex
against SymbolLists in the Alphabet that this PatternFactory
was defined against.
- complement(Symbol) - Static method in class org.biojava.bio.seq.DNATools
-
Complement the symbol.
- complement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
-
Retrieve a complement view of list.
- COMPLEMENT - Static variable in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- complement(Symbol) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Complement the symbol.
- complement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Retrieve a complement view of list.
- complement(Symbol) - Static method in class org.biojava.bio.seq.RNATools
-
Complement the symbol.
- complement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
-
Retrieve a complement view of list.
- complementTable() - Static method in class org.biojava.bio.seq.DNATools
-
Get a translation table for complementing DNA symbols.
- complementTable() - Static method in class org.biojava.bio.seq.NucleotideTools
-
Get a translation table for complementing Nucleotide symbols.
- complementTable() - Static method in class org.biojava.bio.seq.RNATools
-
Get a translation table for complementing DNA symbols.
- completeCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
-
indicate that a cycle of training is completed and the
emission/transition matrices should be updated.
- completeCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
-
- completedActivity(Object) - Static method in class org.biojava.bio.program.das.DAS
-
- completedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
-
Notification that an activity is complete.
- COMPONENT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- ComponentFeature - Interface in org.biojava.bio.seq
-
Feature which represents a component in an assembly (contig).
- ComponentFeature.Template - Class in org.biojava.bio.seq
-
Template for constructing a new ComponentFeature.
- ComponentFeature.Template() - Constructor for class org.biojava.bio.seq.ComponentFeature.Template
-
- componentLocation - Variable in class org.biojava.bio.seq.ComponentFeature.Template
-
- componentLocationIterator() - Method in class org.biojava.bio.symbol.MergeLocation
-
- componentSequence - Variable in class org.biojava.bio.seq.ComponentFeature.Template
-
- componentSequenceName - Variable in class org.biojava.bio.seq.ComponentFeature.Template
-
- composeName(Name, Name) - Method in class org.biojava.naming.ObdaContext
-
- composeName(String, String) - Method in class org.biojava.naming.ObdaContext
-
- Composition - Class in org.biojava.bio.molbio
-
Computes composition statistics about a SymbolList.
- Composition() - Constructor for class org.biojava.bio.molbio.Composition
-
- Compound - Class in org.biojava.bio.structure
-
Created by IntelliJ IDEA.
- Compound() - Constructor for class org.biojava.bio.structure.Compound
-
- CompoundRichLocation - Class in org.biojavax.bio.seq
-
An implementation of RichLocation which covers multiple locations,
but on the same strand of the same (optionally circular) sequence.
- CompoundRichLocation(Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
-
Constructs a CompoundRichLocation from the given set of members, with
the default term of "join".
- CompoundRichLocation(ComparableTerm, Collection) - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
-
Constructs a CompoundRichLocation from the given set of members.
- CompoundRichLocation() - Constructor for class org.biojavax.bio.seq.CompoundRichLocation
-
- compute(double) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc.ChargeCalculator
-
computes charge at given pH
- compute(double) - Method in interface org.biojava.utils.math.ComputeObject
-
workhorse method for this class.
- ComputeObject - Interface in org.biojava.utils.math
-
interface for classes that return a single
double precision value for a single double
precision argument.
- cond() - Method in class org.biojava.bio.structure.jama.Matrix
-
Matrix condition (2 norm)
- cond() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Two norm condition number
- conditionedDistributions() - Method in interface org.biojava.bio.dist.OrderNDistribution
-
Get the conditioned distributions.
- CONFIG_FILE - Static variable in class org.biojava.directory.SystemRegistry
-
- CONFIG_LOCATOR - Static variable in class org.biojava.directory.SystemRegistry
-
- conjunctAdd - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
-
- conjunction - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
-
- connect() - Method in interface org.biojava.bibliography.BibRefQuery
-
It creates a connection to a bibliographic repository, or/and it makes
all necessary initialization steps needed for further communication.
- connect(byte[]) - Method in interface org.biojava.bibliography.BibRefQuery
-
It creates a connection to a bibliographic repository, or/and it makes
all necessary initialization steps needed for further communication,
and it makes the collection described by collectionId
the current collection.
- connect() - Method in interface org.biojava.bibliography.BibRefSupport
-
It creates a connection to an object providing the supporting
utilities, or/and it makes all necessary initialization steps
needed for further communication.
- connect() - Method in interface org.biojava.utils.candy.CandyFinder
-
It creates a connection to an object representing a vocabulary
finder, or/and it makes all necessary initialization steps
needed for further communication.
- connectModel() - Method in class org.biojava.bio.dp.ProfileHMM
-
This is called by constructor in setting up the allowed transitions in the model
- connectModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileHMM
-
This is called by constructor in setting up the allowed transitions in the model
- connectToBioSQL(Object) - Static method in class org.biojavax.RichObjectFactory
-
A utility method that configures the RichObjectFactory for use with a Hibernate session.
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- CONSORTIUM_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- Constants - Class in org.biojava.utils
-
Some usefull constants for working with binary files.
- Constants() - Constructor for class org.biojava.utils.Constants
-
- construct(Collection<Location>) - Static method in class org.biojavax.bio.seq.RichLocation.Tools
-
Constructs a RichLocation object based on the given collection of
members.
- constructSubsets() - Method in class org.biojava.utils.automata.DfaBuilder
-
- constructWithCopy(double[][]) - Static method in class org.biojava.bio.structure.jama.Matrix
-
Construct a matrix from a copy of a 2-D array.
- containedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features with locations wholly contained
by the specified Location.
- contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.AbstractOrthoPairCollection
-
- contains(OrthoPairSet) - Method in interface org.biojava.bio.program.homologene.OrthoPairCollection
-
- contains(OrthoPairSet) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
-
- contains(Symbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocation
-
- contains(Location) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- contains(int) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- contains(int) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
-
- contains(Symbol) - Method in interface org.biojava.bio.symbol.Alphabet
-
Returns whether or not this Alphabet contains the symbol.
- contains(int) - Method in class org.biojava.bio.symbol.CircularLocation
-
- contains(Location) - Method in class org.biojava.bio.symbol.CircularLocation
-
- contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- contains(Symbol) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- contains(Location) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- contains(int) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- contains(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- contains(Location) - Method in interface org.biojava.bio.symbol.Location
-
Checks if this location contains the other.
- contains(int) - Method in interface org.biojava.bio.symbol.Location
-
Checks if this location contains a point.
- contains(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return true iff all indices in locB are also contained
by locA.
- contains(int) - Method in class org.biojava.bio.symbol.PointLocation
-
- contains(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
- contains(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It checks if a given entry exists in this vocabulary.
- contains(Object) - Method in class org.biojava.utils.MergingSet
-
- contains(Object) - Method in class org.biojava.utils.SmallSet
-
- contains(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Checks if this location contains a point.
- contains(Location) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Checks if this location contains the other.
- contains(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Checks if this location contains a point.
- contains(Location) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Checks if this location contains the other.
- contains(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Checks if this location contains a point.
- contains(Location) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Checks if this location contains the other.
- contains(Note) - Method in class org.biojavax.EmptyRichAnnotation
-
Returns true if the given note exists in this annotation.
- contains(Object) - Method in class org.biojavax.ga.util.WeightedSet
-
- contains(Note) - Method in interface org.biojavax.RichAnnotation
-
Returns true if the given note exists in this annotation.
- contains(Note) - Method in class org.biojavax.SimpleRichAnnotation
-
Returns true if the given note exists in this annotation.
- CONTAINS_PREFIX - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- containsAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
-
- containsFeature(Feature) - Method in class org.biojava.bio.program.das.DASSequence
-
- containsFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
-
Check if the feature is present in this holder.
- containsFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
containsFeature() will return true if this seq contains the feature in question, or
if if the original (non reverse complement) sequence contains the feature;
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.MergeFeatureHolder
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- containsFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
- containsFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Check if the feature is present in this holder.
- containsFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Check if the feature is present in this holder.
- containsFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
Returns true if the given
FeatureFilter is already contained in this
renderer.
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- containsImpl(AtomicSymbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- containsKey(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
-
- containsKey(Object) - Method in class org.biojava.utils.OverlayMap
-
- containsKey(Object) - Method in class org.biojava.utils.SmallMap
-
- containsName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Tests for the presence of a name in a given class.
- containsName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Tests for the presence of a name in a given class.
- containsNode(FiniteAutomaton.Node) - Method in class org.biojava.utils.automata.Nfa
-
- containsProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
-
- containsProperty(Object) - Method in interface org.biojava.bio.Annotation
-
Returns whether there the property is defined.
- containsProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
-
- containsProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
-
- containsProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
-
Returns whether there the property is defined.
- containsProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
-
Deprecated.
- containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
Detects whether a particular table is present in the database.
- containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
-
Deprecated.
- containsTable(DataSource, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- containsTerm(String) - Method in class org.biojava.ontology.IntegerOntology
-
- containsTerm(String) - Method in interface org.biojava.ontology.Ontology
-
Determines if this ontology currently contains a term named name
- containsTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
-
- containsTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Determines if this ontology currently contains a term named name
- containsTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Returns wether a transition exists or not.
- containsTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- containsTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
-
- containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
-
- containsTriple(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
-
See if a triple exists in this ontology
- containsTriple(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
-
- containsTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
See if a triple exists in this ontology
- CONTENT - Static variable in interface org.biojava.bio.symbol.Alignment
-
Signals that SymbolLists will be added to or removed from an alignment.
- contextForLabel(SequenceRenderContext, Object) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- CONTIG_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- contributors - Variable in class org.biojava.bibliography.BibRef
-
The authors and contributors are responsible for creating the contents of the cited resource.
- convert() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
-
- convert() - Method in class org.biojava.bio.program.PdbToXMLConverter
-
- convert(FeatureFilter) - Static method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Tools
-
Convert a non-BioSQL FeatureFilter into a BioSQL one.
- convert_3code_1code(String) - Static method in class org.biojava.bio.structure.StructureTools
-
convert three character amino acid codes into single character
e.g.
- convertValueToText(Object, boolean, boolean, boolean, int, boolean) - Method in class org.biojava.bio.gui.FeatureTree
-
Labels Sequence objects with their name, Annotations with
the tag Annotations, Features with the tag Features and other objects
with the toString value.
- COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- COORDINATE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- coordinateDisplayOn(boolean) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
-
coordinateDisplayOn toggles the display of
sequence coordinates.
- CoordManager - Class in org.biojava.bio.structure.gui.util
-
a class that manages the conversion of sequence coordinate system to
JPanel drawing coordinates
- CoordManager() - Constructor for class org.biojava.bio.structure.gui.util.CoordManager
-
- copy() - Method in class org.biojava.bio.structure.jama.Matrix
-
Make a deep copy of a matrix
- COPYRIGHT_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- cost - Variable in class org.biojava.bibliography.BiblioWebResource
-
The cost of accessing the resource.
- CostMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
-
A matrix with the size length(sequence1) times length(sequence2)
- Count - Interface in org.biojava.bio.dist
-
An encapsulation of a count over the Symbols within an alphabet.
- CountedBufferedReader - Class in org.biojava.utils.io
-
- CountedBufferedReader(Reader) - Constructor for class org.biojava.utils.io.CountedBufferedReader
-
- countFeatures() - Method in class org.biojava.bio.program.das.DASSequence
-
- countFeatures() - Method in interface org.biojava.bio.seq.FeatureHolder
-
Count how many features are contained.
- countFeatures() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- countFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- countFeatures() - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- countFeatures() - Method in class org.biojava.bio.seq.MergeFeatureHolder
-
- countFeatures() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- countFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- countFeatures() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- countFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
- countFeatures() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Count how many features are contained.
- countFeatures() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Count how many features are contained.
- COUNTS - Static variable in interface org.biojava.bio.dist.Count
-
Whenever a component count changes the values that would be returned by
getCount, they should fire a ChangeEvent with this object as the type.
- countToDistribution(Count) - Static method in class org.biojava.bio.dist.DistributionTools
-
Make a distribution from a count.
- coverage - Variable in class org.biojava.bibliography.BibRef
-
It defines an extent or scope of the content of the cited resource.
- coverage(Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return the number of positions which are covered by a Location
- CRC64Checksum - Class in org.biojavax.utils
-
Utility class that calculates a CRC64 checksum on a stream of bytes.
- CRC64Checksum() - Constructor for class org.biojavax.utils.CRC64Checksum
-
- create(File) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
-
Creates a new Chromatogram object from the named file.
- create(InputStream) - Static method in class org.biojava.bio.chromatogram.ChromatogramFactory
-
Creates a new Chromatogram object from the supplied stream.
- create(File) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
-
Create a new ABIF object from a file.
- create(InputStream) - Static method in class org.biojava.bio.program.abi.ABIFChromatogram
-
Create a new ABIF object from a stream of bytes.
- create(File) - Static method in class org.biojava.bio.program.scf.SCF
-
- create(InputStream, long) - Static method in class org.biojava.bio.program.scf.SCF
-
- CREATE_DATE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- CREATE_DUMMYSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
-
- CREATE_REALSEQ - Static variable in class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
-
- CREATE_REL_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- createBinary(String) - Static method in class org.biojavax.ga.util.GATools
-
Creates a SymbolList in the GABinary Alphabet
- createBioStore() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
createBioStore creates a BioStore
reflecting the current state of the factory and returns a
reference to it.
- createDistribution(Alphabet) - Method in interface org.biojava.bio.dist.DistributionFactory
-
Generate a new Distribution as requested.
- createDistribution(Alphabet) - Method in class org.biojava.bio.dist.DistributionFactory.DefaultDistributionFactory
-
- createDistribution(Alphabet) - Method in class org.biojava.bio.dist.OrderNDistributionFactory
-
Creates an OrderNDistribution of the appropriate type.
- createDNA(String) - Static method in class org.biojava.bio.seq.DNATools
-
Return a new DNA SymbolList for
dna.
- createDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
-
Return a new DNA Sequence for
dna.
- createDP(MarkovModel) - Method in interface org.biojava.bio.dp.DPFactory
-
- createDP(MarkovModel) - Method in class org.biojava.bio.dp.DPFactory.DefaultFactory
-
- createDummy(String, String) - Static method in class org.biojava.bio.seq.SequenceTools
-
Create a new Sequence that has no annotation, no features and a zero-length
symbol list.
- createDummy(Alphabet, int, Symbol, String, String) - Static method in class org.biojava.bio.seq.SequenceTools
-
Create a new Sequence that contains a single symbol repeated over and over.
- createDummySequence(String, Alphabet, int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- createEmblParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.program.das.DASSequence
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.CircularView
-
Over rides ViewSequence to allow the use of locations that have
coordinates outside of the sequence length (which are needed to
describe locations that overlap the origin of a circular sequence).
- createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.FeatureHolder
-
Create a new Feature, and add it to this FeatureHolder.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.DummySequence
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
createFeature() will call createFeature() on the underlying Sequence.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- createFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
Deprecated.
Please use new 1-arg createFeature instead.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- createFeature(Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Create a projected feature with properties matching the template.
- createFeature(Feature, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Create a new projected feature.
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- createFeature(Feature, Feature.Template) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- createFeature(Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Create a new Feature, and add it to this FeatureHolder.
- createFeature(Feature.Template) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Create a new Feature, and add it to this FeatureHolder.
- createFeatureHolder() - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- createFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
Create a new template of the appropriate type.
- createFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
-
- createGappedDNASequence(String, String) - Static method in class org.biojava.bio.seq.DNATools
-
Get a new dna as a GappedSequence
- createGappedProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
-
Get a new protein as a GappedSequence
- createGFFRecord(Feature, String) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Internal method to create a GFFRecord
from an individual Feature.
- createImmutableAlignment(Map) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
A factory method for creating new immutable alignments, particularly
for use as base call alignments.
- createImmutableSymbolList(Alphabet, List) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
A factory method for creating new symbol lists with a given alphabet.
- createInnerBounds(CircularRendererContext) - Static method in class org.biojava.bio.gui.sequence.GUITools
-
- createList(List) - Static method in class org.biojava.utils.ListTools
-
- createList(Object[]) - Static method in class org.biojava.utils.ListTools
-
- createMatches() - Method in class org.biojava.bio.symbol.SimpleAtomicSymbol
-
- createMMcifInfoList(File[], File, File) - Method in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
-
parses a set of PDB files and writes info into a file
the file is tab separated and has the following columns:
name length resolution depositionDate modificationDate technique title classification filename
binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup
This method needs to be run, before a DBSearch can be performed, since the files created by this method
are required for the DBSearch
- createNodeSet() - Method in class org.biojava.utils.automata.FiniteAutomaton
-
- createNodeSet() - Method in interface org.biojava.utils.automata.NfaBuilder
-
- createNodeSet() - Method in class org.biojava.utils.automata.NfaSubModel
-
- createNucleotide(String) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Return a new Nucleotide SymbolList for
nucleotide.
- createNucleotideSequence(String, String) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Return a new Nucleotide Sequence for
nucleotide.
- createOntology(String, String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- createOntology(String, String) - Method in interface org.biojava.ontology.OntologyFactory
-
Creates a new Ontology
- createOntologyTerm(Ontology) - Method in class org.biojava.ontology.Ontology.Impl
-
- createOrthologue(Taxon, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create an orthologue.
- createOrthologue(int, String, String, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create an orthologue.
- createOrthologue(Taxon, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- createOrthologue(int, String, String, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create a computed orthology entry.
- createOrthoPair(Orthologue, Orthologue, String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create a curated orthology entry.
- createOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- createOrthoPair(Orthologue, Orthologue, String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- createOrthoPairSet() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Create a Homologene Group.
- createOrthoPairSet() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- createOuterBounds(CircularRendererContext, double) - Static method in class org.biojava.bio.gui.sequence.GUITools
-
- createPDBInfoList(File[], File, File) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
-
parses a set of PDB files and writes info into a file
the file is tab separated and has the following columns:
name length resolution depositionDate modificationDate technique title classification filename
binaryDirectory: a directory in which binary files containing the atoms will be places, to provide a speedup
This method needs to be run, before a DBSearch can be performed, since the files created by this method
are required for the DBSearch
- createPhred(SymbolList, SymbolList) - Static method in class org.biojava.bio.program.phred.PhredTools
-
Merges a Symbol List from the DNA alphabet with a SymbolList from the
[0..99] subset of the IntegerAlphabet into a SymbolList from
the PHRED alphabet.
- createProtease(SymbolList, boolean, SymbolList, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
Creates and registers a new Protease.
- createProtease(SymbolList, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- createProtease(String, boolean, String, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- createProtease(String, boolean, String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- createProtein(String) - Static method in class org.biojava.bio.seq.ProteinTools
-
Return a new Protein SymbolList for protein.
- createProteinSequence(String, String) - Static method in class org.biojava.bio.seq.ProteinTools
-
Return a new PROTEIN Sequence for
protein.
- createRecord(GFFDocumentHandler, List, String, String) - Method in class org.biojava.bio.program.gff.GFFParser
-
Actually turns a list of tokens, some value string and a comment into a
GFFRecord and informs
handler.
- createRecord(GFF3DocumentHandler, List, String, String, Ontology, Ontology) - Method in class org.biojava.bio.program.gff3.GFF3Parser
-
Actually turns a list of tokens, some value string and a comment into a
GFF3Record and informs
handler.
- createRegex(SymbolList) - Static method in class org.biojava.bio.symbol.MotifTools
-
createRegex creates a regular expression which
matches the SymbolList.
- createRenderer(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- createRenderer(int) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
-
- createRichSequence(String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the default namespace.
- createRichSequence(String, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the specified namespace.
- createRichSequence(Namespace, String, String, Alphabet) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the specified namespace.
- createRichSequence(String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the default namespace.
- createRichSequence(Namespace, String, SymbolList) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Create a new RichSequence in the specified namespace.
- createRNA(String) - Static method in class org.biojava.bio.seq.RNATools
-
Return a new RNA SymbolList for
rna.
- createRNASequence(String, String) - Static method in class org.biojava.bio.seq.RNATools
-
Return a new RNA Sequence for
rna.
- createSequence(SymbolList, String, String, Annotation) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
-
- createSequence(SymbolList, String, String, Annotation) - Method in interface org.biojava.bio.seq.SequenceFactory
-
Deprecated.
Creates a sequence using these parameters.
- createSequence(SymbolList, String, String, Annotation) - Static method in class org.biojava.bio.seq.SequenceTools
-
- createSeriesList(String, String, int) - Static method in class org.biojava.utils.ListTools
-
Create a new SeriesList with the given leader, trailer and size.
- createState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- createSubcontext(Name) - Method in class org.biojava.naming.ObdaContext
-
- createSubcontext(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
-
- createSubcontext(String) - Method in class org.biojava.naming.ObdaContext
-
- createSubcontext(String, Attributes) - Method in class org.biojava.naming.ObdaContext
-
- createSwissprotParserListener(TagValueListener) - Static method in class org.biojava.bio.program.tagvalue.Formats
-
- createSymbol(String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generate a new AtomicSymbol instance with a name and Annotation.
- createSymbol(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generate a new AtomicSymbol instance with a name and an Empty Annotation.
- createSymbol(char, String, Annotation) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.
Use the two-arg version of this method instead.
- createSymbol(char, Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.
use the new version, without the token argument
- createSymbol(Annotation, List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generates a new Symbol instance that represents the tuple of Symbols in
symList.
- createSymbol(char, Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.
use the three-arg version of this method instead.
- createSymbol(Annotation, Set, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generates a new Symbol instance that represents the tuple of Symbols in
symList.
- createTaxon(int, String) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
-
add a Taxon
- createTaxon(String, String) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- createTaxon(String, String) - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.
Create a new orphan Taxon with a given scientific and common
name.
- createTaxon(String, String) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- createTemplate() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
generates a very basic Template for the feature with
SmallAnnotation in the annotation field.
- createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
-
- createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
-
- createTemplate() - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
-
- createTemplate() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
generates a very basic Template for the feature with
SmallAnnotation in the annotation field.
- createTerm(String) - Method in class org.biojava.ontology.IntegerOntology
-
- createTerm(String, String) - Method in class org.biojava.ontology.IntegerOntology
-
- createTerm(String, String, Object[]) - Method in class org.biojava.ontology.IntegerOntology
-
- createTerm(String) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String, String, Object[]) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology.
- createTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
-
- createTerm(String, String) - Method in class org.biojava.ontology.Ontology.Impl
-
- createTerm(String, String, Object[]) - Method in class org.biojava.ontology.Ontology.Impl
-
- createTerm(String, String, Object[]) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology.
- createTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology.
- createTerm(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology.
- createTransition(State, State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Makes a transition between two states legal.
- createTransition(State, State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- createTransition(State, State) - Method in class org.biojava.bio.dp.WMAsMM
-
- createTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.IntegerOntology
-
- createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.ontology.Ontology
-
Creates a new Triple.
- createTriple(Term, Term, Term, String, String) - Method in class org.biojava.ontology.Ontology.Impl
-
- createTriple(Term, Term, Term, String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Creates a new Triple.
- createType(String, FeatureFilter, Set) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
Create a new type in this repository.
- createUnigene(URL) - Method in class org.biojava.bio.program.unigene.FlatFileUnigeneFactory
-
- createUnigene(URL) - Method in class org.biojava.bio.program.unigene.SQLUnigeneFactory
-
- createUnigene(URL) - Method in interface org.biojava.bio.program.unigene.UnigeneFactory
-
- createUnigene(URL) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
-
Create a new UnigeneDB instance referred to by a URL.
- createURL(Object) - Method in interface org.biojava.utils.net.URLFactory
-
createURL returns a URL which is relevant to the
object in a way specified by the implementation.
- createVariable(String, String) - Method in class org.biojava.ontology.IntegerOntology
-
- createVariable(String, String) - Method in interface org.biojava.ontology.Ontology
-
Create a new term in this ontology that is used as a variable.
- createVariable(String, String) - Method in class org.biojava.ontology.Ontology.Impl
-
- createVariable(String, String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Create a new term in this ontology that is used as a variable.
- createVirtualCBAtom(AminoAcid) - Static method in class org.biojava.bio.structure.Calc
-
creates a virtual C-beta atom.
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptAllFilter
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLAcceptNoneFilter
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
- criterionAliasMap() - Method in interface org.biojavax.bio.db.biosql.BioSQLFeatureFilter
-
Returns a map of property names (keys) to aliases (values), if the criterion
returned by asCriterion() uses aliases at all.
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
-
- criterionAliasMap() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
- CROSS_OVER_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
-
- CROSS_PROB - Static variable in interface org.biojavax.ga.functions.CrossOverFunction
-
- CrosshairRenderer - Class in org.biojava.bio.gui.sequence
-
CrosshairRenderer draws a crosshair, optionally
with coordinates.
- CrosshairRenderer() - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
-
Creates a new CrosshairRenderer in light grey with
coordinates displayed.
- CrosshairRenderer(Paint) - Constructor for class org.biojava.bio.gui.sequence.CrosshairRenderer
-
Creates a new CrosshairRenderer of the specified
colour, with coordinates displayed.
- CrossOverFunction - Interface in org.biojavax.ga.functions
-
Crosses two chromosomes.
- CrossOverFunction.NoCross - Class in org.biojavax.ga.functions
-
A place holder CrossOverFunction that doesn't perform cross overs
- CrossOverFunction.NoCross() - Constructor for class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- CrossProductTokenization - Class in org.biojava.bio.seq.io
-
Tokenization for cross-product alphabets.
- CrossProductTokenization(Alphabet) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
-
- CrossProductTokenization(Alphabet, List) - Constructor for class org.biojava.bio.seq.io.CrossProductTokenization
-
- CROSSREF - Static variable in interface org.biojavax.bio.seq.RichFeature
-
- CrossRef - Interface in org.biojavax
-
Represents a cross reference to another database.
- CROSSREF - Static variable in interface org.biojavax.DocRef
-
- CrossReferenceResolutionException - Exception in org.biojavax
-
An exception that indicates that an attempt to resolve a CrossRef
has failed.
- CrossReferenceResolutionException() - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException
- CrossReferenceResolutionException(String) - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException with a
message.
- CrossReferenceResolutionException(String, Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException with a
message and a cause.
- CrossReferenceResolutionException(Throwable) - Constructor for exception org.biojavax.CrossReferenceResolutionException
-
Creates a new instance of CrossReferenceResolutionException with a
cause.
- CrossReferenceResolver - Interface in org.biojavax
-
This interface returns symbols or sequence for a given cross-reference.
- crossReferences - Variable in class org.biojava.bibliography.BibRef
-
It is an array of identifiers, all of them pointing to the same cited source
but usually stored in different bibliographic repositories.
- crypticVariable - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
-
- cState() - Method in class org.biojava.bio.program.hmmer.FullHmmerProfileHMM
-
Gets the c loop state
- CURATED - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
- CURATED - Static variable in interface org.biojava.bio.program.homologene.SimilarityType
-
- currentCol() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
The current column of the matrix.
- currentCol() - Method in class org.biojava.bio.dp.onehead.SmallCursor
-
- currentRes() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
The current symbol.
- CUT_COMPOUND - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
CUT_COMPOUND a cut type where the enzyme cuts in
two positions relative to the recognition site.
- CUT_SIMPLE - Static variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
CUT_SIMPLE a cut type where the enzyme cuts in one
position relative to the recognition site.
- cutType - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
- cys() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Cysteine (C)
- g() - Static method in class org.biojava.bio.seq.DNATools
-
- g() - Static method in class org.biojava.bio.seq.NucleotideTools
-
- g() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Glycine
- g() - Static method in class org.biojava.bio.seq.RNATools
-
- GACross - Interface in org.biojavax.ga.functions
-
Holds the results of a CrossOver event, objects of this type are made by
CrossOverFunctions
- GACrossResult - Interface in org.biojavax.ga.functions
-
Holds the results of a CrossOver event, objects of this type are made by
CrossOverFunctions
- GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
-
- GAME_ANNOTATION_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
-
Description of the Field
- GAME_ASPECT_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEAspectHandler
-
- GAME_ASPECT_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
-
- GAME_DBXREF_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEDbxrefHandler
-
Description of the Field
- GAME_DBXREF_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler
-
- GAME_DESCRIPTION_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
-
- GAME_FEATURE_SET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
-
Description of the Field
- GAME_FEATURE_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
-
Description of the Field
- GAME_FEATURESET_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
-
- GAME_FEATURESET_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSetPropHandler
-
- GAME_FEATURESPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
-
- GAME_GENE_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
-
Description of the Field
- GAME_GENE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
-
- GAME_MAP_POS_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
-
- GAME_NAME_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMENamePropHandler
-
- GAME_PROPERTY_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMEPropertyHandler
-
Description of the Field
- GAME_RESIDUES_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
-
- GAME_SEQ_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqHandler
-
Description of the Field
- GAME_SEQ_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
-
- GAME_SEQ_REL_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
-
Description of the Field
- GAME_SEQREL_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESeqRelPropHandler
-
- GAME_SPAN_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game12.GAMESpanHandler
-
Description of the Field
- GAME_SPAN_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMESpanPropHandler
-
- GAME_TYPE_PROP_HANDLER_FACTORY - Static variable in class org.biojava.bio.seq.io.game.GAMETypePropHandler
-
- GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <annotation> element
- GAMEAnnotationHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <annotation> element
- GAMEAspectHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <aspect> element
- GAMEAspectPropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <aspect> element
- GAMEDbxrefHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <dbxref> element
- GAMEDbxrefPropHandler - Class in org.biojava.bio.seq.io.game
-
Deals with database crossreferences
- GAMEDbxrefPropHandler.DbXrefElement - Class in org.biojava.bio.seq.io.game
-
- GAMEDescriptionPropHandler - Class in org.biojava.bio.seq.io.game
-
StAX handler for GAME <description> elements.
- GAMEDescriptionPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
-
- GAMEFeatureCallbackItf - Interface in org.biojava.bio.seq.io.game
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game
-
Handles the <feature_set> element
- GAMEFeatureSetHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <feature_set> element
this element is used to represent transcripts.
- GAMEFeatureSetPropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME element
- GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game
-
Handles the <feature_span> element
- GAMEFeatureSpanHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <feature_span> element
- GAMEFeatureSpanHandler.SeqRelHandler - Class in org.biojava.bio.seq.io.game12
-
- GAMEFormat - Class in org.biojava.bio.seq.io
-
A rudimentary read-only GAME 1.2 Format object.
- GAMEFormat() - Constructor for class org.biojava.bio.seq.io.GAMEFormat
-
- GAMEGeneHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <annotation> element
- GAMEGenePropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <gene> element
- GAMEHandler - Class in org.biojava.bio.seq.io.game
-
Handles the root GAME element
- GAMEHandler() - Constructor for class org.biojava.bio.seq.io.game.GAMEHandler
-
- GAMEHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the root GAME element
- GAMEHandler(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.game12.GAMEHandler
-
Constructor for the GAMEHandler object
- GAMEMapPosPropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <map_position> element
Currently, it just ignores it!
- GAMENameCallbackItf - Interface in org.biojava.bio.seq.io.game
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- GAMENamePropHandler - Class in org.biojava.bio.seq.io.game
-
StAX handler for the GAME <name> element.
- GAMENamePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMENamePropHandler
-
- GAMEPropertyHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <dbxref> element
- GAMEResiduesPropHandler - Class in org.biojava.bio.seq.io.game
-
StAX handler for GAME <residues> elements.
- GAMEResiduesPropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
-
- GAMESeqHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <seq> element
- GAMESeqPropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <seq> element
- GAMESeqRelHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <> element
- GAMESeqRelPropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <aspect> element
- GAMESpanHandler - Class in org.biojava.bio.seq.io.game12
-
Handles the GAME <> element.
- GAMESpanPropHandler - Class in org.biojava.bio.seq.io.game
-
Handles the GAME <span> element
Currently, it just ignores it!
- GAMETranscriptCallbackItf - Interface in org.biojava.bio.seq.io.game
-
An interface that can be tested for by nested handlers
when trying to do a callback.
- GAMETypePropHandler - Class in org.biojava.bio.seq.io.game
-
StAX handler for GAME <type> elements.
- GAMETypePropHandler(StAXFeatureHandler) - Constructor for class org.biojava.bio.seq.io.game.GAMETypePropHandler
-
- GAP_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- GapArray - Class in org.biojava.bio.structure.align.helper
-
- GapArray() - Constructor for class org.biojava.bio.structure.align.helper.GapArray
-
- GapDistribution - Class in org.biojava.bio.dist
-
This distribution emits gap symbols.
- GapDistribution(Alphabet) - Constructor for class org.biojava.bio.dist.GapDistribution
-
Get a GapDistribution for an alphabet.
- GappedRenderer - Class in org.biojava.bio.gui.sequence
-
A renderer that will display a gapped sequence as a discontinuous series of
regions.
- GappedRenderer() - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
-
- GappedRenderer(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.GappedRenderer
-
- GappedSequence - Interface in org.biojava.bio.seq
-
Extension of GappedSymbolList which also projects features
into the gapped coordinate system.
- GappedSymbolList - Interface in org.biojava.bio.symbol
-
This extends SymbolList with API for manipulating, inserting and deleting
gaps.
- gappedToLocation(Location) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Translates a Location from the gapped view into the underlying sequence.
- gappedView(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
-
Create a new gapped sequence for a sequence.
- GAPS - Static variable in interface org.biojava.bio.alignment.EditableAlignment
-
- GAStoppingCriteria - Interface in org.biojavax.ga
-
Used by a GeneticAlgorithm.run() method
to determine when the algorithm should stop
- GAStoppingCriteria.MaximumGeneration - Class in org.biojavax.ga
-
Simple Implementation of GAStoppingCriteria, signals
a GeneticAlgorithm to stop after n generations
- GAStoppingCriteria.MaximumGeneration(int) - Constructor for class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
-
Public Constructer
- GATools - Class in org.biojavax.ga.util
-
Utility methods for the GA library
- GATools() - Constructor for class org.biojavax.ga.util.GATools
-
- GCG - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GCG indicates that the sequence format is GCG.
- ge - Variable in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.HibernateFeatureFilter
-
- GENBANK - Static variable in class org.biojava.bio.program.tagvalue.LineSplitParser
-
A LineSplitParser pre-configured to process GENBANK-style flat files.
- GENBANK - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GENBANK indicates that the sequence format is
GENBANK.
- GENBANK_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GENBANK_DNA premade GENBANK | AA.
- GENBANK_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GENBANK_DNA premade GENBANK | DNA.
- GENBANK_FORMAT - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
The name of this format
- GENBANK_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GENBANK_DNA premade GENBANK | RNA.
- GenbankFileFormer - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- GenbankFileFormer() - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
Creates a new GenbankFileFormer using
System.out stream.
- GenbankFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
Creates a new GenbankFileFormer using the
specified stream.
- GenbankFormat - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat
- GenbankFormat() - Constructor for class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- GenbankFormat - Class in org.biojavax.bio.seq.io
-
Format reader for GenBank files.
- GenbankFormat() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat
-
- GenbankFormat.Terms - Class in org.biojavax.bio.seq.io
-
Implements some GenBank-specific terms.
- GenbankFormat.Terms() - Constructor for class org.biojavax.bio.seq.io.GenbankFormat.Terms
-
- GenbankLocationParser - Class in org.biojavax.bio.seq.io
-
Parses Genbank location strings into RichLocation objects.
- GenbankProcessor - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- GenbankProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.
- GenbankProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.
- GenbankProcessor.Factory - Class in org.biojava.bio.seq.io
-
Deprecated.
Factory which wraps sequence builders in a GenbankProcessor
- GenbankProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.GenbankProcessor.Factory
-
Deprecated.
- GenbankRichSequenceDB - Class in org.biojavax.bio.db.ncbi
-
This class contains functions accessing DNA sequences in Genbank format.
- GenbankRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
The default constructor delegates to the parent class.
- GenbankSequenceDB - Class in org.biojava.bio.seq.db
-
This class contains functions accessing DNA sequences in Genbank format.
- GenbankSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenbankSequenceDB
-
- GenbankXmlFormat - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat
- GenbankXmlFormat() - Constructor for class org.biojava.bio.seq.io.GenbankXmlFormat
-
Deprecated.
- GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- GENE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- GENELOCATION_NAME_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- GENELOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- GenEmblFeatureComparator - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- GenEmblPropertyComparator - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- GENENAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- generate(int) - Method in class org.biojava.bio.dp.DP
-
Generates an alignment from a model.
- generate() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Generates a comment string based on the current values of the
internal fields.
- generateAuthorString(List, boolean) - Static method in class org.biojavax.DocRefAuthor.Tools
-
Takes a set of authors and creates a comma-separated string.
- generateBackwardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
-
- generateCallboxes() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Precomputes the Rectangle2Ds that are the in-memory
representation of the callboxes.
- generateChangeSupport() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- generateChangeSupport() - Method in class org.biojava.utils.AbstractChangeable
-
Called the first time a ChangeSupport object is needed.
- generateCrossProductAlphaFromName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Generates a new CrossProductAlphabet from the give name.
- generateDrawableCallboxes(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Precomputes the callboxes in screen coordinates.
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.Annotatable.AnnotationForwarder
-
Deprecated.
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.dist.Distribution.NullModelForwarder
-
Deprecated.
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.PairwiseSequenceRenderer.PairwiseRendererForwarder
-
generateEvent generates events in response to
layout change and repaint requests.
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
-
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.MergeAnnotation.PropertyForwarder
-
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.OverlayAnnotation.PropertyForwarder
-
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
-
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditScreener
-
- generateEvent(ChangeEvent) - Method in class org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
-
- generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder
-
Return the new event to represent the originating event ce.
- generateEvent(ChangeEvent) - Method in class org.biojava.utils.ChangeForwarder.Retyper
-
- generateForardClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
-
- generateOrderNSequence(String, OrderNDistribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
-
Deprecated.
use generateSequence() or generateSymbolList() instead.
- generateRecord(byte[], Object) - Method in class org.biojava.utils.FileAsList
-
- generateSequence(String, Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
-
Produces a sequence by randomly sampling the Distribution.
- generateSubpaths() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Precomputes the GeneralPaths used to draw the
traces.
- generateSymbolList(Distribution, int) - Static method in class org.biojava.bio.dist.DistributionTools
-
Produces a SymbolList by randomly sampling a Distribution.
- generateViterbiClass(DP) - Method in class org.biojava.bio.dp.twohead.DPCompiler
-
- GENERIC_PROVIDER - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A name of a provider type.
- GENESYNONYM_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- GeneticAlgorithm - Interface in org.biojavax.ga
-
The class that runs the cycles of reproduction, evolution and selection,
potentially on multiple Populations
- GENETICCODE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
- GeneticCodes - Class in org.biojava.bio.seq
-
Collects the references to translation methods in one place.
- GENPEPT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GENPEPT indicates that the sequence format is
GENPEPT.
- GenpeptFormat - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- GenpeptFormat() - Constructor for class org.biojava.bio.seq.io.GenpeptFormat
-
Deprecated.
- GenpeptRichSequenceDB - Class in org.biojavax.bio.db.ncbi
-
This class contains functions accessing Peptide sequences in Genpept format.
- GenpeptRichSequenceDB() - Constructor for class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
The default constructor delegates to the parent class.
- GenpeptSequenceDB - Class in org.biojava.bio.seq.db
-
- GenpeptSequenceDB() - Constructor for class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- get(String) - Method in class org.biojava.bio.program.indexdb.BioStore
-
- get(String, String) - Method in class org.biojava.bio.program.indexdb.BioStore
-
- get(String) - Method in interface org.biojava.bio.program.indexdb.IndexStore
-
get returns a record specified by a primary
identifier.
- get(String, String) - Method in interface org.biojava.bio.program.indexdb.IndexStore
-
get returns a list of Records by
searching against the primary identifiers if the namespace
argument is equal to the primary namespace or otherwise by
searching the secondary namespaces.
- get(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
-
get the Transition associated with the specified tag.
- get(int, int) - Method in class org.biojava.bio.structure.jama.Matrix
-
Get a single element.
- get(int) - Method in class org.biojava.stats.svm.SparseVector
-
Retrieve the value at dimension dim.
- get(Object) - Method in interface org.biojava.utils.cache.CacheMap
-
Retrieve the Object associated with the key, or null if either no value has
been associated or if the key's value has been cleared by the cache.
- get() - Method in interface org.biojava.utils.cache.CacheReference
-
- get(Object) - Method in class org.biojava.utils.cache.ChangeableCache
-
- get(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
-
- get(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
-
- get(Object) - Method in class org.biojava.utils.cache.WeakValueHashMap
-
- get(int) - Method in class org.biojava.utils.FileAsList
-
- get(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- get() - Method in class org.biojava.utils.io.LargeBuffer
-
- get(int) - Method in class org.biojava.utils.ListTools.Doublet
-
- get(int) - Method in class org.biojava.utils.ListTools.SeriesList
-
- get(int) - Method in class org.biojava.utils.ListTools.Triplet
-
- get(Object) - Method in class org.biojava.utils.OverlayMap
-
- get(int) - Method in class org.biojava.utils.SingletonList
-
- get(Object) - Method in class org.biojava.utils.SmallMap
-
- get1LetterCode(String) - Static method in class org.biojava.bio.structure.StructureTools
-
convert a three letter code into single character.
- get3PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
-
- get5PrimeEnd() - Method in class org.biojava.bio.symbol.CircularLocation
-
The point at which indicates the 5' end of the Location.
- get_() - Method in class org.biojava.bio.proteomics.StructureTools
-
- get_structure() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
-
returns the Structure object.
- getA() - Method in class org.biojava.bio.molbio.DNAComposition
-
Get the relative compositon of 'A'.
- getA() - Method in class org.biojava.utils.ListTools.Doublet
-
- getA() - Method in class org.biojava.utils.ListTools.Triplet
-
- getAbsorpt_coefficient_mu() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_T_max() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_T_min() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_correction_type() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getAbsorpt_process_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getAbsorptionMax() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property absorptionMax.
- getAbsorptionNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property absorptionNote.
- getAccession() - Method in interface org.biojava.bio.program.homologene.Orthologue
-
get the Accession ID associated with this orthologue.
- getAccession() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getAccession(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getAccession(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getAccession() - Method in interface org.biojavax.bio.BioEntry
-
Returns the accession of this bioentry.
- getAccession() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the accession of this bioentry.
- getAccession() - Method in interface org.biojavax.CrossRef
-
Returns the accession of the object that the crossref refers to.
- getAccession() - Method in class org.biojavax.SimpleCrossRef
-
Returns the accession of the object that the crossref refers to.
- getAcronym() - Method in interface org.biojavax.Namespace
-
If the namespace has an acronym, this will return it.
- getAcronym() - Method in class org.biojavax.SimpleNamespace
-
If the namespace has an acronym, this will return it.
- getAddedFeatures() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getAddHandler() - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Get the GFFDocumentHandler for adding to this
set.
- getAdditionalAccessionTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the secondary/tertiary/additional accession term
- getAddPos() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Retrieve the current value of addPos.
- getAddress(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
Get the URL object for locating sequence object using eutils.
- getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
Get the URL object for locating sequence object using eutils.
- getAddress(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getAddress(String, String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getAddress(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getAddress(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getAddress(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
- getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Get the URL object for locating sequence object using eutils.
- getAddress(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Get the URL object for locating sequence object using eutils.
- getAdvance() - Method in interface org.biojava.bio.dp.EmissionState
-
Determine the number of symbols this state advances along
one or more symbol lists.
- getAdvance() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getAE(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- getAligMap() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- getAligMat() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getAligMat(int, int) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getAligMat() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getAlign_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getAlignedStructure(Structure, Structure) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
create an artifical Structure object that contains the two
structures superimposed onto each other.
- getAlignLength(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getAlignLength(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
This method is good if one wants to reuse the alignment calculated by this
class in another BioJava class.
- getAlignment(SymbolList, SymbolList) - Method in class org.biojava.bio.alignment.SequenceAlignment
-
This method also performs a sequence alignment of the two given sequences
but it returns an Alignment object instead of the score.
- getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
-
- getAlignment() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
-
Deprecated.
- getAlignment() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
-
Gets the Alignment - one of LEADING, TRAILING or CENTER.
- getAlignment(SymbolList) - Static method in class org.biojava.bio.program.abi.ABITools
-
View a symbol list over the QUALITY alphabet as an alignment.
- getAlignment(int) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
-
Returns Alignment at position ...
- getAlignment() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return an alignment of (possibly part of) the query sequence
against (possibly part of) this hit sequence.
- getAlignment() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getAlignment() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getAlignment() - Method in interface org.biojava.bio.seq.homol.Homology
-
Retrieve the Alignment that specifies how the homologous regions are
aligned.
- getAlignment() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
-
getAlignment returns the Alignment of
two similar features.
- getAlignment() - Method in class org.biojava.bio.seq.homol.SimpleHomology
-
getAlignment returns the alignment, which uses the
HomologyFeatures as keys.
- getAlignment() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
-
getAlignment returns the alignment between the two
features.
- getAlignment() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
-
- getAlignmentAtoms(Structure) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
- getAlignments() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
-
connect to a DAS alignment service and retreive alignments.
- getAlignments(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
-
connect to a DAS alignment service and retreive data.
- getAlignments(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
-
Returns the alignments.
- getAlignments() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
-
Returns the alignments.
- getAlignments() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
-
Returns the alignments.
- getAlignments() - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
return the alternative alignments that can be found for the two structures
- getAlignmentString() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
- getAlignmentString() - Method in class org.biojava.bio.alignment.SequenceAlignment
-
- getAlignmentString() - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- getAlignmentStyles() - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
Returns a fragment of HTML that defines the FONT
styles to be used in the alignment markup.
- getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getAlignUnits(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getAlignUnits(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getAll() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
-
All sequences that map to this cluster.
- getAll() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getAll() - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- getAll() - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
- getAllAmbiguitySymbol(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Return the ambiguity symbol which matches all symbols in
a given alphabet.
- getAllBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns all citations from the current collection as a
(possibly big) array.
- getAllBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns all citations from the current collection as a
(possibly big) array, perhaps with a limited number of attributes.
- getAllBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns all citations from the current collection as an XML stream.
- getAllDataRecords() - Method in class org.biojava.bio.program.abi.ABIFParser
-
Obtain all data records.
- getAllEntries() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It returns all available vocabulary entries.
- getAllEnzymes() - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getAllEnzymes returns an unmodifable set of all
available enzymes.
- getAllIDs() - Method in interface org.biojava.bibliography.BibRefQuery
-
A convenient method returning just identifiers of all current citations.
- getAllMMcif(File) - Method in class org.biojava.bio.structure.server.PrepareMMcifIndexFile
-
- getAllNames() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It return all names (entry identifiers) available in this vocabulary.
- getAllNodes(UkkonenSuffixTree.SuffixNode, ArrayList, boolean) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getAllPDB(File) - Method in class org.biojava.bio.structure.server.PrepareIndexFile
-
get all PDBfiles from a directory
- getAllProteases() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getAllScientificNames(Connection) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Returns all the scientific names, which are currently stored in the
database.
- getAllSymbols(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Return a set containing all possible symbols which can be
considered members of a given alphabet, including ambiguous
symbols.
- getAllVocabularies() - Method in interface org.biojava.utils.candy.CandyFinder
-
It returns all available vocabularies.
- getAllVocabularyNames() - Method in interface org.biojava.utils.candy.CandyFinder
-
It returns names of all vocabularies known to this vocabulary
finder.
- getAlpha(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- getAlpha(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- getAlpha(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getAlphabet() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- getAlphabet() - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- getAlphabet() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
Gives the alphabet used by this matrix.
- getAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
- getAlphabet() - Method in interface org.biojava.bio.dist.Count
-
The alphabet from which this Count is over.
- getAlphabet() - Method in interface org.biojava.bio.dist.Distribution
-
The alphabet from which this spectrum emits symbols.
- getAlphabet() - Method in class org.biojava.bio.dist.GapDistribution
-
- getAlphabet() - Method in class org.biojava.bio.dist.IndexedCount
-
- getAlphabet() - Method in class org.biojava.bio.dist.PairDistribution
-
- getAlphabet() - Method in class org.biojava.bio.dist.SimpleDistribution
-
- getAlphabet() - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- getAlphabet() - Method in class org.biojava.bio.dist.UniformDistribution
-
- getAlphabet() - Method in class org.biojava.bio.dp.SimpleStatePath
-
- getAlphabet() - Method in class org.biojava.bio.dp.SimpleWeightMatrix
-
- getAlphabet() - Method in interface org.biojava.bio.dp.WeightMatrix
-
The alphabet for the sequences that this weight matrix models.
- getAlphabet() - Method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- getAlphabet() - Method in class org.biojava.bio.program.das.DASSequence
-
- getAlphabet() - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
-
- getAlphabet() - Method in interface org.biojava.bio.program.ssaha.DataStore
-
The alphabet of symbol lists that can be searched against this
DataStore.
- getAlphabet() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getAlphabet() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getAlphabet() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getAlphabet() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getAlphabet() - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
- getAlphabet() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- getAlphabet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- getAlphabet() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- getAlphabet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
-
- getAlphabet() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getAlphabet() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getAlphabet() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getAlphabet() - Method in class org.biojava.bio.seq.io.AlternateTokenization
-
- getAlphabet() - Method in class org.biojava.bio.seq.io.CharacterTokenization
-
- getAlphabet(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
getAlphabet accepts a value which represents a
sequence format and returns the relevant
FiniteAlphabet object.
- getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolReader
-
Find the alphabet of all symbols which may be returned by
this SymbolReader.
- getAlphabet() - Method in interface org.biojava.bio.seq.io.SymbolTokenization
-
The alphabet to which this tokenization applies.
- getAlphabet() - Method in class org.biojava.bio.seq.io.WordTokenization
-
- getAlphabet() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
-
Gets the protein alphabet
- getAlphabet() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- getAlphabet() - Method in interface org.biojava.bio.symbol.AlphabetIndex
-
Retrieve the alphabet that this indexes.
- getAlphabet() - Method in class org.biojava.bio.symbol.ChunkedSymbolList
-
- getAlphabet() - Method in class org.biojava.bio.symbol.DNAAmbPack
-
- getAlphabet() - Method in class org.biojava.bio.symbol.DNANoAmbPack
-
- getAlphabet() - Method in class org.biojava.bio.symbol.DummySymbolList
-
- getAlphabet() - Method in class org.biojava.bio.symbol.PackedSymbolList
-
- getAlphabet() - Method in interface org.biojava.bio.symbol.Packing
-
The FiniteAlphabet this packing is for.
- getAlphabet() - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- getAlphabet() - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- getAlphabet() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
Get the alphabet of this SymbolList.
- getAlphabet() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
-
- getAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
-
- getAlphabet() - Method in class org.biojava.bio.symbol.SuffixTree
-
Return the Alphabet containing all Symbols which might be found in
this SuffixTree.
- getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolList
-
The alphabet that this SymbolList is over.
- getAlphabet() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
-
- getAlphabet() - Method in class org.biojava.utils.regex.Pattern
-
- getAlphabet() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
The alphabet that this SymbolList is over.
- getAlphabet() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
The alphabet that this SymbolList is over.
- getAlphabetIndex(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Get an indexer for a specified alphabet.
- getAlphabetIndex(Symbol[]) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Get an indexer for an array of symbols.
- getAlphabetName() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
- getAlphabets() - Method in interface org.biojava.bio.symbol.Alphabet
-
Return an ordered List of the alphabets which make up a
compound alphabet.
- getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getAlphabets() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getAlphabets() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getAlphabets() - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getAlphabets() - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getAlphabets() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
Gets the components of the Alphabet.
- getAlphaCarbonAngleAlphabet() - Static method in class org.biojava.bio.structure.AlphaCTools
-
Returns a reference to the Alphabet that contains Symbols that represent PHI,
PSI angles.
- getAlphaStar(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getAltAligNumber() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
returns the sequential number of this alternative alignment
- getAlternativeAligs() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getAlternativeAligs() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getAltIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getAltIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getAltLoc() - Method in interface org.biojava.bio.structure.Atom
-
get set alternate Location.
- getAltLoc() - Method in class org.biojava.bio.structure.AtomImpl
-
get alternate Location.
- getAmbiguity(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getAmbiguity(Set) - Method in interface org.biojava.bio.symbol.Alphabet
-
Get a symbol that represents the set of symbols in syms.
- getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getAmbiguity(Set) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getAmbiguity(Set) - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getAmbiguity(Set) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
This is not supported.
- getAmbiguityImpl(Set) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
Backend for getAmbiguity, called when it is actually necessarly to create a new symbol.
- getAminoAcid(String) - Static method in class org.biojava.bio.structure.StandardAminoAcid
-
get a standard amino acid.
- getAminoOneLetter(String) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- getAminoThreeLetter(Character) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- getAminoType() - Method in interface org.biojava.bio.structure.AminoAcid
-
returns the name of the AA, in single letter code.
- getAminoType() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
returns the name of the AA, in single letter code.
- getAngle(int) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
-
Return the angle for an index into a sequence.
- getAngle(int) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getAngleDiff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getAniso_B() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getAnnotatedQuerySeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- getAnnotatedSubjectSeq(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- getAnnotaters() - Method in class org.biojava.bio.program.das.ReferenceServer
-
- getAnnotation() - Method in interface org.biojava.bio.Annotatable
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getAnnotation(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getAnnotation returns an immutable, static
annotation describing the enzyme.
- getAnnotation() - Method in class org.biojava.bio.program.das.DASSequence
-
- getAnnotation() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
getAnnotation returns the Annotation associated
with this hit.
- getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
getAnnotation returns the Annotation associated
with this hit.
- getAnnotation() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
getAnnotation returns the Annotation associated
with this hit.
- getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
getAnnotation returns the Annotation associated
with this hit.
- getAnnotation() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
getAnnotation returns the Annotation associated
with this sub-hit.
- getAnnotation() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getAnnotation() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getAnnotation() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getAnnotation() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getAnnotation() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getAnnotation() - Method in class org.biojava.bio.seq.io.AlternateTokenization
-
- getAnnotation() - Method in class org.biojava.bio.seq.io.CharacterTokenization
-
- getAnnotation() - Method in class org.biojava.bio.seq.io.WordTokenization
-
- getAnnotation() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getAnnotation() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- getAnnotation() - Method in interface org.biojava.bio.structure.Chain
-
get/set the Annotation of a Chain.
- getAnnotation() - Method in class org.biojava.bio.structure.ChainImpl
-
get/set the Annotation of a Chain.
- getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getAnnotation() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getAnnotation() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getAnnotation() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getAnnotation() - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getAnnotation() - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
-
- getAnnotation() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
The SoftMaskedAlphabet has no annotation
- getAnnotation() - Method in class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- getAnnotation() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getAnnotation() - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getAnnotation() - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getAnnotation() - Method in class org.biojava.ontology.Term.Impl
-
- getAnnotation() - Method in class org.biojava.ontology.Triple.Impl
-
- getAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Should return the associated annotation object.
- getAnnotation() - Method in class org.biojavax.SimpleCrossRef
-
Should return the associated annotation object.
- getAnnotations() - Method in class org.biojava.bio.MergeAnnotation
-
Gets an unmodifiable view of the list of Annotations that are part of the
MergeAnnotation.
- getAnnotationType() - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
-
Get the AnnotationType used as a constraint.
- getAnnotationType() - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
-
Return the AnnotationType built by this handler
- getAnnotator() - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Get an annotator that can add GFF features to a
Sequence using the features in this
GFFEntrySet.
- getAnnotator(boolean) - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Get an annotator that can add GFF features to a
Sequence using the features in this
GFFEntrySet.
- getArg_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getArray() - Method in class org.biojava.bio.structure.jama.Matrix
-
Access the internal two-dimensional array.
- getArrayCopy() - Method in class org.biojava.bio.structure.jama.Matrix
-
Copy the internal two-dimensional array.
- getArrowHeadSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getArrowScoop() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getArrowScoop() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- getArrowSize() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getArrowSize() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- getArticleAuthors() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the names of the authors which first published an article about the
AAindex entry.
- getArticleTitle() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the title of the article which describes the AAindex entry.
- getAsp_N() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getAsym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAsym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAtcc() - Method in class org.biojava.bio.structure.Compound
-
- getAtom(String) - Method in interface org.biojava.bio.structure.Group
-
Get an atom.
- getAtom(int) - Method in interface org.biojava.bio.structure.Group
-
Get at atom by position.
- getAtom(String) - Method in class org.biojava.bio.structure.HetatomImpl
-
get an atom throws StructureException if atom not found.
- getAtom(int) - Method in class org.biojava.bio.structure.HetatomImpl
-
return an atom by its position in the internal List.
- getAtomArray(Structure, String[]) - Static method in class org.biojava.bio.structure.StructureTools
-
Returns an array of the requested Atoms from the Structure object.
- getAtomCAArray(Structure) - Static method in class org.biojava.bio.structure.StructureTools
-
Returns an Atom array of the CA atoms.
- getAtomGroup(int) - Method in interface org.biojava.bio.structure.Chain
-
return the Group at position X.
- getAtomGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
-
return the group at position .
- getAtomGroups() - Method in interface org.biojava.bio.structure.Chain
-
Return all groups that have been specified in the ATOM section of this chain .
- getAtomGroups(String) - Method in interface org.biojava.bio.structure.Chain
-
Return a List of all groups of a special type (e.g.
- getAtomGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
-
Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
- getAtomGroups() - Method in class org.biojava.bio.structure.ChainImpl
-
Return all groups that have been specified in the ATOM section of this chain .
- getAtomLength() - Method in interface org.biojava.bio.structure.Chain
-
Return the number of Groups in the ATOM records of the chain.
- getAtomLength() - Method in class org.biojava.bio.structure.ChainImpl
-
Return the number of Groups in the ATOM records of the chain.
- getAtoms() - Method in interface org.biojava.bio.structure.Group
-
Get list of atoms.
- getAtoms() - Method in class org.biojava.bio.structure.HetatomImpl
-
get all atoms of this group .
- getAtomSequence() - Method in interface org.biojava.bio.structure.Chain
-
Return the sequence of amino acids as it has been provided in the ATOM records.
- getAtomSequence() - Method in class org.biojava.bio.structure.ChainImpl
-
Return the sequence of amino acids as it has been provided in the ATOM records.
- getAttributes(Name) - Method in class org.biojava.naming.ObdaContext
-
- getAttributes(Name, String[]) - Method in class org.biojava.naming.ObdaContext
-
- getAttributes(String) - Method in class org.biojava.naming.ObdaContext
-
- getAttributes(String, String[]) - Method in class org.biojava.naming.ObdaContext
-
- getAuth_asym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getAuth_atom_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getAuth_comp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getAuth_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAuth_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAuth_seq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getAuth_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getAuth_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getAuthority() - Method in interface org.biojavax.Namespace
-
This method will return the authority that governs the namespace.
- getAuthority() - Method in class org.biojavax.SimpleNamespace
-
This method will return the authority that governs the namespace.
- getAuthorityId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
-
Return the authority id for this identifier.
- getAuthorList() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the list of Authors of the JournalArticle
- getAuthorList() - Method in interface org.biojavax.DocRef
-
Returns the authors of the document reference as a set of DocRefAuthor
implementation instances.
- getAuthorList() - Method in class org.biojavax.SimpleDocRef
-
Returns the authors of the document reference as a set of DocRefAuthor
implementation instances.
- getAuthors() - Method in interface org.biojavax.DocRef
-
Returns the authors of the document reference.
- getAuthors() - Method in class org.biojavax.SimpleDocRef
-
Returns the authors of the document reference.
- getAutomaton() - Method in class org.biojava.utils.automata.FiniteAutomaton
-
- getAutomaton() - Method in interface org.biojava.utils.automata.NfaBuilder
-
- getAutomaton() - Method in class org.biojava.utils.automata.NfaSubModel
-
- getB() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getB() - Method in class org.biojava.utils.ListTools.Doublet
-
- getB() - Method in class org.biojava.utils.ListTools.Triplet
-
- getB_iso_max() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getB_iso_mean() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getB_iso_min() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getB_iso_or_equiv() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getB_iso_or_equiv_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getBackboneAtomArray(Structure) - Static method in class org.biojava.bio.structure.StructureTools
-
Returns an Atom array of the MainChain atoms.
- getBackwardTransitions() - Method in class org.biojava.bio.dp.DP
-
- getBackwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
-
- getBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Return the total number of base calls.
- getBaseCalls() - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Returns an alignment that describes the base calls for this chromatogram.
- getBasecalls() - Method in class org.biojava.bio.program.abi.ABITrace
-
Returns an int[] array that represents the basecalls - each int in the
array corresponds to an x-coordinate point in the graph that is a peak (a base location).
- getBaseColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the color that will be used to draw the trace for the
given DNA symbol.
- getBaseFillColor(Symbol) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the color that will be used to fill in the callboxes for
calls with the given symbol.
- getBases() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getBases() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getBases() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getbaseURL() - Method in class org.biojava.bio.seq.db.FetchURL
-
- getBeadDepth() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
getBeadDepth returns the depth of a single bead
produced by this renderer.
- getBeadDepth() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
-
getBeadDepth returns the depth of a single bead
produced by the renderer.
- getBeadDepth() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
- getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
getBeadDisplacement returns the displacement of
beads from the centre line of the renderer.
- getBeadDisplacement() - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
-
getBeadDisplacement returns the displacement of
beads from the centre line of the renderer.
- getBeadDisplacement() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
- getBeadFill() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
getBeadFill returns the bead fill paint.
- getBeadOutline() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
getBeadOutline returns the bead outline paint.
- getBeadStroke() - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
getBeadStroke returns the bead outline stroke.
- getBibRefAsXML(BibRef) - Method in interface org.biojava.bibliography.BibRefQuery
-
A convenient utility method converting a given citation to its
XML representation.
- getBibRefCount() - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns the number of citations in the current collection.
- getBibRefs() - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns an enumeration of all citations from the current collection.
- getBibRefs(String[]) - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns an enumeration of all citations from the current collection,
perhaps with a limited number of attributes.
- getBibRefsAsXML() - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns an enumeration of all citations from the current collection.
- getBinaryAlphabet() - Static method in class org.biojavax.ga.util.GATools
-
Gets a Reference to the FlyWeight GA_Binary Alphabet.
- getBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Retrieve a single BioEntry by its id.
- getBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- getBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
- getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractBioEntryDB
-
- getBioEntryIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getBioEntryIterator() - Method in interface org.biojavax.bio.db.BioEntryDB
-
Returns a BioEntryIterator over all BioEntrys in the database.
- getBioEntrys(Set) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getBioEntrys(Set) - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Retrieve multiple BioEntry by their ids.
- getBioEntrys(Set, BioEntryDB) - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Retrieve multiple BioEntry into a specific sequence database.
- getBioEntrys(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- getBioEntrys(Set) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
- getBioEntrys(Set, BioEntryDB) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
- getBiol_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getBiologicalUnit() - Method in class org.biojava.bio.structure.Compound
-
- getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
Returns the an object indicating the style of biosequence storage
that this database should employ.
- getBioSequenceStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- getBJSequence() - Method in interface org.biojava.bio.structure.Chain
-
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
- getBJSequence() - Method in class org.biojava.bio.structure.ChainImpl
-
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
- getBlockAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
-
define the alignment Block Annotation Type.
- getBlockDepth() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- getBlockDepth() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- getBlockPainter() - Method in class org.biojava.bio.gui.DistributionLogo
-
- getBlockPainter() - Method in interface org.biojava.bio.gui.LogoContext
-
- getBlocks() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
get all Annotations of type "Block".
- getBlockWidth() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.Aggregator
-
- getBoundaryFinder() - Method in class org.biojava.bio.program.tagvalue.MultiTagger
-
- getBounds() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
- getBounds() - Method in interface org.biojava.bio.gui.glyph.Glyph
-
- getBounds() - Method in class org.biojava.bio.gui.glyph.HelixGlyph
-
- getBounds() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
-
- getBounds() - Method in class org.biojava.bio.gui.glyph.TurnGlyph
-
- getBounds() - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
-
- getBounds() - Method in interface org.biojava.bio.gui.LogoContext
-
- getBuilderFactory(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
getBuilderFactory accepts a value which represents
a sequence format and returns the relevant
SequenceBuilderFactory object.
- getC() - Method in class org.biojava.bio.molbio.DNAComposition
-
Get the relative compositon of 'C'.
- getC() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getC() - Method in interface org.biojava.bio.structure.AminoAcid
-
get C atom.
- getC() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
get C atom.
- getC() - Method in class org.biojava.stats.svm.SMOTrainer
-
- getC() - Method in class org.biojava.utils.ListTools.Triplet
-
- getCA() - Method in interface org.biojava.bio.structure.AminoAcid
-
get CA atom.
- getCA() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
get CA atom.
- getCacheSize() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- getCacheSize() - Method in interface org.biojava.bio.structure.server.StructureServer
-
- getCallboxBounds(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the screen-coordinate bounds of the callbox for a given call.
- getCallboxBounds(int, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the bounds of the callbox for a given call.
- getCallboxCount() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the number of callboxes, regenerating them if necessary.
- getCallContaining(Point2D, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the 0-based index of the call containing a given
point.
- getCallContaining(Point2D) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
- getCallContaining(float, boolean) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
- getCallContaining(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
- getCAOnly(List<Chain>) - Static method in class org.biojava.bio.structure.io.CAConverter
-
Convert a List of chain objects to another List of chains, containing C-alpha atoms only.
- getCAOnly(Chain) - Static method in class org.biojava.bio.structure.io.CAConverter
-
Convert a Chain to a new Chain containing C-alpha atoms only.
- getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
-
Get the cardinality constraint used to validate the number of property
values.
- getCardinalityConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
-
Get the cardinality constraint used to validate the number of property
values.
- getCartn_x() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getCartn_x_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getCartn_y() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getCartn_y_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getCartn_z() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getCartn_z_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getCategory() - Method in class org.biojava.ontology.Synonym
-
- getCB() - Method in interface org.biojava.bio.structure.AminoAcid
-
get CB atom.
- getCB() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
get CB atom.
- getCell(int[]) - Method in interface org.biojava.bio.dp.DPMatrix
-
- getCell(int[]) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- getCell(int[]) - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
-
- getCell() - Method in class org.biojava.bio.structure.Compound
-
- getCellLine() - Method in class org.biojava.bio.structure.Compound
-
- getCellularLocation() - Method in class org.biojava.bio.structure.Compound
-
- getCenter(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
- getCenter1() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getCenter2() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getCenterVector(Atom[]) - Static method in class org.biojava.bio.structure.Calc
-
Returns the Vector that needs to be applied to shift a set of atoms
to the Centroid.
- getCentroid(Atom[]) - Static method in class org.biojava.bio.structure.Calc
-
Returns the center of mass of the set of atoms.
- getChain() - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- getChain(int) - Method in interface org.biojava.bio.structure.Structure
-
retrieve a chain by it's position within the Structure .
- getChain(int, int) - Method in interface org.biojava.bio.structure.Structure
-
retrieve a chain by it's position within the Structure and model number.
- getChain(int) - Method in class org.biojava.bio.structure.StructureImpl
-
retrieve a chain by it's position within the Structure.
- getChain(int, int) - Method in class org.biojava.bio.structure.StructureImpl
-
retrieve a chain by it's position within the Structure and model number.
- getChainByPDB(String) - Method in interface org.biojava.bio.structure.Structure
-
request a chain by it's PDB code
by default takes only the first model
- getChainByPDB(String, int) - Method in interface org.biojava.bio.structure.Structure
-
request a chain by it's PDB code
by default takes only the first model
- getChainByPDB(String, int) - Method in class org.biojava.bio.structure.StructureImpl
-
- getChainByPDB(String) - Method in class org.biojava.bio.structure.StructureImpl
-
- getChainedEvent() - Method in class org.biojava.utils.ChangeEvent
-
Return the event which caused this to be fired, or null
if this change was not caused by another event.
- getChainId() - Method in class org.biojava.bio.structure.Compound
-
Returns the chain id value.
- getChainId() - Method in class org.biojava.bio.structure.DBRef
-
The chain ID of the corresponding chain.
- getChainID1() - Method in class org.biojava.bio.structure.SSBond
-
- getChainID2() - Method in class org.biojava.bio.structure.SSBond
-
- getChainInfoFile() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getChains() - Method in class org.biojava.bio.structure.Compound
-
get the chains that are part of this Compound
- getChains() - Method in interface org.biojava.bio.structure.Structure
-
retrieve all chains - if it is a NMR structure will return the chains of the first model.
- getChains(int) - Method in interface org.biojava.bio.structure.Structure
-
retrieve all chains of a model.
- getChains(int) - Method in class org.biojava.bio.structure.StructureImpl
-
retrieve all chains of a model.
- getChains() - Method in class org.biojava.bio.structure.StructureImpl
-
- getChange() - Method in class org.biojava.utils.ChangeEvent
-
Return an object which is to be the new value of some property,
or is to be added to a collection.
- getChangeEvent() - Method in exception org.biojava.utils.ChangeVetoException
-
Return the ChangeEvent which is being vetoed.
- getChanger() - Method in class org.biojava.bio.AnnotationChanger
-
getMapper returns the ValueChanger being
used to remap the Annotation.
- getChanger(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
-
Get the Changer currently registered to handle a tag.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractDistribution
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getChangeSupport lazily instantiates a helper for
change listeners.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getChangeSupport lazily instantiates a helper for
change listeners.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.MergeAnnotation
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.OverlayAnnotation
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.program.das.DASSequence
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
-
- getChangeSupport() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getChangeSupport() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.AbstractSymbol
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getChangeSupport(ChangeType) - Method in class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- getChangeSupport(ChangeType) - Method in class org.biojava.ontology.AbstractTerm
-
- getChangeSupport(ChangeType) - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getChangeSupport(ChangeType) - Method in class org.biojava.utils.AbstractChangeable
-
Called to retrieve the ChangeSupport for this object.
- getChangeTable() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
- getChangeTypes(Class) - Static method in class org.biojava.utils.ChangeType
-
Get all ChangeType objects defined within a class.
- getChar(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- getChar() - Method in class org.biojava.utils.io.LargeBuffer
-
- getCharacter() - Method in class org.biojava.utils.RepeatedCharSequence
-
- getCharacterOffset() - Method in exception org.biojava.utils.ParserException
-
Get the character offset in the line where an error was detected.
- getChild() - Method in class org.biojava.bio.seq.FeatureFilter.Not
-
- getChild(SuffixTree.SuffixNode, Symbol) - Method in class org.biojava.bio.symbol.SuffixTree
-
Get a child of a SuffixTree.SuffixNode, constructing a new
one if need be.
- getChild(SuffixTree.SuffixNode, int) - Method in class org.biojava.bio.symbol.SuffixTree
-
Get the n'th child of a node.
- getChild() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Not
-
- getChild1() - Method in class org.biojava.bio.CollectionConstraint.And
-
Get the first child CollectionConstraint.
- getChild1() - Method in class org.biojava.bio.CollectionConstraint.Or
-
Get the first child CollectionConstraint.
- getChild1() - Method in class org.biojava.bio.PropertyConstraint.And
-
Get the first child PropertyConstraint.
- getChild1() - Method in class org.biojava.bio.PropertyConstraint.Or
-
Get the first child PropertyConstraint.
- getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.And
-
- getChild1() - Method in class org.biojava.bio.seq.FeatureFilter.Or
-
- getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
-
- getChild1() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
-
- getChild2() - Method in class org.biojava.bio.CollectionConstraint.And
-
Get the seccond child CollectionConstraint.
- getChild2() - Method in class org.biojava.bio.CollectionConstraint.Or
-
Get the seccond child CollectionConstraint.
- getChild2() - Method in class org.biojava.bio.PropertyConstraint.And
-
Get the seccond child PropertyConstraint.
- getChild2() - Method in class org.biojava.bio.PropertyConstraint.Or
-
Get the seccond child PropertyConstraint.
- getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.And
-
- getChild2() - Method in class org.biojava.bio.seq.FeatureFilter.Or
-
- getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.And
-
- getChild2() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.Or
-
- getChildren() - Method in class org.biojava.bio.taxa.SimpleTaxon
-
Deprecated.
- getChildren() - Method in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
The children of this Taxon.
- getChildren() - Method in class org.biojava.bio.taxa.WeakTaxon
-
Deprecated.
- getChildrenOf(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Returns all children of the specified taxon.
- getChildrenOf(Connection, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Returns the children as a Stack of this given taxon.
- getChildrenRaw() - Method in class org.biojava.bio.taxa.WeakTaxon
-
Deprecated.
- getChromatogram() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Accessor for the in-use chromatogram.
- getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getChromNum(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getChromNum(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getChromosome(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getChromosome() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getChromosome(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getChromosomes() - Method in interface org.biojavax.ga.functions.GACross
-
Gets the chromosomes after the cross
- getChromosomes() - Method in interface org.biojavax.ga.functions.GACrossResult
-
Gets the chromosomes after the cross
- getChromosomes() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
-
- getChromosomes() - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- getChromosomes() - Method in interface org.biojavax.ga.Organism
-
Gets the organisms 'chromosome' sequences
- getChymotrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getCircular() - Method in interface org.biojavax.bio.seq.RichSequence
-
Is the sequence circular? Circularity has implications for work with
locations and any coordinate work eg symbolAt(int i).
- getCircular() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Is the sequence circular? Circularity has implications for work with
locations and any coordinate work eg symbolAt(int i).
- getCircularLength() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the circular length of this location.
- getCircularLength() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
Retrieves the circular length of this location.
- getCircularLength() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the circular length of this location.
- getCircularLength() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the circular length of this location.
- getClassification() - Method in class org.biojava.bio.structure.PDBHeader
-
- getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getClassifyId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getClassifyId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getClassifySystem(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getClassifySystem(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getClassifyType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getClassifyType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getClassLoader(Object) - Static method in class org.biojava.utils.ClassTools
-
Get the classloader which loaded the class of obj.
- getClassLoader(Class) - Static method in class org.biojava.utils.ClassTools
-
Get the classloader which loaded clazz.
- getClassNumber(int) - Method in interface org.biojava.bio.EcNumber
-
Get the class number associated with the particular level of the ec number.
- getClassNumber(int) - Method in class org.biojava.bio.EcNumber.Impl
-
- getCleaveageResidues() - Method in class org.biojava.bio.proteomics.Protease
-
The list of residues that the protease will cleave at.
- getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getCloneId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getCloneId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getCloneLibrary(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getCloneLibrary(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getCluster(String) - Method in interface org.biojava.bio.program.unigene.UnigeneDB
-
Fetch a cluster by its cluster id.
- getCluster() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
get the number of the cluster this alignment belongs to
- getCluster() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getCNBr() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getCodonAlphabet() - Static method in class org.biojava.bio.seq.DNATools
-
Gets the (DNA x DNA x DNA) Alphabet
- getCodonAlphabet() - Static method in class org.biojava.bio.seq.RNATools
-
Gets the (RNA x RNA x RNA) Alphabet
- getCodonPref() - Method in class org.biojava.bio.symbol.CodonPrefFilter.ByName
-
- getCodonPreference(String) - Static method in class org.biojava.bio.symbol.CodonPrefTools
-
get the specified codon preference.
- getCodonPrefs() - Method in class org.biojava.bio.symbol.CodonPrefFilter.AcceptAll
-
- getCol() - Method in class org.biojava.bio.structure.align.helper.IndexPair
-
- getCollapsing() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
Returns true if this class collapses to zero depth when there are
no visible features.
- getCollectionConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.CollectionConstraintHandler
-
- getCollectionId() - Method in interface org.biojava.bibliography.BibRefQuery
-
It returns an identification of the current query collection.
- getColourClass(String) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
Returns the colour class for the specified colour (in hex).
- getCols() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getCols() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getColumn(int) - Method in class org.biojava.bio.dp.SimpleWeightMatrix
-
- getColumn(int) - Method in interface org.biojava.bio.dp.WeightMatrix
-
Retrieve a column as an EmissionState.
- getColumnDimension() - Method in class org.biojava.bio.structure.jama.Matrix
-
Get column dimension.
- getColumnPackedCopy() - Method in class org.biojava.bio.structure.jama.Matrix
-
Make a one-dimensional column packed copy of the internal array.
- getCommands() - Method in class org.biojava.utils.process.ExternalProcess
-
Gets the command line including the path or name of the external program
and its command line arguments.
- getComment() - Method in interface org.biojava.bio.AnnotationType
-
Get the comment for the whole AnnotationType.
- getComment(Object) - Method in interface org.biojava.bio.AnnotationType
-
Get the comment for a particular property.
- getComment() - Method in class org.biojava.bio.AnnotationType.Impl
-
- getComment(Object) - Method in class org.biojava.bio.AnnotationType.Impl
-
- getComment() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The feature comment.
- getComment() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getComment() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the user comment for the AAindex entry.
- getComment() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
-
- getComment() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
-
Getter for property comment.
- getComment() - Method in interface org.biojavax.Comment
-
Returns the comment part of this comment.
- getComment() - Method in class org.biojavax.SimpleComment
-
Returns the comment part of this comment.
- getComments() - Method in class org.biojava.bio.program.scf.SCF
-
Returns the comments fields as a Properties mapping.
- getComments() - Method in interface org.biojavax.bio.BioEntry
-
Returns a set of all comments associated with this bioentry.
- getComments() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns a set of all comments associated with this bioentry.
- getCommentType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property commentType.
- getCommonName() - Method in class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- getCommonName() - Method in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
The common name of the Taxon.
- getComp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getComparator() - Method in class org.biojava.utils.FileAsList
-
- getComponentList(boolean) - Method in class org.biojava.bio.symbol.MergeLocation
-
Gets the component locations that make up this one
- getComponentLocation() - Method in interface org.biojava.bio.seq.ComponentFeature
-
Return a location which identifies a portion of the component
sequence which is to be included in the assembly.
- getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- getComponentLocationSet() - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
-
- getComponentName() - Method in class org.biojava.bio.seq.FeatureFilter.ByComponentName
-
- getComponentSequence() - Method in interface org.biojava.bio.seq.ComponentFeature
-
Get the sequence object which provides a component of this
feature's parent sequence.
- getComponentSequenceName() - Method in interface org.biojava.bio.seq.ComponentFeature
-
Get the name of the component sequence.
- getCompoundById(String) - Method in interface org.biojava.bio.structure.Structure
-
request a particular compound by its id
- getCompoundById(String) - Method in class org.biojava.bio.structure.StructureImpl
-
- getCompounds() - Method in interface org.biojava.bio.structure.Structure
-
get all the Compounds that are defined in the PDB Header
- getCompounds() - Method in class org.biojava.bio.structure.StructureImpl
-
- getConditionedAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
Get the conditioned alphabet.
- getConditionedAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution
-
Get the conditioned alphabet.
- getConditioningAlphabet() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
Get the conditioning alphabet of this distribution.
- getConditioningAlphabet() - Method in interface org.biojava.bio.dist.OrderNDistribution
-
Get the conditioning alphabet of this distribution.
- getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getConfidence(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getConfidence(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Composite
-
- getConfigLocator() - Method in interface org.biojava.directory.RegistryConfiguration
-
getConfigLocator returns a locator for the
configuration.
- getConfigLocator() - Method in class org.biojava.directory.RegistryConfiguration.Impl
-
- getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Composite
-
- getConfiguration() - Method in interface org.biojava.directory.RegistryConfiguration
-
getConfiguration returns a mapping of registry
database names to collections of tag-value pairs.
- getConfiguration() - Method in class org.biojava.directory.RegistryConfiguration.Impl
-
- getConnections() - Method in interface org.biojava.bio.structure.Structure
-
Returns the connections value.
- getConnections() - Method in class org.biojava.bio.structure.StructureImpl
-
Returns the connections value.
- getConstant() - Method in class org.biojava.stats.svm.PolynomialKernel
-
- getConstant() - Method in class org.biojava.stats.svm.SigmoidKernel
-
- getConstraint(Object) - Method in interface org.biojava.bio.AnnotationType
-
Retrieve the constraint that will be applied to all
properties with a given key.
- getConstraint(Object) - Method in class org.biojava.bio.AnnotationType.Impl
-
- getContacts() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getContainsTerm() - Static method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Gets the default CONTAINS term used for defining the relationship between features.
- getContentHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
correct this later
- getContext(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- getContext() - Method in class org.biojava.stats.svm.TrainingEvent
-
- getContig() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
-
- getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
See if empty tags are treated as a continuation of previous tags or as a
new tag with the value of the empty string.
- getContinueOnEmptyTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Report whether empty tags will be treated as continuations of the last non
-empty tag.
- getCoordinates() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
-
getCoordinates returns the hotspot coordinates.
- getCoords() - Method in interface org.biojava.bio.structure.Atom
-
get the coordinates.
- getCoords() - Method in class org.biojava.bio.structure.AtomImpl
-
get the coordinates as a double[3] array .
- getCopyrightTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the copyright term
- getCoreOntology() - Static method in class org.biojava.ontology.OntoTools
-
Get the Ontology that defines our core "central dogma".
- getCorrelation_coeff_Fo_to_Fc() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getCorrelation_coeff_Fo_to_Fc_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getCount(AtomicSymbol) - Method in interface org.biojava.bio.dist.Count
-
Return the counts for a given Symbol.
- getCount(DistributionTrainerContext, AtomicSymbol) - Method in interface org.biojava.bio.dist.DistributionTrainer
-
Get the current count for this state.
- getCount(Distribution, Symbol) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Return the number of counts of a particular symbol which will be used
to train the specified distribution.
- getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.IgnoreCountsTrainer
-
- getCount(AtomicSymbol) - Method in class org.biojava.bio.dist.IndexedCount
-
- getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution.Trainer
-
- getCount(DistributionTrainerContext, AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainer
-
Deprecated.
- getCount(Distribution, Symbol) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- getCount() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It returns a number of entries contained in this vocabulary.
- getCovered() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getCRC() - Method in interface org.biojavax.DocRef
-
Returns a CRC64 checksum of this document reference, allowing for easy
comparisons with other document references.
- getCRC() - Method in class org.biojavax.SimpleDocRef
-
Returns a CRC64 checksum of this document reference, allowing for easy
comparisons with other document references.
- getCreate_co() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getCreateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getCreateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getCreateOnUnderlyingSequence() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getCrossOverFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
-
- getCrossOverFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACross
-
Returns the collection of cross over locations from the last cross
- getCrossOverPositions() - Method in interface org.biojavax.ga.functions.GACrossResult
-
Returns the collection of cross over locations from the last cross
- getCrossOverPositions() - Method in class org.biojavax.ga.functions.SimpleGACrossResult
-
- getCrossOverProbs() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
-
- getCrossOverProbs() - Method in interface org.biojavax.ga.functions.CrossOverFunction
-
- getCrossOverProbs() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- getCrossProductAlphabet(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Retrieve a CrossProductAlphabet instance over the alphabets in aList.
- getCrossProductAlphabet(List, String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Attempts to create a cross product alphabet and register it under a name.
- getCrossProductAlphabet(List, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Retrieve a CrossProductAlphabet instance over the alphabets in aList.
- getCrossRef() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the crossref associated with this location.
- getCrossRef() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
Retrieves the crossref associated with this location.
- getCrossRef() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the crossref associated with this location.
- getCrossRef() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the crossref associated with this location.
- getCrossref() - Method in interface org.biojavax.DocRef
-
The document reference may refer to an object in another database.
- getCrossRef() - Method in interface org.biojavax.RankedCrossRef
-
Return the cross reference associated with this object.
- getCrossref() - Method in class org.biojavax.SimpleDocRef
-
The document reference may refer to an object in another database.
- getCrossRef() - Method in class org.biojavax.SimpleRankedCrossRef
-
Return the cross reference associated with this object.
- getCrossResults() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
-
Get a List containing details of all the cross over events during the run.
- getCrystals_number() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getCurrentChain() - Method in class org.biojava.bio.structure.AtomIterator
-
Get the chain that contains the current atom.
- getCurrentChain() - Method in class org.biojava.bio.structure.GroupIterator
-
Get the current Chain.
- getCurrentCycle() - Method in interface org.biojava.stats.svm.TrainingContext
-
- getCurrentFeature() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- getCurrentFeature() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- getCurrentFeature() - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Gets the feature currently being created.
- getCurrentFeature() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Gets the feature currently being created.
- getCurrentModel() - Method in class org.biojava.bio.structure.AtomIterator
-
Get the model number of the model containing the current atom.
- getCurrentModel() - Method in class org.biojava.bio.structure.GroupIterator
-
Get the model number of the current model.
- getCurrentScore() - Method in class org.biojava.bio.dp.AbstractTrainer
-
- getCurrentScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
-
- getCutoff() - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
-
- getCutType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getCutType returns the type of cut produced by the
enzyme.
- getCycle() - Method in class org.biojava.bio.dp.AbstractTrainer
-
- getCycle() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
-
- getD() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
-
Return the block diagonal eigenvalue matrix
- getDataAccess() - Method in class org.biojava.bio.program.abi.ABIFParser
-
Returns the accessor for the raw data being parsed by this parser.
- getDataBase() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getDatabase() - Method in class org.biojava.bio.structure.DBRef
-
The database of the db-ref.
- getDatabase(String) - Method in class org.biojava.directory.Registry
-
getDatabase retrieves a database instance known by
a name String.
- getDatabaseName() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property databaseName.
- getDatabaseURLGenerators() - Method in class org.biojava.bio.program.blast2html.DefaultURLGeneratorFactory
-
- getDatabaseURLGenerators() - Method in interface org.biojava.bio.program.blast2html.URLGeneratorFactory
-
Returns a list of 0, 1 or more DatabaseURLGenerator
The first is used to link from the id in the summary table, all are
used as a list of links in the detail section.
- getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
-
Getter for the Ensembl-specific 'dataClass' term
- getDataClassTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the Ensembl-specific 'dataClass' term
- getDataClassTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the DataClass term
- getDataRecord(String, int) - Method in class org.biojava.bio.program.abi.ABIFParser
-
Get the entry from the file TOC with the given name and tag number.
- getDataSource(String, String, String, String) - Static method in class org.biojava.utils.JDBCPooledDataSource
-
- getDataSources() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
Get the current set of all currently registered data sources.
- getDataStore(File) - Method in class org.biojava.bio.program.ssaha.CompactedDataStoreFactory
-
- getDataStore(File) - Method in interface org.biojava.bio.program.ssaha.DataStoreFactory
-
Get a pre-built data store associated with a file.
- getDataStore(File) - Method in class org.biojava.bio.program.ssaha.MappedDataStoreFactory
-
- getDataStore(File) - Method in class org.biojava.bio.program.ssaha.NIODataStoreFactory
-
- getDataType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getDate() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getDate_original() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getDateAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the date annotated term
- getDateCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the date created term
- getDateUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the date updated term
- getDB() - Method in class org.biojava.bio.program.das.ReferenceServer
-
- getDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
retrieve the DB that has just been built
- getDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- getDB() - Method in class org.biojava.bio.seq.db.FetchURL
-
- getDb_align_beg() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getDb_align_end() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getDb_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getDb_name() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getDbAccession() - Method in class org.biojava.bio.structure.DBRef
-
Sequence database accession code.
- getDbCode() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- getDBHelper(Connection) - Static method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
Returns a DBHelper implementation suitable for a particular
database.
- getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getDbId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- getDbId() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getDbId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getDbIdCode() - Method in class org.biojava.bio.structure.DBRef
-
Sequence database identification code.
- getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
-
- getDbIds() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
return a set of DbId
- getDbname() - Method in interface org.biojavax.CrossRef
-
Returns the name of the database the cross reference refers to.
- getDbname() - Method in class org.biojavax.SimpleCrossRef
-
Returns the name of the database the cross reference refers to.
- getDBRefs() - Method in interface org.biojava.bio.structure.Structure
-
get the list of database references
- getDBRefs() - Method in class org.biojava.bio.structure.StructureImpl
-
- getDBSearchParameters() - Static method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getDbSeqBegin() - Method in class org.biojava.bio.structure.DBRef
-
Initial sequence number of the
database seqment.
- getDbSeqEnd() - Method in class org.biojava.bio.structure.DBRef
-
Ending sequence position of the database segment.
- getDBTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Attempts to get a Taxon object corresponding to the specified
taxon_id (i.e.
- getDbXrefId() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
-
- getDbxrefList(String, int, int) - Method in class org.biojava.ontology.obo.OboFileParser
-
- getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocation
-
- getDecorator(Class) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getDecorator(Class) - Method in interface org.biojava.bio.symbol.Location
-
Checks the decorator chain for an instance of decoratorClass
and return it if found.
- getDecorator(Class) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Checks the decorator chain for an instance of decoratorClass
and return it if found.
- getDecorator(Class) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Checks the decorator chain for an instance of decoratorClass
and return it if found.
- getDecorator(Class) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Checks the decorator chain for an instance of decoratorClass
and return it if found.
- getDefaultChanger() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
Get the changer that will be applied to values of tags with no specific
handler registered.
- getDefaultConstraint() - Method in interface org.biojava.bio.AnnotationType
-
Get the CollectionConstraint that will be applied to all properties without
an explicit binding.
- getDefaultConstraint() - Method in class org.biojava.bio.AnnotationType.Impl
-
- getDefaultCrossReferenceResolver() - Static method in class org.biojavax.RichObjectFactory
-
Returns the default cross ref resolver object.
- getDefaultFactory() - Static method in class org.biojava.ontology.OntoTools
-
- getDefaultFormat() - Method in class org.biojava.bio.program.phred.PhredFormat
-
Deprecated.
- getDefaultFormat() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- getDefaultFormat() - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
- getDefaultFormat() - Method in class org.biojava.bio.seq.io.GAMEFormat
-
Deprecated.
- getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenbankXmlFormat
-
Deprecated.
- getDefaultFormat() - Method in class org.biojava.bio.seq.io.GenpeptFormat
-
Deprecated.
- getDefaultFormat() - Method in interface org.biojava.bio.seq.io.SequenceFormat
-
Deprecated.
new implementations should only write a single
format.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.FastaFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultFormat() - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.
- getDefaultNamespace() - Static method in class org.biojavax.RichObjectFactory
-
Returns the default namespace object.
- getDefaultOntology() - Static method in class org.biojavax.RichObjectFactory
-
Returns the default ontology object.
- getDefaultPaint() - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
-
- getDefaultParameters() - Static method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getDefaultPositionResolver() - Static method in class org.biojavax.RichObjectFactory
-
Returns the default position resolver object.
- getDefaultRichSequenceHandler() - Static method in class org.biojavax.RichObjectFactory
-
Returns the default sequence resolver object.
- getDefaultSplitter() - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
Get the splitter that will be applied to values of tags with no specific
handler registered.
- getDelegate() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
-
- getDelegate() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
-
- getDelegate() - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- getDelegate() - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper
-
get listener to which all calls will be delegated
- getDelegate() - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
Retrieve the delegate that is wrapped.
- getDelegate() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
Retrieve the delegate that is wrapped.
- getDelegate() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
The compound alpha that holds the symbols used by this wrapper
- getDelegateParser() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- getDelete() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Returns the current expenses of a single delete operation.
- getDelete(int) - Method in class org.biojava.bio.dp.ProfileHMM
-
Retrieves the delete state for column indx.
- getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
Returns the an object indicating the style of deletion that
this database should employ.
- getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
-
Deprecated.
- getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
-
- getDeleteStyle() - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
-
Deprecated.
- getDensityCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getDepDate() - Method in class org.biojava.bio.structure.PDBHeader
-
- getDepth() - Method in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
-
- getDepth() - Method in class org.biojava.bio.dp.twohead.LightPairDPCursor
-
Gets the Depth attribute of the LightPairDPCursor object
- getDepth() - Method in interface org.biojava.bio.dp.twohead.PairDPCursor
-
retrieve the depth of this cursor
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
getDepth calculates the depth required by this
renderer to display its beads.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeatureFilteringRenderer
-
- getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
-
- getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
-
- getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularMLR
-
- getDepth(CircularRendererContext) - Method in class org.biojava.bio.gui.sequence.CircularPaddedRenderer
-
- getDepth(CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularRenderer
-
Get the depth needed for this renderer.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
-
getDepth calculates the depth required by this
renderer to display its beads.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
Returns the depth property of this class.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- getDepth(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
-
getDepth returns the total depth of a list of
SequenceRenderers.
- getDepth(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LineInfo
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
getDepth calculates the depth required by this
renderer to display its beads.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
getDepth calculates the depth required by this
renderer to display its beads.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
-
- getDepth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
-
Retrieve the depth of this renderer when rendering src.
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
-
- getDepth() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- getDepth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
-
- getDepthScaler() - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
-
Retrieve the current DepthScaler.
- getDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
This gives you the description of this matrix if there is one.
- getDescription() - Method in class org.biojava.bio.program.das.DataSource
-
- getDescription() - Method in class org.biojava.bio.program.fastq.Fastq
-
Return the description of this FASTQ formatted sequence.
- getDescription() - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Return the description for this FASTQ formatted sequence builder.
- getDescription() - Method in enum org.biojava.bio.program.fastq.FastqVariant
-
Return the description of this FASTQ sequence format variant.
- getDescription() - Method in class org.biojava.bio.program.homologene.SimilarityType.PlaceHolder
-
- getDescription() - Method in interface org.biojava.bio.program.homologene.Taxon
-
returns the name of the Taxon
- getDescription() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
-
- getDescription() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the description for the AAindex entry.
- getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getDescription(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getDescription(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getDescription() - Method in class org.biojava.bio.structure.PDBHeader
-
- getDescription() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
-
- getDescription() - Method in class org.biojava.ontology.IntegerOntology
-
- getDescription() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getDescription() - Method in interface org.biojava.ontology.Ontology
-
Return a human-readable description of this ontology, or the empty
string if none is available
- getDescription() - Method in class org.biojava.ontology.Ontology.Impl
-
- getDescription() - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getDescription() - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getDescription() - Method in interface org.biojava.ontology.Term
-
Return a human-readable description of this term, or the empty string if
none is available.
- getDescription() - Method in class org.biojava.ontology.Term.Impl
-
- getDescription() - Method in class org.biojava.ontology.Triple.Impl
-
- getDescription() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It returns a description of this vocabulary.
- getDescription() - Method in interface org.biojavax.bio.BioEntry
-
Returns a description of this sequence.
- getDescription() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns a description of this sequence.
- getDescription() - Method in interface org.biojavax.Namespace
-
Returns a description of this namespace.
- getDescription() - Method in interface org.biojavax.ontology.ComparableOntology
-
Return a human-readable description of this ontology.
- getDescription() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Return a human-readable description of this ontology.
- getDescription() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Return a human-readable description of this term, or the empty string if
none is available.
- getDescription() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return a human-readable description of this term, or the empty string if
none is available.
- getDescription() - Method in class org.biojavax.SimpleNamespace
-
Returns a description of this namespace.
- getDescriptors() - Method in interface org.biojavax.ontology.ComparableTriple
-
Returns all descriptors.
- getDescriptors() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Returns all descriptors.
- getDetails() - Method in class org.biojava.bio.structure.Compound
-
- getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getDetails() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getDetailsHandler() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Return a handler for the XFF details element.
- getDFA() - Method in class org.biojava.utils.automata.DfaBuilder
-
- getDiagonalAtK(Atom[], int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
- getDiagonalDistance() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getDiagonalDistance2() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getDictionary() - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
-
- getDimAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
-
Retrieve the dimension at a specific index.
- getDimensionRatio() - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
-
getDimensionRatio returns the maximum ratio of
long dimension to short dimension of the bead.
- getDinucleotideAlphabet() - Static method in class org.biojava.bio.symbol.CodonPrefTools
-
returns an RNA dinucleotide alphabet.
- getDirection() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getDirection returns the direction in which this
context expects the sequence to be rendered - HORIZONTAL or
VERTICAL.
- getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Retrieve the current rendering direction.
- getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getDirection() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the current rendering direction.
- getDirection() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Gets the direction in which this context expects sequences to be rendered
- HORIZONTAL or VERTICAL.
- getDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getDirection() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getDirection() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getDirection returns the direction in which this
context expects sequences to be rendered - HORIZONTAL or
VERTICAL.
- getDisplayName() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns the name of this taxon entry in the form:
scientific (common)
or if there is no common name:
scientific
- getDisplayName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Returns the name of this taxon entry in the form:
scientific (common)
or if there is no common name:
scientific
or if there are no scientific names at all, the empty string.
- getDistance(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
calculate distance between two atoms.
- getDistanceBetweenFeatures() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
matrix of all distances between two sets of 3d coords"
- getDistanceMatrix(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getDistanceMatrix() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
The distance matrix this alignment is based on
- getDistDataSource() - Method in class org.biojava.bio.program.das.DataSource
-
- getDistDataSource() - Method in class org.biojava.bio.program.das.ReferenceServer
-
- getDistMat() - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
return the difference of distance matrix between the two structures
- getDistribution(Symbol) - Method in interface org.biojava.bio.dist.OrderNDistribution
-
- getDistribution() - Method in interface org.biojava.bio.dp.EmissionState
-
Get the Distribution associated with this state.
- getDistribution() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getDistribution() - Method in class org.biojava.bio.gui.DistributionLogo
-
Retrieve the currently rendered dist.
- getDistribution() - Method in interface org.biojava.bio.gui.LogoContext
-
- getDistribution() - Method in class org.biojava.bio.molbio.Composition
-
Returns the distribution backing this class.
- getDivision() - Method in interface org.biojavax.bio.BioEntry
-
Returns the division of this bioentry.
- getDivision() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the division of this bioentry.
- getDNA() - Method in class org.biojava.bio.program.phred.PhredSequence
-
Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
- getDNA() - Static method in class org.biojava.bio.seq.DNATools
-
Return the DNA alphabet.
- getDNAAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
-
- getDNADistribution(double) - Static method in class org.biojava.bio.seq.DNATools
-
return a SimpleDistribution of specified GC content.
- getDNAOneLetter(String) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- getDNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Creates a DNA symbol tokenizer.
- getDNASequence(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
-
Get the called DNA sequence from a chromatogram.
- getDNATwoLetter(Character) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- getDNAxDNA() - Static method in class org.biojava.bio.seq.DNATools
-
Gets the (DNA x DNA) Alphabet
- getDNAxDNADistribution(double, double) - Static method in class org.biojava.bio.seq.DNATools
-
return a (DNA x DNA) cross-product Distribution with specified
DNA contents in each component Alphabet.
- getDocumentReference() - Method in interface org.biojavax.RankedDocRef
-
Represents a reference to a document.
- getDocumentReference() - Method in class org.biojavax.SimpleRankedDocRef
-
Represents a reference to a document.
- getDoi() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the value of DOI field.
- getDotStatesIndex() - Method in class org.biojava.bio.dp.DP
-
- getDouble(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- getDouble() - Method in class org.biojava.utils.io.LargeBuffer
-
- getDoublePivot() - Method in class org.biojava.bio.structure.jama.LUDecomposition
-
Return pivot permutation vector as a one-dimensional double array
- getDoubleValue(Symbol) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
-
- getDoubleValue(Symbol) - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
-
- getDownstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getDownstreamCut returns the cut site within or
downstream of the recognition site.
- getDownstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getDownstreamEndType returns the double-stranded
end type produced by the primary (intra-site or downstream)
cut.
- getDP() - Method in class org.biojava.bio.dp.AbstractTrainer
-
- getDP() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
-
- getDTDHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- getE() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getEcNumber(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getEcNumber(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getEcNums() - Method in class org.biojava.bio.structure.Compound
-
- getEdgeLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getEdgeLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
Tree navigation methods
- getEditDistance() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
This gives the edit distance according to the given parameters of this
certain object.
- getEditorList() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the list of editors of the JournalArticle
- getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getElementId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getElementId() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- getElementId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getElementIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getElementIds() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getElementIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getElideComments() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Is the format going to emit events when comments data or remarks from
bibliographic references are read?
- getElideComments() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Is the format going to emit events when comments data or remarks from
bibliographic references are read?
- getElideFeatures() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Is the format going to emit events when feature data is read?
- getElideFeatures() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Is the format going to emit events when feature data is read?
- getElideReferences() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Is the format going to emit events when bibliographic reference data is read?
- getElideReferences() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Is the format going to emit events when bibliographic reference data is read?
- getElideSymbols() - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
Return a flag indicating if symbol data will be skipped
when parsing streams.
- getElideSymbols() - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- getElideSymbols() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Is the format going to emit events when sequence data is read?
- getElideSymbols() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Is the format going to emit events when sequence data is read?
- getEmblBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Get a default SequenceBuilderFactory for handling EMBL
files.
- getEMBLTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
-
Getter for the EMBL term
- getEMBLxmlTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the EMBLxml term
- getEmission(Symbol, ScoreType) - Method in class org.biojava.bio.dp.onehead.SingleDP
-
This method is public for the benefit of training algorithms,
and in the future we should look at a better way of exposing
the emissions cache.
- getEmissions(List) - Method in class org.biojava.bio.dp.twohead.EmissionCache
-
- getEmissions(List, boolean) - Method in class org.biojava.bio.dp.twohead.EmissionCache
-
Retrieve the emission scores from the cache for every EmissionState
for the specified symbols.
- getEnd() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The end of this feature within the source sequence.
- getEnd() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getEnd() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getEnd() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getEnd() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- getEnd() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- getEnd() - Method in class org.biojava.utils.automata.FiniteAutomaton
-
- getEnd() - Method in interface org.biojava.utils.automata.NfaBuilder
-
- getEnd() - Method in class org.biojava.utils.automata.NfaSubModel
-
- getEnd() - Method in interface org.biojavax.bio.seq.Position
-
Returns the end of the range of bases this base could lie in.
- getEnd() - Method in class org.biojavax.bio.seq.SimplePosition
-
Returns the end of the range of bases this base could lie in.
- getEnd() - Method in interface org.biojavax.RankedDocRef
-
The end position in the sequence that this reference is referred to from.
- getEnd() - Method in class org.biojavax.SimpleRankedDocRef
-
The end position in the sequence that this reference is referred to from.
- getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Get the current string indicating that a record has ended.
- getEndOfRecord() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Get the explicit end-of-record string.
- getEngineered() - Method in class org.biojava.bio.structure.Compound
-
- getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getEntity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getEntityResolver() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
This class has an EntityResolver that
resolves the public ID specifying the
NCBI DTDs to resource files within the
BioJava libraries.
- getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getEntry_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- getEntryByName(String) - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It returns a selected vocabulary entry.
- getEnvironment() - Method in class org.biojava.naming.ObdaContext
-
- getEnvironmentProperties() - Method in class org.biojava.utils.process.ExternalProcess
-
Gets environment variables for the external process.
- getEnzyme(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getEnzyme returns an enzyme by name.
- getEnzyme() - Method in interface org.biojava.bio.molbio.RestrictionSite
-
getEnzyme returns the enzyme which cuts at this
site.
- getEnzyme() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
-
- getEpsilon() - Method in class org.biojava.stats.svm.SMOTrainer
-
- getEqr() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
returns the number of euqivalent residues in this alignment
- getEquivalent() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getErrorHandler() - Method in class org.biojava.bio.program.gff.GFFParser
-
Find the error handler used by this parser.
- getErrorHandler() - Method in class org.biojava.bio.program.gff3.GFF3Parser
-
Find the error handler used by this parser.
- getErrorHandler() - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- getErrorHandler() - Method in class org.biojava.utils.process.ExternalProcess
-
Gets the output error handler which is responsible for the standard error
output of the external process.
- getErrString() - Method in class org.biojava.utils.ExecRunner
-
Returns the error string if exec(String) was invoked.
- getEvalCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the overall E-value of this hit.
- getEValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the E-value of this sub-hit.
- getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getEValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getEValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getEvent() - Method in class org.biojava.utils.ChangeListener.ChangeEventRecorder
-
- getEvents() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property events.
- getEvidenceAttrTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the evidence attr term
- getEvidenceCategoryTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the evidence category term
- getEvidenceDateTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the evidence date term
- getEvidenceTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the evidence type term
- getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getExonIds(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getExonIds(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getExpressionSystem() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemAtccNumber() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemCell() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemCellLine() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemCellularLocation() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemGene() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemOrgan() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemOrganelle() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemOtherDetails() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemPlasmid() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemStrain() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemTaxId() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemTissue() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemVariant() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemVector() - Method in class org.biojava.bio.structure.Compound
-
- getExpressionSystemVectorType() - Method in class org.biojava.bio.structure.Compound
-
- getExtendedName() - Method in interface org.biojavax.DocRefAuthor
-
Returns the extended version of the authors name.
- getExtendedName() - Method in class org.biojavax.SimpleDocRefAuthor
-
Returns the extended version of the authors name.
- getFactory(String, FiniteAutomaton) - Method in class org.biojava.utils.automata.ArrayStateMachineToolkit
-
- getFactory() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Getter for property factory.
- getFactory() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Getter for property factory.
- getFastaBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Get a default SequenceBuilderFactory for handling FASTA
files.
- getFeature() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The feature type filed.
- getFeature() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
Retrieve the current feature.
- getFeature() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getFeature(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- getFeature() - Method in class org.biojava.bio.seq.FeatureFilter.ByFeature
-
- getFeature() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the feature this location is associated with.
- getFeature() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the feature this location is associated with.
- getFeature() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the feature this location is associated with.
- getFeatureDescTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the FeatureDesc term
- getFeatureFilter(int) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- getFeatureFilter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Return the current FeatureFilter.
- getFeatureFilter() - Method in interface org.biojava.bio.seq.io.filterxml.XMLFilterHandler.FilterHandler
-
- getFeatureFromOriginal(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
getFeatureFromOriginal() Since you can not create a feature on a projectedFeature at this time, I am
including this method so that you can get the corresponding feature from the original sequence.
- getFeatureHolder() - Method in interface org.biojava.bio.gui.sequence.FeatureSource
-
- getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
A utility function to retrieve the feature holder delegate, creating it if
necessary.
- getFeatureHolder() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getFeatureID(Feature) - Method in class org.biojava.bio.program.xff.BasicXFFHelper
-
- getFeatureID(Feature) - Method in interface org.biojava.bio.program.xff.XFFHelper
-
- getFeatureListener() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Return the object which receives startFeature/endFeature notifications.
- getFeatureListener() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
Return current feature listener
- getFeatureListener() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
Return current feature listener
- getFeatureOriginalTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the feature original term
- getFeatureRealizer() - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
-
Returns the FeatureRealizer set by "setFeatureRealizer".
- getFeatureRefTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the feature ref term
- getFeatureRelationshipSet() - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
-
Returns the set of relationships held in this feature holder.
- getFeatureRelationshipSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Returns the set of relationships held in this feature holder.
- getFeatureRenderer() - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
getFeatureRenderer returns the currently active
renderer.
- getFeatures() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
-
The features to render.
- getFeatures() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getFeatures returns all of the
Features belonging to the currently rendered
Sequence.
- getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getFeatures() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- getFeatures() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
The features to render.
- getFeatures() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getFeatures() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getFeatures() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getFeatures returns all of the
Features belonging to the currently rendered
Sequence.
- getFeatures(FeatureFilter) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
-
Get all features matching a FeatureFilter provided by this DistDataSource.
- getFeatures(String, FeatureFilter, boolean) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
-
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
- getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
-
- getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
-
- getFeatures(FeatureFilter) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
-
- getFeatures(String, FeatureFilter, boolean) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
-
- getFeatures() - Method in interface org.biojava.bio.seq.homol.Homology
-
Retrieve the set of features that mark homologous regions.
- getFeatures() - Method in class org.biojava.bio.seq.homol.SimpleHomology
-
getFeatures returns the constituent
HomologyFeatures which are also used as the keys
in the alignment.
- getFeatures() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getFeatures() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
Returns the list of features in this featureholder.
- getFeatureSet() - Method in interface org.biojavax.bio.seq.RichSequence
-
The features for this sequence.
- getFeatureSet() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
The features for this sequence.
- getFeatureSource() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- getFeatureStatusTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the feature status term
- getFeatureTemplate() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
Get the template for the feature being constructed.
- getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getFeatureType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getFeatureType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getFeatureVariationTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the feature variation term
- getField() - Method in class org.biojava.utils.ChangeType
-
Return a Field object where this change type is declared.
- getFile() - Method in interface org.biojava.bio.program.indexdb.Record
-
getFile returns the random access file in which
the record belongs.
- getFile() - Method in class org.biojava.bio.program.indexdb.Record.Impl
-
- getFile() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
getFile returns the File wrapped.
- getFile() - Method in interface org.biojava.bio.seq.db.Index
-
The file to retrieve from.
- getFile() - Method in class org.biojava.bio.seq.db.SimpleIndex
-
- getFile() - Method in class org.biojava.utils.io.RAF
-
- getFileIndex(File) - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getFilePath() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getFilePointer() - Method in class org.biojava.utils.io.CountedBufferedReader
-
- getFilePointer() - Method in class org.biojava.utils.io.RandomAccessReader
-
getFilePointer returns the effective position of
the pointer in the underlying RandomAccessFile.
- getFiles() - Method in class org.biojava.bio.seq.db.BioIndex
-
- getFiles() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getFiles() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Retrieve the Set of files that are currently indexed.
- getFiles() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getFill() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getFill() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getFill() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- getFill() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- getFill() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- getFillColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Get the background color of the label area.
- getFillPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
Returns the paint properties of this glyph.
- getFilter() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- getFilter() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getFilter() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
getFilter returns the current filter.
- getFilter() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByAncestor
-
- getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByChild
-
- getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByDescendant
-
- getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.ByParent
-
- getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyChildren
-
- getFilter() - Method in class org.biojava.bio.seq.FeatureFilter.OnlyDescendants
-
- getFinderName() - Method in interface org.biojava.utils.candy.CandyFinder
-
It returns a name of this vocabulary finder.
- getFirstIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Getter for property firstIntActID.
- getFirstOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair
-
gets the first orthologue in the orthology
relationship.
- getFirstOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getFitness() - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- getFitness() - Method in interface org.biojavax.ga.Organism
-
Returns the current fitness of this organism.
- getFitnessFunction() - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
-
- getFitnessFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
-
Returns the fitness function, i.e.
- getFitnessFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getFloat(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- getFloat() - Method in class org.biojava.utils.io.LargeBuffer
-
- getFloatOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Helper method for converting a Number-valued
option into a float primitive.
- getFont() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getFont() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Gets the Font attribute of the SequenceRenderContext object
- getFont() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getFont() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getFormat(String) - Static method in class org.biojava.bio.program.formats.FormatTools
-
Attempt to find aformat for a format identifer string.
- getFormat() - Method in class org.biojava.bio.seq.db.BioIndex
-
- getFormat() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getFormat() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Retrieve the format of the index file.
- getFormat() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getFormula() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getFormula_weight() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getFormula_weight() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getForwarders(ChangeType) - Method in class org.biojava.utils.Unchangeable
-
- getForwardRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getForwardRegex returns a regular expression which
matches the forward strand of the recognition site.
- getForwardTransitions() - Method in class org.biojava.bio.dp.DP
-
- getForwardTransitionScores(ScoreType) - Method in class org.biojava.bio.dp.DP
-
- getFragCompat() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getFragment(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
get a continue subset of Atoms based by the starting position and the length
- getFragment() - Method in class org.biojava.bio.structure.Compound
-
- getFragmentFromIdxList(Atom[], int[]) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
get a subset of Atoms based by their positions
- getFragmentLength() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getFragmentMiniDistance() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getFragmentNoClone(Atom[], int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
get a continue subset of Atoms based by the starting position and the length
does not clone the original atoms.
- getFragmentPairs() - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
get the results of step 1 - the FragmentPairs used for seeding the alignment
- getFragmentPairs() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getFragmentPairs() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- getFrame() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The frame of the feature.
- getFrame() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- getFrame() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getFrame() - Method in class org.biojava.bio.seq.FeatureFilter.FrameFilter
-
Retrieve the reading frame this filter matches.
- getFrame() - Method in interface org.biojava.bio.seq.Frame
-
A method to get the frame information of the implementing object
- getFrame() - Method in class org.biojava.bio.seq.FramedFeature.ReadingFrame
-
- getFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
-
- getFrequency() - Method in interface org.biojava.bio.symbol.CodonPref
-
returns a Distribution giving the
frequency of codons (sums to one over the
totality of codons).
- getFrequency() - Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getFrequencyForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref
-
returns a Distribution giving the
frequency of synonymous codons.
- getFrequencyForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getFrequencyOfNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution
-
returns the frequency with which
synonymous codons start with a
specified pair of bases.
- getFrom() - Method in exception org.biojava.bio.dp.IllegalTransitionException
-
- getFTIdTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the FTId term
- getFullAtomSequence(List<Group>) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
returns the full sequence of the Atom records of a chain
with X instead of HETATMSs.
- getFullName() - Method in interface org.biojava.bio.structure.Atom
-
get full name of atom e.g.
- getFullName() - Method in class org.biojava.bio.structure.AtomImpl
-
get full name of atom e.g.
- getFuzzyEnd() - Method in interface org.biojavax.bio.seq.Position
-
Returns true if the position has a fuzzy end.
- getFuzzyEnd() - Method in class org.biojavax.bio.seq.SimplePosition
-
Returns true if the position has a fuzzy end.
- getFuzzyStart() - Method in interface org.biojavax.bio.seq.Position
-
Returns true if the position has a fuzzy start.
- getFuzzyStart() - Method in class org.biojavax.bio.seq.SimplePosition
-
Returns true if the position has a fuzzy start.
- getG() - Method in class org.biojava.bio.molbio.DNAComposition
-
Get the relative compositon of 'G'.
- getG() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getGapExt() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Returns the current expenses of any extension of a gap operation.
- getGapExtCol() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getGapExtCol() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getGapExtension() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getGapExtRow() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getGapExtRow() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getGapOpen() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getGapOpenCol() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getGapOpenCol() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getGapOpenRow() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getGapOpenRow() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getGaps() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
return the number of gaps in this alignment
- getGapSymbol() - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getGapSymbol() - Method in interface org.biojava.bio.symbol.Alphabet
-
Get the 'gap' ambiguity symbol that is most appropriate for this alphabet.
- getGapSymbol() - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Get the special `gap' Symbol.
- getGapSymbol(List) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Get the gap symbol appropriate to this list of alphabets.
- getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getGapSymbol() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getGapSymbol() - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getGapSymbol() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
- getGenbankBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Get a default SequenceBuilderFactory for handling GenBank
files.
- getGenBankTerm() - Static method in class org.biojavax.bio.seq.io.GenbankFormat.Terms
-
Getter for the Genbank term
- getGene() - Method in class org.biojava.bio.structure.Compound
-
- getGeneNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the GeneName term
- getGenerateSequenceHeader() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Discover if per-sequence header lines will be generated.
- getGeneration() - Method in interface org.biojavax.ga.GeneticAlgorithm
-
- getGeneration() - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
-
The current generation
- getGeneSynonymTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the GeneSynonym term
- getGeneticCode(String) - Static method in class org.biojava.bio.seq.RNATools
-
Retrieve a TranslationTable by name.
- getGeneticCode(int) - Static method in class org.biojava.bio.seq.RNATools
-
Retrieve a TranslationTable by number.
- getGeneticCode() - Method in interface org.biojava.bio.symbol.CodonPref
-
the genetic code that this codon
preference is based on.
- getGeneticCode() - Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns the genetic code of this taxon, which may be null if not known.
- getGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Returns the genetic code of this taxon, which may be null if not known.
- getGeneticCodeName() - Method in interface org.biojava.bio.symbol.CodonPref
-
get the name of the genetic code
- getGeneticCodeName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getGeneticCodeNames() - Static method in class org.biojava.bio.seq.RNATools
-
Retrieve a Set containing the name of each genetic code.
- getGenomicTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
-
Getter for the Ensembl-specific 'genomic' term
- getGenpeptBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Get a default SequenceBuilderFactory for handling Genpept
files.
- getGlu_C_bicarbonate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getGlu_C_phosphate() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getGlyphForFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
Returns the
Glyph object which is assigned to the given feature
filter.
- getGraphics() - Method in interface org.biojava.bio.gui.LogoContext
-
- getGroup(int) - Method in interface org.biojava.bio.structure.Chain
-
Deprecated.
use getAtomGroup or getSeqResGroup instead
- getGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
-
Deprecated.
use getAtomGroup or getSeqResGroup instead
- getGroup_PDB() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getGroupAttributes() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
A Map containing the group / attribute information.
- getGroupAttributes() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getGroupByPDB(String) - Method in interface org.biojava.bio.structure.Chain
-
get a group by its PDB residue numbering.
- getGroupByPDB(String) - Method in class org.biojava.bio.structure.ChainImpl
-
- getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getGroupOrder(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getGroupOrder(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getGroups(String) - Method in interface org.biojava.bio.structure.Chain
-
Deprecated.
use getAtomGroups or getSeqResGroups instead
- getGroups() - Method in interface org.biojava.bio.structure.Chain
-
Deprecated.
use getAtomGroups or getSeqResGroups instead
- getGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
-
Deprecated.
use getAtomGroups instead
- getGroups() - Method in class org.biojava.bio.structure.ChainImpl
-
Deprecated.
use getAtomGroups instead
- getGroupsByPDB(String, String) - Method in interface org.biojava.bio.structure.Chain
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(String, String, boolean) - Method in interface org.biojava.bio.structure.Chain
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(String, String, boolean) - Method in class org.biojava.bio.structure.ChainImpl
-
Get all groups that are located between two PDB residue numbers.
- getGroupsByPDB(String, String) - Method in class org.biojava.bio.structure.ChainImpl
-
Get all groups that are located between two PDB residue numbers.
- getH() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getH() - Method in class org.biojava.bio.structure.jama.QRDecomposition
-
Return the Householder vectors
- getHandler(SeqSimilarityStAXAdapter) - Method in interface org.biojava.bio.program.ssbind.StAXHandlerFactory
-
getHandler returns an appropriate
StAXContentHandler implementation containing a
reference to a parent context.
- getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.agave.StAXHandlerFactory
-
Return a suitable StAX content handler.
- getHandler(String, String) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
-
Retrieve a FilterHandler for the specified tag name.
- getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game.StAXHandlerFactory
-
Return a suitable StAX content handler.
- getHandler(StAXFeatureHandler) - Method in interface org.biojava.bio.seq.io.game12.StAXHandlerFactory
-
Return a suitable StAX content handler.
- getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
return iterator to callbackStack
- getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
get iterator for current stack starting at the position
below mine.
- getHandlerStackIterator(int) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
return iterator to callbackStack
- getHandlerStackIterator() - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
-
get iterator for current stack starting at the position
below mine.
- getHeader() - Method in interface org.biojava.bio.structure.Chain
-
Returns the Header ( a Compound object) for this chain.
- getHeader() - Method in class org.biojava.bio.structure.ChainImpl
-
Returns the Header ( a Compound object) for this chain.
- getHeader() - Method in interface org.biojava.bio.structure.Structure
-
Deprecated.
use getPDBHeader instead
- getHeader() - Method in class org.biojava.bio.structure.StructureImpl
-
get Header data.
- getHeader() - Method in class org.biojavax.bio.seq.io.FastaFormat
-
- getHeaderDefinitions() - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
-
Returns the appropriate style and javascript definitions for this
renderer.
- getHeaderVars() - Method in class org.biojava.bio.structure.Compound
-
- getHeight() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the height of the whole graphic (in pixels).
- getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
getHeightScaling returns the state of the height
scaling policy.
- getHeightScaling() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
getHeightScaling returns the state of the height
scaling policy.
- getHetero() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- getHetero() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- getHibernateSession() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
-
- getHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- getHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
-
Return all hits in this sequence similarity search result.
- getHits() - Method in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- getHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getHomologeneID() - Method in interface org.biojava.bio.program.homologene.Orthologue
-
get the Homologene ID.
- getHomologeneID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getHomology() - Method in interface org.biojava.bio.seq.homol.HomologyFeature
-
- getHomology() - Method in class org.biojava.bio.seq.impl.SimpleHomologyFeature
-
- getHorizontalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the in-use horizontal scale factor.
- getI() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getID() - Method in interface org.biojava.bio.program.indexdb.Record
-
getID returns the primary identifier of the
record.
- getID() - Method in class org.biojava.bio.program.indexdb.Record.Impl
-
- getID() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
-
The public unigene ID.
- getID() - Method in interface org.biojava.bio.seq.db.Index
-
The ID of the sequence at this position in this file.
- getID() - Method in class org.biojava.bio.seq.db.SimpleIndex
-
- getId() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- getID() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
-
- getId() - Method in class org.biojava.bio.structure.AtomImpl
-
Get the Hibernate database ID.
- getId() - Method in interface org.biojava.bio.structure.Chain
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.bio.structure.ChainImpl
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.bio.structure.Compound
-
get the ID used by Hibernate
- getId() - Method in class org.biojava.bio.structure.DBRef
-
Get the ID used by Hibernate.
- getId() - Method in class org.biojava.bio.structure.HetatomImpl
-
the Hibernate database ID
- getId() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getId() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getId() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
-
- getId() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getId() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getId() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getId() - Method in class org.biojava.bio.structure.PDBHeader
-
Get the ID used by Hibernate.
- getId() - Method in interface org.biojava.bio.structure.Structure
-
get the ID used by Hibernate
- getId() - Method in class org.biojava.bio.structure.StructureImpl
-
get the ID used by Hibernate
- getID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Getter for property ID.
- getId() - Method in class org.biojavax.bio.seq.SimplePosition
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.bio.SimpleBioEntry
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.SimpleComment
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.SimpleCrossRef
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.SimpleDocRef
-
Gets the Hibernate ID.
- getId() - Method in class org.biojavax.SimpleNamespace
-
Gets the Hibernate ID.
- getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getIdAlias(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getIdAlias(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getIdbnsBegin() - Method in class org.biojava.bio.structure.DBRef
-
Insertion code of initial residue of the segment, if PDB is the
reference.
- getIdbnsEnd() - Method in class org.biojava.bio.structure.DBRef
-
Insertion code of the ending
residue of the segment, if PDB is
the reference.
- getIdCode() - Method in class org.biojava.bio.structure.DBRef
-
get the idCode for this entry
- getIdCode() - Method in class org.biojava.bio.structure.PDBHeader
-
The PDB code for this protein structure.
- getIdentifier() - Method in interface org.biojava.utils.lsid.Identifiable
-
Return the identifier of this object.
- getIdentifier() - Method in interface org.biojavax.bio.BioEntry
-
Returns the identifier of this bioentry.
- getIdentifier() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the identifier of this bioentry.
- getIdentifier() - Method in interface org.biojavax.ontology.ComparableTerm
-
Returns the (optional) identifier associated with this term.
- getIdentifier() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Returns the (optional) identifier associated with this term.
- getIDMaker() - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
Retrieve the IDMaker associated with this database.
- getIDMaker() - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
Retrieve the IDMaker associated with this database.
- getIDs() - Method in class org.biojava.bio.seq.db.BioIndex
-
- getIDs() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getIDs() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Retrieve the set of all current IDs.
- getIDs() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getIdx1() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
the positions of the structure equivalent positions in atom set 1
- getIdx1() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
get the identical position in the alignment
- getIdx2() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
the positions of the structure equivalent atoms in atom set 2
- getIdx2() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
get the identical position in the alignment
- getIdxlist() - Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- getImage(int, int) - Method in class org.biojava.bio.program.abi.ABITrace
-
Returns a BufferedImage that represents the entire trace.
- getImagEigenvalues() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
-
Return the imaginary parts of the eigenvalues
- getImageMap() - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
-
getImageMap returns the current image map.
- getImageMap() - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
getImageMap returns the current image map.
- getImageMap() - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
-
getImageMap returns the current image map.
- getImplementationNames(Class) - Static method in class org.biojava.utils.Services
-
Return a Set of names of implementations of the
given service interface in the classloader from
which BioJava was loaded.
- getImplementationNames(Class, ClassLoader) - Static method in class org.biojava.utils.Services
-
Return a List of names of implementations of the
given service interface available in a given
classloader.
- getIndex(double) - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
-
Calculate the position in the sequence relating to the angle.
- getIndex(double) - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getIndex() - Method in class org.biojava.bio.structure.align.helper.GapArray
-
- getIndexStore() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
Retrieve the IndexStore.
- getInitialContext(Hashtable) - Method in class org.biojava.naming.ObdaInitialContextFactory
-
- getInitialK() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getInitials() - Method in class org.biojava.bio.structure.Author
-
- getInnerMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getInnerMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getInput() - Method in interface org.biojava.utils.process.OutputHandler
-
Gets the input stream.
- getInput() - Method in class org.biojava.utils.process.StreamPipe
-
Gets the input stream
- getInput() - Method in class org.biojava.utils.process.WriterOutputHandler
-
Gets the input stream.
- getInputHandler() - Method in class org.biojava.utils.process.ExternalProcess
-
Gets the input handler which is responsible for the standard input
of the external process.
- getInputStream(String) - Method in class org.biojava.utils.io.InputStreamProvider
-
get an InputStream for this file
- getInputStream(File) - Method in class org.biojava.utils.io.InputStreamProvider
-
get an InputStream for the file
- getInsCode1() - Method in class org.biojava.bio.structure.SSBond
-
- getInsCode2() - Method in class org.biojava.bio.structure.SSBond
-
- getINSDseqTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
-
Getter for the INSDseq term
- getInsert() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Returns the current expenses of a single insert operation.
- getInsert(int) - Method in class org.biojava.bio.dp.ProfileHMM
-
Retrieves the insert state at column indx.
- getInsertBegin() - Method in class org.biojava.bio.structure.DBRef
-
Initial insertion code of the PDB sequence segment.
- getInsertEnd() - Method in class org.biojava.bio.structure.DBRef
-
Ending insertion code of the PDB sequence segment.
- getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
Returns the id value created during the last insert
command.
- getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.HypersonicDBHelper
-
Deprecated.
- getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.MySQLDBHelper
-
Deprecated.
- getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.PostgreSQLDBHelper
-
- getInsertID(Connection, String, String) - Method in class org.biojava.bio.seq.db.biosql.UnknownDBHelper
-
Deprecated.
- getInstance() - Static method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity
-
Retrieve the singleton instance of this class.
- getInstance() - Static method in class org.biojava.bio.dist.IgnoreCountsTrainer
-
Returns the global singleton instance of the IgnoreCountsTrainer.
- getInstance() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getInstance() - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilterFactory
-
- getInstance() - Static method in class org.biojava.bio.symbol.DoubleAlphabet
-
Retrieve the single DoubleAlphabet instance.
- getInstance() - Static method in class org.biojava.bio.symbol.IntegerAlphabet
-
Retrieve the single IntegerAlphabet instance.
- getInstance(FiniteAlphabet) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
Generates a soft masked Alphabet where lowercase tokens are assumed to be
soft masked.
- getInstance(FiniteAlphabet, SoftMaskedAlphabet.MaskingDetector) - Static method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
Creates a compound alphabet that is a hybrid of the alphabet that is to
be soft masked and a binary alphabet that indicates if any
Symbol is soft masked or not.
- getInstance() - Static method in class org.biojava.bio.taxa.EbiFormat
-
Deprecated.
- getInstance() - Static method in class org.biojava.naming.ObdaUriParser
-
- getInstance(Class) - Static method in class org.biojava.utils.walker.WalkerFactory
-
Make a WalkerFactory that handles a Visitor for
a class of type typeClazz.
- getInstance() - Static method in class org.biojava.utils.walker.WalkerFactory
-
- getInt(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- getInt() - Method in class org.biojava.utils.io.LargeBuffer
-
- getIntegerOntology() - Static method in class org.biojava.ontology.OntoTools
-
Get the Ontology that defines integers.
- getInteractions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property interactions.
- getInternalSymbolList() - Method in interface org.biojavax.bio.seq.RichSequence
-
A special function that returns the SymbolList that this RichSequence is
based around.
- getInternalSymbolList() - Method in class org.biojavax.bio.seq.SimpleRichSequence
-
A special function that returns the SymbolList that this RichSequence is
based around.
- getInternalSymbolList() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
A special function that returns the SymbolList that this RichSequence is
based around.
- getIntFromSymbolList(SymbolList, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
-
- getIntOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Helper method for converting a Number-valued
option into an int primitive.
- getInvTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns a new AffineTransform describing the transformation from
output space to chromatogram space.
- getIsoelectricPoint(SymbolList) - Static method in class org.biojava.bio.proteomics.IsoelectricPointCalc
-
Static public method to compute the pI for a polypeptide in
denaturating and reduced conditions with both free ends.
- getIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property isoforms.
- getIsoIDs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Getter for property isoIDs.
- getIsoschizomers(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getIsoschizomers returns an unmodifable set of the
isoschizomers of this enzyme.
- getItem() - Method in interface org.biojava.stats.svm.ItemValue
-
- getItem() - Method in class org.biojava.stats.svm.SimpleItemValue
-
- getIterator() - Method in class org.biojava.utils.ListTools.Doublet
-
- getIterator() - Method in class org.biojava.utils.ListTools.Triplet
-
- getJoiner() - Method in class org.biojava.bio.program.tagvalue.Aggregator
-
- getJoinRMSCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.DBHelper
-
Deprecated.
Returns the an object indicating the style of table joining that
this database should employ.
- getJoinStyle() - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- getJoinTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
-
Getter for the "join" term
- getJournalArticle() - Method in interface org.biojava.bio.structure.Structure
-
get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalArticle() - Method in class org.biojava.bio.structure.StructureImpl
-
get the associated publication as defined by the JRNL records in a PDB
file.
- getJournalName() - Method in class org.biojava.bio.structure.JournalArticle
-
- getJournalReference() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets a reference to the journal which published the article about the
AAindex entry.
- getKernel() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- getKernel() - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- getKernel() - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getKernel() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Retrieve the currently used kernel
- getKernelValue(int, int) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getKey() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
-
- getKey() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
-
- getKey() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
-
- getKey() - Method in class org.biojava.bio.seq.FeatureFilter.HasAnnotation
-
- getKey() - Method in class org.biojava.utils.cache.KeyedWeakReference
-
- getKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
- getKeys() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
- getKeys() - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
- getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getKeyword(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getKeyword(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getKeywordTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the keyword term
- getKineticsNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property kineticsNote.
- getKmpNextTable() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
-
Returns the table of border lengths
- getKMs() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property KMs.
- getL() - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
-
Return triangular factor.
- getL() - Method in class org.biojava.bio.structure.jama.LUDecomposition
-
Return lower triangular factor
- getLabel() - Method in interface org.biojava.bio.alignment.AlignmentElement
-
- getLabel() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
-
- getLabel() - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- getLabel() - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
-
- getLabel() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
return the label of this class.
- getLabel() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
-
- getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getLabel(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getLabel(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getLabel(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getLabel() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
-
- getLabel() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Getter for property label.
- getLabel_alt_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getLabel_asym_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getLabel_atom_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getLabel_comp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getLabel_entity_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getLabel_seq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getLabelGlyph(SequenceRenderContext, FontRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
-
- getLabelMaker() - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- getLabels() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- getLabels() - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
getLabels will return a list of labels in left to right order
- getLabels() - Method in class org.biojava.bio.dp.SimpleStatePath
-
- getLabels() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- getLabels() - Method in interface org.biojava.bio.symbol.Alignment
-
The list of SymbolLists in the alignment.
- getLabels() - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- getLabels() - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- getLabelsAt(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- getLambda() - Method in class org.biojava.stats.svm.DiagonalAddKernel
-
Retrieve the scale factor.
- getLast() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
-
Get the last complete annotation built.
- getLastScore() - Method in class org.biojava.bio.dp.AbstractTrainer
-
- getLastScore() - Method in interface org.biojava.bio.dp.TrainingAlgorithm
-
- getLeader() - Method in class org.biojava.utils.ListTools.SeriesList
-
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getLeadingBorder returns the leading border of the
primary sequence.
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Retrieve the object that encapsulates the leading border area - the space
before sequence information is rendered.
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the object that encapsulates the leading border area - the space
before sequence information is rendered.
- getLeadingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Gets the LeadingBorder attribute of the SequenceRenderContext object.
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getLeadingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getLeadingBorder returns the leading border.
- getLeadingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getLeftValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Gets the left value.
- getLeftValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Gets the left value.
- getLength() - Method in interface org.biojava.bio.program.indexdb.Record
-
getLength returns the length of the record in
bytes.
- getLength() - Method in class org.biojava.bio.program.indexdb.Record.Impl
-
- getLength() - Method in class org.biojava.bio.search.SeqContentPattern
-
Get the current length.
- getLength() - Method in interface org.biojava.bio.seq.db.Index
-
The entry can be slurped out of the file by grabbing length bytes from
start.
- getLength() - Method in class org.biojava.bio.seq.db.SimpleIndex
-
- getLength() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getLength() - Method in interface org.biojava.bio.structure.Chain
-
Deprecated.
please use getAtomLength or getLengthSeqRes instead
- getLength() - Method in class org.biojava.bio.structure.ChainImpl
-
Deprecated.
use getAtomLength instead
- getLength() - Method in class org.biojava.bio.symbol.CircularLocation
-
- getLength() - Method in class org.biojava.utils.RepeatedCharSequence
-
- getLengthAminos() - Method in interface org.biojava.bio.structure.Chain
-
Deprecated.
use getAtomGroups("amino").size() instead.
- getLengthAminos() - Method in class org.biojava.bio.structure.ChainImpl
-
returns the length of the AminoAcids in the ATOM records of this chain.
- getLevel() - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
return current stack level.
- getLevel() - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
return current stack level.
- getLimit() - Method in class org.biojava.utils.cache.FixedSizeCache
-
- getLine() - Method in exception org.biojava.utils.ParserException
-
Get the text of the line where the exception occured.
- getLineNumber() - Method in exception org.biojava.utils.ParserException
-
Get the line number in the stream where this exception occured.
- getLines() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the number of lines that the sequence will be rendered over.
- getLineWidth() - Method in class org.biojava.bio.program.phred.PhredFormat
-
Retrive the current line width.
- getLineWidth() - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
Retrive the current line width.
- getLineWidth() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Retrive the current line width.
- getLineWidth() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Retrive the current line width.
- getLinkURL() - Method in class org.biojava.bio.program.das.DASLink
-
- getListener() - Method in class org.biojava.bio.program.tagvalue.ParserListener
-
getListener returns the listener of the pair.
- getListener() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
return the TagValueListener assigned to this State.
- getListener() - Method in interface org.biojava.bio.program.tagvalue.StateMachine.State
-
- getListener(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- getListeners(ChangeType) - Method in class org.biojava.utils.Unchangeable
-
- getLITDBEntryNumbers() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Gets the list of literature database identifiers for the AAindex entry.
- getLoc() - Method in interface org.biojava.bio.alignment.AlignmentElement
-
- getLoc() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
-
- getLocation() - Method in class org.biojava.bio.program.indexdb.BioStore
-
getLocation returns the directory where the index
is located.
- getLocation() - Method in interface org.biojava.bio.seq.Feature
-
The location of this feature.
- getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ContainedByLocation
-
- getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.OverlapsLocation
-
- getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowContainedByLocation
-
- getLocation() - Method in class org.biojava.bio.seq.FeatureFilter.ShadowOverlapsLocation
-
- getLocation() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getLocation() - Method in class org.biojava.bio.seq.RemoteFeature.Region
-
Retrieve the Location of the Region.
- getLocation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
The location of this feature.
- getLocation() - Method in interface org.biojavax.DocRef
-
Returns a textual description of the document reference.
- getLocation() - Method in interface org.biojavax.RankedDocRef
-
If this object was constructed using a location instead of two integers,
then this method will return that location.
- getLocation() - Method in class org.biojavax.SimpleDocRef
-
Returns a textual description of the document reference.
- getLocation() - Method in class org.biojavax.SimpleRankedDocRef
-
- getLocationHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getLocationSequenceTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the location seq term
- getLocator() - Method in exception org.biojava.utils.ParserException
-
Get a locator for the stream which caused this exception.
- getLocusID() - Method in interface org.biojava.bio.program.homologene.Orthologue
-
get the locus ID associated with this orthologue.
- getLocusID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getLogoFont() - Method in class org.biojava.bio.gui.TextBlock
-
Retrieve the current font.
- getLogoFont() - Method in class org.biojava.bio.gui.TextLogoPainter
-
Retrieve the current font.
- getLogoPainter() - Method in class org.biojava.bio.gui.DistributionLogo
-
Retrieve the current logo painter.
- getLong(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- getLong() - Method in class org.biojava.utils.io.LargeBuffer
-
- getLs_d_res_high() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_d_res_low() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_number_parameters() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_all() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_number_reflns_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_number_restraints() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_percent_reflns_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_percent_reflns_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_all() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free_error() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_free_error_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_R_factor_R_work() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_redundancy_reflns_obs() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_wR_factor_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLs_wR_factor_R_work() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getLSID() - Method in class org.biojava.bio.program.formats.Embl
-
- getLSID() - Method in class org.biojava.bio.program.formats.Enzyme
-
- getLSID() - Method in interface org.biojava.bio.program.formats.Format
-
Retrieve the LSID associated with this format.
- getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Compound
-
- getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
-
- getLSID() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
-
- getLSID() - Method in class org.biojava.bio.program.formats.Swissprot
-
- getLys_C() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getMagicalState(Alphabet, int) - Static method in class org.biojava.bio.dp.MagicalState
-
- getMagicalState() - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- getMapAll() - Method in class org.biojava.bio.molbio.RestrictionMapper
-
getMapAll returns whether all sites should be
marked, including those which have recognition sites within the
sequence, but cut outside it.
- getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMapLocation(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMapLocation(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMapper() - Method in class org.biojava.bio.AnnotationRenamer
-
getMapper returns the TagMapper being
used to remap the Annotation.
- getMapper() - Method in class org.biojava.bio.program.tagvalue.TagRenamer
-
Retrieve the mapper used to rename tags
- getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMapPosition(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMapPosition(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMapType() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getMapURL() - Method in class org.biojava.bio.program.das.DataSource
-
- getMaskedAlphabet() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
Gets the Alphabet upon which masking is being applied
- getMaskingDetector() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
Getter for the MaskingDetector
- getMass(SymbolList, String, boolean) - Static method in class org.biojava.bio.proteomics.MassCalc
-
getMass calculates the mass of this peptide.
- getMass(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
-
Get the Mass of this peptide.
- getMatch() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Returns the current expenses of a single match operation.
- getMatch(int) - Method in class org.biojava.bio.dp.ProfileHMM
-
Retrieve the match state at column indx.
- getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMatchAlign(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMatchAlign(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMatchDesc(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMatchDesc(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMatches() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getMatches() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getMatches() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getMatches() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getMatches() - Method in interface org.biojava.bio.symbol.Symbol
-
The alphabet containing the symbols matched by this ambiguity symbol.
- getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMatchRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMatchRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMatrices() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
Returns the matrices.
- getMatrix() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getMatrix() - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- getMatrix(int, int, int, int) - Method in class org.biojava.bio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int[], int[]) - Method in class org.biojava.bio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int, int, int[]) - Method in class org.biojava.bio.structure.jama.Matrix
-
Get a submatrix.
- getMatrix(int[], int, int) - Method in class org.biojava.bio.structure.jama.Matrix
-
Get a submatrix.
- getMatrixAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
-
define the rotation matrix annotation type
- getMax() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
The maximum score in this matrix.
- getMax() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getMax(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getMax() - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Gets the max intensity from all the traces.
- getMax(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Gets the max intensity on the trace for the specified nucleotide.
- getMax() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getMax() - Method in class org.biojava.bio.symbol.CircularLocation
-
This will give you the coordinate of the maximum point contained by this
Location.
- getMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getMax() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- getMax() - Method in interface org.biojava.bio.symbol.Location
-
The maximum position contained.
- getMax() - Method in class org.biojava.bio.symbol.PointLocation
-
- getMax() - Method in class org.biojava.bio.symbol.RangeLocation
-
- getMax() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
The maximum position contained.
- getMax() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
The maximum position contained.
- getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
-
Resolves the maximum possible base for this position.
- getMax(Position) - Method in interface org.biojavax.bio.seq.PositionResolver
-
Resolves the maximum possible base for this position.
- getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
-
Resolves the maximum possible base for this position.
- getMax(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
-
Resolves the maximum possible base for this position.
- getMax() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
The maximum position contained.
- getMaxCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern
-
Get the maximum counts required for a symbol.
- getMaxCrossOvers() - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
-
- getMaxCrossOvers() - Method in interface org.biojavax.ga.functions.CrossOverFunction
-
- getMaxCrossOvers() - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- getMaxGenerations() - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
-
- getMaxIter() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getMaxPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the end position of this location.
- getMaxPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
Retrieves the end position of this location.
- getMaxPosition() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the end position of this location.
- getMaxPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the end position of this location.
- getMaxrefine() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getMaxRunTimeExceeded() - Method in class org.biojava.utils.ExecRunner
-
Returns whether the maximum runtime was exceeded or not.
- getMaxRunTimeSecs() - Method in class org.biojava.utils.ExecRunner
-
Returns the maximum run time in seconds for this object.
- getMaxScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
-
getMaxScore returns the maximum score
accepted.
- getMaxSize() - Method in class org.biojava.utils.cache.FixedSizeMap
-
- getMaxValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getMergeAnnotation() - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
- getMerged() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
Return a list of merged DBs.
- getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
See if tags are being merged.
- getMergeSameTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Report whether empty tags will be treated as continuations of the last non
-empty tag.
- getMessage() - Method in class org.biojava.utils.ParseErrorEvent
-
Find the message about this event
- getMetaData() - Method in class org.biojava.bio.program.indexdb.BioStore
-
- getMetaData() - Method in interface org.biojava.bio.program.indexdb.IndexStore
-
getMetaData returns a data structure which
represents an OBDA "config.dat" flatfile indexing configuration
file.
- getMethod() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
-
Get the Method used.
- getMethod() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getMethod() - Method in class org.biojava.bio.structure.PDBHeader
-
- getMethod_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- getMin() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
The minimum score of this matrix.
- getMin() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getMin() - Method in class org.biojava.bio.symbol.CircularLocation
-
This will give you the coordinate of the minimum point contained by this
Location.
- getMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getMin() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- getMin() - Method in interface org.biojava.bio.symbol.Location
-
The minimum position contained.
- getMin() - Method in class org.biojava.bio.symbol.PointLocation
-
- getMin() - Method in class org.biojava.bio.symbol.RangeLocation
-
- getMin() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
The minimum position contained.
- getMin() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
The minimum position contained.
- getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.AverageResolver
-
Resolves the minimum possible base for this position.
- getMin(Position) - Method in interface org.biojavax.bio.seq.PositionResolver
-
Resolves the minimum possible base for this position.
- getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MaximalResolver
-
Resolves the minimum possible base for this position.
- getMin(Position) - Method in class org.biojavax.bio.seq.PositionResolver.MinimalResolver
-
Resolves the minimum possible base for this position.
- getMin() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
The minimum position contained.
- getMinCounts(AtomicSymbol) - Method in class org.biojava.bio.search.SeqContentPattern
-
Get the minimum counts required for a symbol.
- getMinIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
get the lowest level of identity observed
in this Group
- getMinIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- getMinimumLeader(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
-
getMinimumLeader returns the maximum value of
getMinimumLeader() for a list of SequenceRenderers.
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
-
Retrieve the minimum leading distance for this renderer when rendering src.
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
-
- getMinimumLeader(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GappedRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- getMinimumTrailer(List, List) - Method in class org.biojava.bio.gui.sequence.LayeredRenderer
-
getMinimumTrailer returns the maximum value of
getMinimumTrailer() for a list of SequenceRenderers.
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RulerRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderer
-
Retrieve the minimum trailing distance for this renderer when rendering src.
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StopRenderer
-
- getMinimumTrailer(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
-
- getMinimumWidth(SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.LabelRenderer
-
Retrieve the minimum space required to render the label.
- getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.LabelRenderer.RenderNothing
-
- getMinimumWidth(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
-
- getMinPosition() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the start position of this location.
- getMinPosition() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
Retrieves the start position of this location.
- getMinPosition() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the start position of this location.
- getMinPosition() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the start position of this location.
- getMinScore() - Method in class org.biojava.bio.seq.FeatureFilter.ByPairwiseScore
-
getMinScore returns the minimum score
accepted.
- getMinValue() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getMismatches() - Method in class org.biojava.bio.search.MaxMismatchPattern
-
- getMitoGeneticCode() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns the mitochondrial genetic code of this taxon, which may be null
if not known.
- getMitoGeneticCode() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Getter for property mitoGeneticCode.
- getMod_type() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getModDate() - Method in class org.biojava.bio.structure.PDBHeader
-
- getModel() - Method in class org.biojava.bio.dp.DP
-
- getModel() - Method in interface org.biojava.bio.dp.ModelInState
-
The model that is inside this state.
- getModel() - Method in class org.biojava.bio.dp.SimpleModelInState
-
- getModel() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
-
- getModel(int) - Method in interface org.biojava.bio.structure.Structure
-
retrieve all Chains belonging to a model .
- getModel(int) - Method in class org.biojava.bio.structure.StructureImpl
-
retrieve all Chains belonging to a model .
- getModifiable() - Method in class org.biojava.utils.MergingSet
-
- getMolecularWeight(SymbolList) - Static method in class org.biojava.bio.proteomics.MassCalc
-
Calculate the molecular weight of a protein, making estimates whenever it is
possible like averaging mass values for ambiguity symbols or counting
zero when gaps are encountered.
- getMolecularWeight() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property molecularWeight.
- getMolId() - Method in class org.biojava.bio.structure.Compound
-
Returns the mol id value.
- getMolName() - Method in class org.biojava.bio.structure.Compound
-
- getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getMolType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getMolType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getMolTypeTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
getter for the MolType term
- getMolWeightError() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property molWeightError.
- getMolWeightMethod() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property molWeightMethod.
- getMolWeightRangeEnd() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property molWeightRangeEnd.
- getMolWeightRangeStart() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property molWeightRangeStart.
- getMon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- getMon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getMon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getMon_nstd_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getMon_nstd_parent_comp_id() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getMoreSearches() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- getMoreSearches() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- getMoreSearches() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- getMoreSearches() - Method in class org.biojava.bio.search.SearchContentAdapter
-
- getMoreSearches() - Method in class org.biojava.bio.search.SearchContentFilter
-
- getMoreSearches() - Method in interface org.biojava.bio.search.SearchContentHandler
-
getMoreSearches returns the state of the
SearchContentHandler with respect to further
searches from its data source.
- getMoreSearches() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- getMotifs() - Method in class org.biojava.bio.program.Meme
-
- getMouseEvent() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
-
Get the mouse event that caused this.
- getMultiplier() - Method in class org.biojava.stats.svm.PolynomialKernel
-
- getMultiplier() - Method in class org.biojava.stats.svm.SigmoidKernel
-
- getMutation() - Method in class org.biojava.bio.structure.Compound
-
- getMutationFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
-
- getMutationFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getMutationProbs() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
-
- getMutationProbs() - Method in interface org.biojavax.ga.functions.MutationFunction
-
- getMutationProbs() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- getMutationSpectrum() - Method in class org.biojavax.ga.functions.AbstractMutationFunction
-
- getMutationSpectrum() - Method in interface org.biojavax.ga.functions.MutationFunction
-
- getMutationSpectrum() - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- getMyComponents(Name) - Method in class org.biojava.naming.ObdaContext
-
- getN() - Method in interface org.biojava.bio.structure.AminoAcid
-
get N atom.
- getN() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
get N atom.
- getName() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
Every substitution matrix has a name like "BLOSUM30" or "PAM160".
- getName() - Method in interface org.biojava.bio.annodb.AnnotationDB
-
The name of this AnnotationDB.
- getName() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
- getName() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
-
- getName() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
-
- getName() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
- getName() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
-
- getName() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getName() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getName returns the enzyme name.
- getName() - Method in class org.biojava.bio.program.das.DASSequence
-
- getName() - Method in class org.biojava.bio.program.das.DASSequenceDB
-
- getName() - Method in class org.biojava.bio.program.das.DASSequenceDBProvider
-
- getName() - Method in class org.biojava.bio.program.das.DataSource
-
- getName() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
retrieves name of this group.
- getName() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- getName() - Method in class org.biojava.bio.program.indexdb.BioStore
-
The name of this store or null if the name has not been set.
- getName() - Method in class org.biojava.bio.proteomics.Protease
-
Gets the name of this Protease
- getName() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
-
- getName() - Method in class org.biojava.bio.seq.db.BioIndex
-
- getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- getName() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
-
Deprecated.
- getName() - Method in class org.biojava.bio.seq.db.CachingSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
getName returns the database name as defined
within the EMBL CD-ROM index.
- getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
-
- getName() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
Get the name of this sequence database.
- getName() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Retrieve the name of this store.
- getName() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getName() - Method in interface org.biojava.bio.seq.db.SequenceDBLite
-
Get the name of this sequence database.
- getName() - Method in class org.biojava.bio.seq.db.SubSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getName() - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
-
- getName() - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
-
The name of this repository.
- getName() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getName() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
-
Get the name of this type.
- getName() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- getName() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getName() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getName() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getName() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getName() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getName() - Method in interface org.biojava.bio.seq.Sequence
-
The name of this sequence.
- getName() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- getName() - Method in interface org.biojava.bio.structure.Atom
-
get trimmed version of atom name, e.g.
- getName() - Method in class org.biojava.bio.structure.AtomImpl
-
Gets this object's name.
- getName() - Method in interface org.biojava.bio.structure.Chain
-
get and set the name of this chain (Chain id in PDB file ).
- getName() - Method in class org.biojava.bio.structure.ChainImpl
-
get and set the name of this chain (Chain id in PDB file ).
- getName() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getName() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- getName() - Method in interface org.biojava.bio.structure.Structure
-
get biological name of Structure.
- getName() - Method in class org.biojava.bio.structure.StructureImpl
-
get biological name of Structure.
- getName() - Method in interface org.biojava.bio.symbol.Alphabet
-
Get the name of the alphabet.
- getName() - Method in interface org.biojava.bio.symbol.CodonPref
-
get name of object
- getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getName() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getName() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getName() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getName() - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getName() - Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getName() - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
-
- getName() - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getName() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
The name of the Alphabet
- getName() - Method in interface org.biojava.bio.symbol.Symbol
-
The long name for the symbol.
- getName() - Method in interface org.biojava.bio.symbol.SymbolPropertyTable
-
- getName() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- getName() - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.
Name for this TaxonFactory.
- getName() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- getName() - Method in interface org.biojava.directory.SequenceDBProvider
-
The name of this provider.
- getName() - Method in class org.biojava.ontology.IntegerOntology
-
- getName() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getName() - Method in interface org.biojava.ontology.Ontology
-
Return the name of this ontology
- getName() - Method in class org.biojava.ontology.Ontology.Impl
-
- getName() - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getName() - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getName() - Method in class org.biojava.ontology.Synonym
-
- getName() - Method in interface org.biojava.ontology.Term
-
Return the name of this term.
- getName() - Method in class org.biojava.ontology.Term.Impl
-
- getName() - Method in class org.biojava.ontology.Triple.Impl
-
- getName() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It returns a name of this vocabulary.
- getName() - Method in class org.biojava.utils.ChangeType
-
Return the name of this change.
- getName() - Method in class org.biojava.utils.regex.Pattern
-
return the String label associated with this pattern.
- getName() - Method in interface org.biojavax.bio.BioEntry
-
Returns the name of this bioentry.
- getName() - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Get the name of this sequence database.
- getName() - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- getName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByName
-
- getName() - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getName() - Method in class org.biojavax.bio.db.HashBioEntryDB
-
- getName() - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getName() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
- getName() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
- getName() - Method in interface org.biojavax.bio.seq.RichFeature
-
Returns the name of this feature.
- getName() - Method in class org.biojavax.bio.seq.RichLocation.Strand
-
Returns the string symbol of this strand.
- getName() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Returns the name of this feature.
- getName() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the name of this bioentry.
- getName() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Returns this name.
- getName() - Method in interface org.biojavax.DocRefAuthor
-
Returns a textual description of the authors name.
- getName() - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- getName() - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- getName() - Method in interface org.biojavax.ga.Organism
-
Gets the organisms name
- getName() - Method in interface org.biojavax.ga.Population
-
- getName() - Method in interface org.biojavax.Namespace
-
The name of the namespace is immutable and must be set by the constructor
of the instantiating class.
- getName() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Return the name of this ontology
- getName() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Return the name of this term.
- getName() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return the name of this term.
- getName() - Method in class org.biojavax.SimpleDocRefAuthor
-
Returns a textual description of the authors name.
- getName() - Method in class org.biojavax.SimpleNamespace
-
The name of the namespace is immutable and must be set by the constructor
of the instantiating class.
- getNameClass() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Returns the class of this name.
- getNameClasses() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns all the name classes available for a taxon.
- getNameClasses() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Returns all the name classes available for a taxon.
- getNamedIsoforms() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
-
Getter for property namedIsoforms.
- getNameHierarchy() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns the taxonomy hierarchy of this taxon entry in the form:
least specific; more specific; ...; most specific.
- getNameHierarchy() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Returns the taxonomy hierarchy of this taxon entry in the form:
most specific; less specific; ...; least specific.
- getNameInNamespace() - Method in class org.biojava.naming.ObdaContext
-
- getNameParser(Name) - Method in class org.biojava.naming.ObdaContext
-
- getNameParser(String) - Method in class org.biojava.naming.ObdaContext
-
- getNames() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getNames() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Getter for property names.
- getNames(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns all the names available for a taxon in a given class.
- getNames(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Returns all the names available for a taxon in a given class.
- getNameSet() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
- getNamesMap() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
- getNamespace() - Method in interface org.biojavax.bio.BioEntry
-
Returns the namespace of this bioentry.
- getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Getter for property namespace.
- getNamespace() - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Getter for property namespace.
- getNamespace() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the namespace of this bioentry.
- getNamespaceId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
-
Return the namespace id for this identifier
within the authority.
- getNameToSymbol() - Method in class org.biojava.bio.seq.io.NameTokenization
-
- getNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Gets the NCBI taxon ID.
- getNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Gets the NCBI taxon ID.
- getNCutters(int) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getNCutters returns an unmodifable set of all
enzymes with a cut site of size n.
- getNdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getNdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getNegShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Retrieve the shape used to represent negative points.
- getNestedKernel() - Method in class org.biojava.stats.svm.NestedKernel
-
Retrieve the currently nested SVMKernel.
- getNestedValue(NestedValue, String, int) - Method in class org.biojava.ontology.obo.OboFileParser
-
- getNewTag(Object) - Method in interface org.biojava.bio.program.tagvalue.PropertyChanger
-
getNewTag returns the tag which substitutes the
specified value.
- getNewTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
-
- getNodeRank() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Gets the node rank of this taxon.
- getNodeRank() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Gets the node rank of this taxon.
- getNodes() - Method in class org.biojava.utils.automata.FiniteAutomaton
-
get all Nodes within this instance.
- getNodes() - Method in interface org.biojava.utils.automata.NfaBuilder
-
- getNodes() - Method in class org.biojava.utils.automata.NfaSubModel
-
- getNonWobbleBases() - Method in interface org.biojava.bio.symbol.WobbleDistribution
-
returns Set containing the nonWobbleBases that
occur in codons that encode this residue
- getNormalizingVector() - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
-
Retrive the current normalizing vector.
- getNotCleaveResidues() - Method in class org.biojava.bio.proteomics.Protease
-
The list of residues that will prevent cleavage if they follow the cleavage
residue.
- getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getNote(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getNote(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getNote() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNote
-
- getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property note.
- getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Getter for property note.
- getNote() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
-
Uses the term and rank to lookup a note in this annotation.
- getNote(Note) - Method in interface org.biojavax.RichAnnotation
-
Uses the term and rank to lookup a note in this annotation.
- getNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
-
Uses the term and rank to lookup a note in this annotation.
- getNoteSet() - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in class org.biojavax.EmptyRichAnnotation
-
Returns an immutable set of all notes in this annotation.
- getNoteSet() - Method in interface org.biojavax.RichAnnotatable
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in interface org.biojavax.RichAnnotation
-
Returns an immutable set of all notes in this annotation.
- getNoteSet() - Method in class org.biojavax.SimpleCrossRef
-
Returns the set of notes associated with this object.
- getNoteSet() - Method in class org.biojavax.SimpleRichAnnotation
-
Returns an immutable set of all notes in this annotation.
- getNrAtoms(Structure) - Static method in class org.biojava.bio.structure.StructureTools
-
Count how many number of Atoms are contained within a Structure object.
- getNrCPUs() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- getNrGroups(Structure) - Static method in class org.biojava.bio.structure.StructureTools
-
Count how many groups are contained within a structure object.
- getNucleotide() - Static method in class org.biojava.bio.seq.NucleotideTools
-
Return the Nucleotide alphabet.
- getNucleotideParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Creates a nucleotide symbol tokenizer.
- getNullModel() - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
- getNullModel() - Method in interface org.biojava.bio.dist.Distribution
-
Retrieve the null model Distribution that this Distribution recognizes.
- getNullModel() - Method in class org.biojava.bio.dist.GapDistribution
-
- getNullModel(Distribution, Distribution) - Static method in class org.biojava.bio.dist.PairDistribution
-
Get a uniform null model over a PairDistribution over [first,second].
- getNullModel() - Method in class org.biojava.bio.dist.PairDistribution
-
- getNullModel() - Method in class org.biojava.bio.dist.SimpleDistribution
-
- getNullModel() - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- getNullModel() - Method in class org.biojava.bio.dist.UniformDistribution
-
- getNullModelWeight() - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Return the number of pseudocounts added to the distribution when training.
- getNullModelWeight() - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- getNum() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getNum() - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- getNumber() - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
-
Return a number (usually, but not always, a motif count)
associated with this node of the tree.
- getNumberExperiments() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Getter for property numberExperiments.
- getNumCount() - Method in interface org.biojava.utils.candy.CandyFinder
-
It returns the number of available vocabularies.
- getNumRes() - Method in class org.biojava.bio.structure.Compound
-
- getO() - Method in interface org.biojava.bio.structure.AminoAcid
-
get O atom.
- getO() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
get O atom.
- getObject() - Method in interface org.biojava.ontology.Triple
-
Return the object term of this triple.
- getObject() - Method in class org.biojava.ontology.Triple.Impl
-
- getObject() - Method in interface org.biojavax.bio.BioEntryRelationship
-
Returns the object of this relationship (ie.
- getObject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
-
Returns the object of this relationship (ie.
- getObject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Returns the object of this relationship (ie.
- getObject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Returns the object of this relationship (ie.
- getObject() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return the object term of this triple.
- getObject(Class, Object[]) - Static method in class org.biojavax.RichObjectFactory
-
Delegates to a RichObjectBuilder to construct/retrieve the object, and returns it.
- getObjectAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
-
define the alignment object Annotation Type.
- getObjectId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
-
Return the object id of this identifier.
- getObjects() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
Returns the Annotation of all objects in this Alignment.
- getOboFileEventListener() - Method in class org.biojava.ontology.obo.OboFileParser
-
- getObsolete() - Method in interface org.biojavax.ontology.ComparableTerm
-
Checks to see if this term is obsolete.
- getObsolete() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Checks to see if this term is obsolete.
- getOccupancy() - Method in interface org.biojava.bio.structure.Atom
-
get occupancy.
- getOccupancy() - Method in class org.biojava.bio.structure.AtomImpl
-
- getOccupancy() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_esd() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getOccupancy_max() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOccupancy_min() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOffset() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
-
Get the angle through which the origin of the sequence is rotated through.
- getOffset() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getOffset() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getOffset() - Method in interface org.biojava.bio.program.indexdb.Record
-
getOffset returns the byte offset in the file at
which the record begins.
- getOffset() - Method in class org.biojava.bio.program.indexdb.Record.Impl
-
- getOldIDHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getOne_letter_code() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getOneLetterCode(ChemComp, ChemicalComponentDictionary) - Static method in class org.biojava.bio.structure.io.mmcif.chem.ChemCompTools
-
- getOntology(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- getOntology() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getOntology() - Method in interface org.biojava.ontology.OntologyTerm
-
Get the remote ontology referenced by this term
- getOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getOntology() - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getOntology() - Method in interface org.biojava.ontology.Term
-
Return the ontology in which this term exists.
- getOntology() - Method in class org.biojava.ontology.Term.Impl
-
- getOntology() - Method in class org.biojava.ontology.Triple.Impl
-
- getOntology() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Return the ontology in which this term exists.
- getOntology() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return the ontology in which this term exists.
- getOps() - Method in class org.biojava.ontology.IntegerOntology
-
- getOps() - Method in interface org.biojava.ontology.Ontology
-
Return the associated OntologyOps.
- getOps() - Method in class org.biojava.ontology.Ontology.Impl
-
- getOps() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Return the associated OntologyOps.
- getOption(ChromatogramGraphic.Option) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the current value for the specified option.
- getOrCreateTerm(String) - Method in interface org.biojavax.ontology.ComparableOntology
-
Looks for a term with the given name and returns it.
- getOrCreateTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Looks for a term with the given name and returns it.
- getOrCreateTriple(Term, Term, Term) - Method in interface org.biojavax.ontology.ComparableOntology
-
Looks for a triple with the given subject object and predicate and returns it.
- getOrCreateTriple(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Looks for a triple with the given subject object and predicate and returns it.
- getOrder() - Method in class org.biojava.stats.svm.PolynomialKernel
-
- getOrderedLocusNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the OrderedLocusName term
- getOrderTerm() - Static method in class org.biojavax.bio.seq.CompoundRichLocation
-
Getter for the "order" term
- getORFNameTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the ORFName term
- getOrgan() - Method in class org.biojava.bio.structure.Compound
-
- getOrganelle() - Method in class org.biojava.bio.structure.Compound
-
- getOrganelleTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Organelle term
- getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getOrganism(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getOrganism(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getOrganismByName(String) - Method in class org.biojavax.ga.impl.SimplePopulation
-
- getOrganismByName(String) - Method in interface org.biojavax.ga.Population
-
Gets the specified organism
- getOrganismCommon() - Method in class org.biojava.bio.structure.Compound
-
- getOrganisms() - Method in class org.biojavax.ga.impl.SimplePopulation
-
- getOrganisms() - Method in interface org.biojavax.ga.Population
-
Gets the Set of Organisms
- getOrganismScientific() - Method in class org.biojava.bio.structure.Compound
-
- getOrganismTaxId() - Method in class org.biojava.bio.structure.Compound
-
- getOrientation() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getOrImportTerm(Term) - Method in interface org.biojavax.ontology.ComparableOntology
-
Looks for a term with the same name as the given term and returns it.
- getOrImportTerm(Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Looks for a term with the same name as the given term and returns it.
- getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Returns an orthologue of specified ID.
- getOrthologue(String) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
-
- getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- getOrthologue(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
-
- getOrthoPairSets() - Method in interface org.biojava.bio.program.homologene.HomologeneDB
-
Get the HomologeneGroups in this database.
- getOrthoPairSets() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getOS(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getOS(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getOtherSeqIdTerm() - Static method in class org.biojavax.bio.seq.io.INSDseqFormat.Terms
-
Getter for the INSDseq term
- getOuterMax() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getOuterMin() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
- getOuterPaint() - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
Returns the paint properties of the outer line of this glyph.
- getOutline() - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- getOutline() - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- getOutline() - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
-
getOutline returns the colour used to draw the
lines.
- getOutline() - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
-
getOutline returns the colour used to draw the
lines.
- getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- getOutline() - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- getOutline() - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- getOutline() - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- getOutput() - Method in interface org.biojava.utils.process.InputHandler
-
Gets the output stream.
- getOutput() - Method in class org.biojava.utils.process.ReaderInputHandler
-
Gets the output stream.
- getOutput() - Method in class org.biojava.utils.process.StreamPipe
-
Gets the output stream.
- getOutputHandler() - Method in class org.biojava.utils.process.ExternalProcess
-
Gets the output handler which is responsible for the standard output
of the external process.
- getOutString() - Method in class org.biojava.utils.ExecRunner
-
Returns the output string if exec(String) was invoked.
- getOverall_FOM_free_R_set() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_FOM_work_R_set() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_B() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_ML() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_Cruickshank_DPI() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverall_SU_R_free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getOverlay() - Method in class org.biojava.bio.OverlayAnnotation
-
Get the map used for the overlay.
- getOverlayMap() - Method in class org.biojava.utils.OverlayMap
-
Return the object containing the overlay mappings.
- getPacking(FiniteAlphabet, boolean) - Static method in class org.biojava.bio.symbol.PackingFactory
-
Get the default packing for an alphabet.
- getPadding() - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
Retrieve the current padding.
- getPaint() - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
-
- getPaint() - Method in class org.biojava.bio.gui.glyph.TurnGlyph
-
- getPanelPos(int) - Method in class org.biojava.bio.structure.gui.util.CoordManager
-
- getParams() - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
get the parameters.
- getParent() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
Get the original sequenceDB from this annotated sequenceDB.
- getParent() - Method in class org.biojava.bio.seq.db.SequenceDBWrapper
-
Return the parent SequenceDB.
- getParent() - Method in interface org.biojava.bio.seq.Feature
-
Return the FeatureHolder to which this feature has been
attached.
- getParent() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getParent() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getParent(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
- getParent() - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getParent(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getParent() - Method in interface org.biojava.bio.structure.Atom
-
Returns the parent Group of the Atom.
- getParent() - Method in class org.biojava.bio.structure.AtomImpl
-
- getParent() - Method in interface org.biojava.bio.structure.Chain
-
Returns the parent Structure of this chain.
- getParent() - Method in class org.biojava.bio.structure.ChainImpl
-
Returns the parent Structure of this chain.
- getParent() - Method in class org.biojava.bio.structure.DBRef
-
Get the structure object that this DBRef relates to.
- getParent() - Method in interface org.biojava.bio.structure.Group
-
Returns the parent Chain of the Group.
- getParent() - Method in class org.biojava.bio.structure.HetatomImpl
-
Returns the parent Chain of the Group
- getParent(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
Get the parent of a component.
- getParent() - Method in class org.biojava.bio.taxa.SimpleTaxon
-
Deprecated.
- getParent() - Method in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
The parent of this Taxon.
- getParent() - Method in class org.biojava.bio.taxa.WeakTaxon
-
Deprecated.
- getParent() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Return the FeatureHolder to which this feature has been
attached.
- getParentDB() - Method in class org.biojava.bio.program.das.DASSequence
-
- getParentMap() - Method in class org.biojava.utils.OverlayMap
-
Return the object containing the fallback mappings.
- getParentNCBITaxID() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Returns the parent NCBI taxon ID, if known.
- getParentNCBITaxID() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Returns the parent NCBI taxon ID, if known.
- getParents() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
-
Get a set of URIs for parent types.
- getParser() - Method in class org.biojava.bio.program.tagvalue.ParserListener
-
getParser returns the parser of the pair.
- getParser(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- getParserListener(TagValueListener) - Method in interface org.biojava.bio.annodb.IndexedAnnotationDB.ParserListenerFactory
-
Get the ParserListener for a TagValueListener.
- getParserListener(TagValueListener) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB.StaticMethodRPFactory
-
- getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Embl
-
- getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Enzyme
-
- getParserListener(TagValueListener) - Method in interface org.biojava.bio.program.formats.Format
-
Retrieve a ParserListener pair for the format that will pass all events
on to a listener.
- getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Compound
-
- getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
-
- getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Ligand.Reaction
-
- getParserListener(TagValueListener) - Method in class org.biojava.bio.program.formats.Swissprot
-
- getParserListenerFactory() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
Get the ParserListenerFactory used by this IndexedAnnotationDB.
- getPartHandler(XFFFeatureSetHandler) - Method in interface org.biojava.bio.program.xff.XFFPartHandlerFactory
-
Return a suitable StAX content handler.
- getPath() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
-
Get the list of SequenceRenderer instances that were passed through to
produce this event
- getPath() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getPath() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getPath() - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- getPath() - Method in class org.biojava.bio.structure.io.PDBFileReader
-
Returns the path value.
- getPath() - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
get the directory path to the files
- getPathEnd(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getPathLength(UkkonenSuffixTree.SuffixNode) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getPathPrefix() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
getPathPrefix returns the abstract path currently
being appended to the raw sequence database filenames extracted
from the binary index.
- getPathSize() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getPathSize() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getPattern() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Get the Pattern currently used to split lines.
- getPattern() - Method in class org.biojava.bio.search.KnuthMorrisPrattSearch
-
- getPattern() - Method in class org.biojava.bio.search.MaxMismatchPattern
-
- getPatterns(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getPatterns returns two Pattern
objects for an enzyme, one matches the forward strand and one
the reverse.
- getPdb_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_mon_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_seq_num() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPdb_strand_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getPdb_strand_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getPDBCode() - Method in interface org.biojava.bio.structure.Group
-
Return the PDBcode (residue number + insertion code ) of this group.
- getPDBCode() - Method in class org.biojava.bio.structure.HetatomImpl
-
Returns the PDBCode.
- getPDBCode() - Method in interface org.biojava.bio.structure.server.StructureEvent
-
- getPDBCode() - Method in class org.biojava.bio.structure.server.StructureEventImpl
-
- getPDBCode() - Method in interface org.biojava.bio.structure.Structure
-
get PDB code of structure.
- getPDBCode() - Method in class org.biojava.bio.structure.StructureImpl
-
get PDB code of structure .
- getPDBHeader(String) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getPDBHeader(String) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- getPDBHeader(String) - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
get the PDB header for a single protein structure
- getPDBHeader() - Method in interface org.biojava.bio.structure.Structure
-
return the header information for this PDB file
- getPDBHeader() - Method in class org.biojava.bio.structure.StructureImpl
-
- getPDBInfoFile() - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getPDBInstallation() - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- getPDBInstallation() - Method in interface org.biojava.bio.structure.server.StructureServer
-
- getPDBline() - Method in interface org.biojava.bio.structure.Atom
-
store the whole line.
- getPDBline() - Method in class org.biojava.bio.structure.AtomImpl
-
get the whole line .
- getPDBName() - Method in interface org.biojava.bio.structure.Group
-
Get the PDB 3 character name for this group.
- getPDBName() - Method in class org.biojava.bio.structure.HetatomImpl
-
Returns the PDBName.
- getPDBresnum1() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getPDBresnum2() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getPDBserial() - Method in interface org.biojava.bio.structure.Atom
-
get PDB atom number.
- getPDBserial() - Method in class org.biojava.bio.structure.AtomImpl
-
get PDB atom number.
- getPdbx_align_begin() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getPdbx_ambiguous_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_auth_seq_align_beg() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_auth_seq_align_end() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_blank_PDB_chainid_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getPdbx_data_cutoff_high_absF() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_high_rms_absF() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_data_cutoff_low_absF() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_db_accession() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getPdbx_db_accession() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_beg_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_db_align_end_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_description() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_descriptor() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getPdbx_ec() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_formal_charge() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getPdbx_formal_charge() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_fragment() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_ideal_coordinates_details() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_ideal_coordinates_missing_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_initial_date() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_isotropic_thermal_model() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_keywords() - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- getPdbx_ls_cross_valid_method() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_F() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_ls_sigma_I() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_method_to_determine_struct() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_model_coordinates_db_code() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_details() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_coordinates_missing_flag() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_model_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getPdbx_model_type_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getPdbx_modified() - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- getPdbx_modified_date() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_mutation() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_number_of_molecules() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getPdbx_overall_ESU_R() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_ESU_R_Free() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_overall_phase_error() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_PDB_id_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_PDB_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getPdbx_PDB_model_num() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getPdbx_processing_site() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_R_Free_selection_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_refine_id() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_release_status() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaced_by() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_replaces() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_seq_align_beg_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_align_end_ins_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_seq_one_letter_code() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- getPdbx_solvent_ion_probe_radii() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_shrinkage_radii() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_solvent_vdw_probe_radii() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_starting_model() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_stereochem_target_val_spec_case() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_stereochemistry_target_values() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getPdbx_strand_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getPdbx_subcomponent_list() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_synonyms() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPdbx_type() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPercentIdentity() - Method in interface org.biojava.bio.program.homologene.OrthoPair
-
get percentage identity.
- getPercentIdentity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getPercId() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getPermutationSize() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getPhase() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getPhase() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getPHDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property PHDependence.
- getPhi(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
-
phi angle.
- getPhiAngle(Symbol) - Static method in class org.biojava.bio.structure.AlphaCTools
-
extracts the Phi angle from a Symbol.
- getPhiPsiSymbol(double, double) - Static method in class org.biojava.bio.structure.AlphaCTools
-
Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet.
- getPhredAlphabet() - Static method in class org.biojava.bio.program.phred.PhredTools
-
Retrieves the PHRED alphabet from the AlphabetManager.
- getPhredSymbol(Symbol, Symbol) - Static method in class org.biojava.bio.program.phred.PhredTools
-
Creates a symbol from the PHRED alphabet by combining a Symbol from the
DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
- getPI(SymbolList, boolean, boolean) - Method in class org.biojava.bio.proteomics.IsoelectricPointCalc
-
Computes isoelectric point of specified peptide.
- getPivot() - Method in class org.biojava.bio.structure.jama.LUDecomposition
-
Return pivot permutation vector
- getPlasmidTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Plasmid term
- getPmid() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the value of PMID field.
- getPolymerType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getPopulation() - Method in interface org.biojavax.ga.GeneticAlgorithm
-
The registered Population
- getPopulation() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getPos() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
-
Get the offset within the sequence - the symbol index.
- getPos() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
-
- getPos(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getPos1() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getPos1() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getPos2() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getPos2() - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- getPosition() - Method in interface org.biojava.bio.molbio.RestrictionSite
-
getPosition returns the common, forward strand cut
site.
- getPosition() - Method in class org.biojava.bio.seq.impl.SimpleRestrictionSite
-
- getPosition1() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getPosition2() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getPositions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getPosShape() - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Retrieve the shape used to represent positive points.
- getPredicate() - Method in interface org.biojava.ontology.Triple
-
Return a Term which defines the type of relationship between the subject and object terms.
- getPredicate() - Method in class org.biojava.ontology.Triple.Impl
-
- getPredicate() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return a Term which defines the type of relationship between the subject and object terms.
- getPrevious() - Method in class org.biojava.utils.ChangeEvent
-
Return the old value of a property being changed.
- getPrimaryKey() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
getPrimaryKey returns the primary identifier
namespace.
- getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
Retrieve the tag currently used as primary key.
- getPrimaryKeyName() - Method in class org.biojava.bio.program.tagvalue.Indexer
-
Retrieve the tag currently used as primary key.
- getPrintStream() - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- getPrintStream() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- getPrintStream() - Method in interface org.biojava.bio.seq.io.SeqFileFormer
-
Deprecated.
getPrintStream returns the
PrintStream to which an instance will write the
formatted data.
- getPrintStream() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
getPrintStream returns the
PrintStream to which an instance of SwissprotFileFormer
will write the formatted data.
- getPrintStream() - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Gets the print stream currently being written to.
- getPrintStream() - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Gets the print stream currently being written to.
- getProbabilityAlphabet() - Static method in class org.biojava.bio.program.scf.SCF
-
- getProjectAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the ProjectAccession term
- getProjectedFeatures() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getProjectionContext() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getProjectionContext() - Method in interface org.biojava.bio.seq.projection.Projection
-
- getPropClass() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getProperties() - Method in class org.biojava.bio.AbstractAnnotation
-
Implement this to return the Map delegate.
- getProperties() - Method in class org.biojava.bio.AnnotationChanger
-
getProperties returns the mapped contents of the
underlying Annotation as a Map.
- getProperties() - Method in class org.biojava.bio.AnnotationRenamer
-
getProperties returns the mapped contents of the
underlying Annotation as a Map.
- getProperties() - Method in interface org.biojava.bio.AnnotationType
-
Retrieve the set of properties for which constraints have been explicity specified.
- getProperties() - Method in class org.biojava.bio.AnnotationType.Impl
-
- getProperties() - Method in class org.biojava.bio.BeanAsAnnotation
-
- getProperties() - Method in class org.biojava.bio.seq.io.ReferenceAnnotation
-
Deprecated.
- getProperties() - Method in class org.biojava.bio.SimpleAnnotation
-
Get the property value pairs in this annotation
- getProperties() - Method in class org.biojava.bio.SmallAnnotation
-
- getProperties() - Method in interface org.biojava.bio.structure.Group
-
return properties.
- getProperties() - Method in class org.biojava.bio.structure.HetatomImpl
-
return properties.
- getProperties(Object) - Method in class org.biojavax.EmptyRichAnnotation
-
Find all the Notes with any rank that match the key.
- getProperties(Object) - Method in interface org.biojavax.RichAnnotation
-
Find all the Notes with any rank that match the key.
- getProperties(Object) - Method in class org.biojavax.SimpleRichAnnotation
-
Deprecated.
- getProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
-
- getProperty(Object) - Method in interface org.biojava.bio.Annotation
-
Retrieve the value of a property by key.
- getProperty(Annotation, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- getProperty(Annotation, Object) - Method in interface org.biojava.bio.AnnotationType
-
Get the Collection of values associated with an Annotation bundle
according to the type we believe it to be.
- getProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
-
- getProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
-
- getProperty(String) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getProperty(Annotation, String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getProperty(Annotation, String) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
ThomasD made this a bit safer...
- getProperty(Annotation, String) - Static method in class org.biojava.bio.seq.io.agave.UtilHelper
-
inhibit the getProperty(key) of Annotation from throw exception when
key does not exist.
- getProperty(String) - Method in interface org.biojava.bio.structure.Group
-
get a single property .
- getProperty(String) - Method in class org.biojava.bio.structure.HetatomImpl
-
get a single property .
- getProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
-
Retrieve the value of a property by key.
- getProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
-
Deprecated.
- getPropertyAsBoolean(String) - Method in class org.biojava.utils.TypedProperties
-
Searches for the property with the specified key in this property list.
- getPropertyAsDouble(String) - Method in class org.biojava.utils.TypedProperties
-
Searches for the property with the specified key in this property list.
- getPropertyAsInteger(String) - Method in class org.biojava.utils.TypedProperties
-
Searches for the property with the specified key in this property list.
- getPropertyAsLong(String) - Method in class org.biojava.utils.TypedProperties
-
Searches for the property with the specified key in this property list.
- getPropertyAsStringList(String, String) - Method in class org.biojava.utils.TypedProperties
-
Searches for the property with the specified key in this property list.
- getPropertyAsStringList(String) - Method in class org.biojava.utils.TypedProperties
-
just like getPropertyAsStringList(String key, String delims) but uses ',' (comma), ';' (semicolon) and '\t' (tab)
as the possible delimiters.
- getPropertyClass() - Method in class org.biojava.bio.PropertyConstraint.ByClass
-
Get the Class used as the constraint.
- getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
-
Get the PropertyConstraint used to validate each property value.
- getPropertyConstraint() - Method in class org.biojava.bio.CollectionConstraint.Contains
-
Get the PropertyConstraint used to validate each property value.
- getPropertyConstraint() - Method in interface org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler.PropertyConstraintHandler
-
- getProps() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getPropType() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.Protease
-
Retrieves a reference to the named Protease.
- getProteaseByName(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
Gets a Protease instance by name.
- getProteaseList() - Static method in class org.biojava.bio.proteomics.Protease
-
Get the list of Protease names defined in the ProteaseManager
(Internally calls ProteaseManager.
- getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
-
Getter for the protein exists term
- getProteinExistsTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the protein exists term
- getProteinParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Creates a protein symbol tokenizer.
- getProteinTypeTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the protein type term
- getPsi(AminoAcid, AminoAcid) - Static method in class org.biojava.bio.structure.Calc
-
psi angle.
- getPsiAngle(Symbol) - Static method in class org.biojava.bio.structure.AlphaCTools
-
extracts the Psi angle from a Symbol.
- getPublicationDate() - Method in class org.biojava.bio.structure.JournalArticle
-
- getPublisher() - Method in class org.biojava.bio.structure.JournalArticle
-
- getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the overall P-value of this hit.
- getPValue() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the P-value of this sub-hit.
- getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getPValue() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getPValue() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getQ() - Method in class org.biojava.bio.structure.jama.QRDecomposition
-
Generate and return the (economy-sized) orthogonal factor
- getQuality() - Method in class org.biojava.bio.program.fastq.Fastq
-
Return the quality scores for this FASTQ formatted sequence.
- getQuality() - Method in class org.biojava.bio.program.phred.PhredSequence
-
Extracts the quality part if the Phred Alphabet and returns it as a SymbolList
over the Integer SubAlphabet from 0..99.
- getQuality() - Method in interface org.biojava.bio.program.phred.Qualitative
-
Retreives the list of quality symbols from the underlying object.
- getQualityAt(int) - Method in class org.biojava.bio.program.phred.PhredSequence
-
- getQualityAt(int) - Method in interface org.biojava.bio.program.phred.Qualitative
-
Retreives the quality symbol for the specified index.
- getQuery() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
-
Returns the query.
- getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the end position of the last sub-hit in the query
sequence.
- getQueryEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the end position of the sub-hit in the query sequence.
- getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getQueryEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getQueryEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getQueryRegion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getQueryRegion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getQuerySeqHolder() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
getQuerySeqHolder returns the database of query
sequences used to retrieve sequences for creation of the
various result objects.
- getQuerySequence() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
-
Returns the query sequence which was used to perform the search.
- getQuerySequence() - Method in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- getQuerySequence() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the start position of the first sub-hit in the query
sequence.
- getQueryStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the start position of the sub-hit in the query sequence.
- getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getQueryStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getQueryStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the strand of the hit with respect to the query
sequence.
- getQueryStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the strand of the sub-hit with respect to the query
sequence.
- getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getQueryStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getQueryStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getR() - Method in class org.biojava.bio.structure.jama.QRDecomposition
-
Return the upper triangular factor
- getRadius() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
-
Get the current radius at which data should be rendered.
- getRadius() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getRadius() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getRange() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getRange returns a RangeLocation
representing the region of the sequence currently being
rendered.
- getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getRange() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- getRange() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
The range of the SymbolList to render.
- getRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getRange() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getRange() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getRange returns a RangeLocation
representing the region of the sequence currently being
rendered.
- getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- getRanges() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- getRanges() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- getRank() - Method in interface org.biojavax.bio.BioEntryRelationship
-
Returns the rank of this relationship.
- getRank() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByRank
-
- getRank() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the rank associated with this location.
- getRank() - Method in interface org.biojavax.bio.seq.RichFeature
-
Returns the rank of this feature.
- getRank() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
-
Gets the rank of this relationship.
- getRank() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the rank associated with this location.
- getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Returns the rank of this feature.
- getRank() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Gets the rank of this relationship.
- getRank() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the rank associated with this location.
- getRank() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Returns the rank of this relationship.
- getRank() - Method in interface org.biojavax.Comment
-
Returns the rank of this comment.
- getRank() - Method in interface org.biojavax.Note
-
Gets the rank that defines this note.
- getRank() - Method in interface org.biojavax.RankedCrossRef
-
Return the rank associated with the cross reference.
- getRank() - Method in interface org.biojavax.RankedDocRef
-
The rank of this reference.
- getRank() - Method in class org.biojavax.SimpleComment
-
Returns the rank of this comment.
- getRank() - Method in class org.biojavax.SimpleNote
-
Gets the rank that defines this note.
- getRank() - Method in class org.biojavax.SimpleRankedCrossRef
-
Return the rank associated with the cross reference.
- getRank() - Method in class org.biojavax.SimpleRankedDocRef
-
The rank of this reference.
- getRankedCrossRefs() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Returns the set of all ranked cross references associated with an object.
- getRankedCrossRefs() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns the set of all ranked cross references associated with an object.
- getRankedCrossRefs() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Returns the set of all ranked cross references associated with an object.
- getRankedCrossRefs() - Method in interface org.biojavax.RankedCrossRefable
-
Returns the set of all ranked cross references associated with an object.
- getRankedDocRefs() - Method in interface org.biojavax.bio.BioEntry
-
Returns a set of all bioentrydocrefs associated with this bioentry.
- getRankedDocRefs() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns a set of all bioentrydocrefs associated with this bioentry.
- getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer
-
Retrieve the reader that can be safely used to index this file.
- getReader() - Method in class org.biojava.bio.program.tagvalue.Indexer2
-
Retrieve the reader that can be safely used to index this file.
- getReader() - Method in class org.biojava.utils.process.ReaderWriterPipe
-
Gets the reader.
- getReadingFrame() - Method in interface org.biojava.bio.seq.FramedFeature
-
return the reading frame of the feature.
- getReadingFrame() - Method in class org.biojava.bio.seq.impl.SimpleFramedFeature
-
- getRealEigenvalues() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
-
Return the real parts of the eigenvalues
- getRealScientificName(Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
This returns the true scientific name of a given taxon, if there is one.
- getRecognitionSequence(String) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getRecognitionSequence returns a string that describes
the recognition site of this enzyme.
- getRecognitionSite() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getRecognitionSite returns the forward strand of
the recognition site.
- getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
getRecordKey returns the field from the record on
which the records were sorted in the index.
- getRecordKey(Object[]) - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
-
getRecordKey returns the field from the record on
which the records were sorted in the index.
- getRecordList() - Method in class org.biojava.bio.program.indexdb.BioStore
-
getRecordList returns all the Records
in the index.
- getRecordType() - Method in interface org.biojava.bio.structure.AminoAcid
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- getRecordType() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
- getRecurse() - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- getRecurse() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
getRecurse returns the recursion flag of the
filter.
- getRecurse() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Return whether features will be filtered recursively or not.
- getRecursive() - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
-
- getRedoxPotential() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property redoxPotential.
- getRef() - Method in interface org.biojava.bio.program.homologene.OrthoPair
-
get reference to evidence for
orthology.
- getRef() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getRef() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the value of REF field.
- getRef_id() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getRefChainId() - Method in class org.biojava.bio.structure.Compound
-
Returns the ref chain id value.
- getReferenceServers() - Method in class org.biojava.bio.program.das.DAS
-
- getRefn() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the value of REFN field.
- getRegions() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- getRegions() - Method in interface org.biojava.bio.seq.RemoteFeature
-
Retrieve the list of Regions that locate this feature both localy and
remotely.
- getRegistryConfiguration() - Method in class org.biojava.directory.Registry
-
getRegistryConfiguration returns the configuration
of the registry.
- getRegistryPath() - Static method in class org.biojava.directory.SystemRegistry
-
Get the list of places that will be searched for registry
files.
- getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getRel() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- getRelAnnotatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the release annotated term
- getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getRelatedAnnot(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getRelatedAnnot(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getRelationships() - Method in interface org.biojavax.bio.BioEntry
-
Returns a set of all relationships associated with this bioentry.
- getRelationships() - Method in class org.biojavax.bio.SimpleBioEntry
-
Returns a set of all relationships associated with this bioentry.
- getRelCreatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the release created term
- getRelUpdatedRecordVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
-
Getter for the RelUpdatedRecordVersion term
- getRelUpdatedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the release updated term
- getRemark() - Method in interface org.biojavax.DocRef
-
If remarks have been made about this document reference, this method
will return them.
- getRemark() - Method in class org.biojavax.SimpleDocRef
-
If remarks have been made about this document reference, this method
will return them.
- getRemoteBioEntry(CrossRef) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
-
Given the CrossRef return the corresponding
BioEntry
- getRemoteBioEntry(CrossRef) - Method in interface org.biojavax.CrossReferenceResolver
-
Given the CrossRef return the corresponding
BioEntry
- getRemoteBioEntry(CrossRef) - Method in class org.biojavax.DummyCrossReferenceResolver
-
Given the CrossRef return the corresponding
BioEntry
- getRemoteFeature() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- getRemoteFeature() - Method in interface org.biojava.bio.seq.RemoteFeature
-
Retrieve the Feature on some assembly Sequence that can represent this
RemoteFeature properly.
- getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.bio.db.biosql.BioSQLCrossReferenceResolver
-
Given a cross reference, return the corresponding symbol list.
- getRemoteSymbolList(CrossRef, Alphabet) - Method in interface org.biojavax.CrossReferenceResolver
-
Given a cross reference, return the corresponding symbol list.
- getRemoteSymbolList(CrossRef, Alphabet) - Method in class org.biojavax.DummyCrossReferenceResolver
-
Given a cross reference, return the corresponding symbol list.
- getRemoteTerm() - Method in interface org.biojava.ontology.RemoteTerm
-
Return the imported term
- getRemoteTerm() - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getRemoteTerms() - Method in interface org.biojava.ontology.OntologyOps
-
Get the set of all remote terms.
- getRenderedWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the width of the graphic as it will be rendered.
- getRenderedWidth(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the width of the graphic as it would be rendered with
the specified horizontal scale.
- getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
-
- getRenderer() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getRenderer() - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
getRenderer return the current renderer.
- getRenderer() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getRenderer returns the current
PairwiseSequenceRenderer.
- getRenderer() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getRenderer() - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- getRenderer() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getRenderer returns the current
SequenceRenderer.
- getRenderingHints() - Method in class org.biojava.bio.gui.DistributionLogo
-
- getRenderingHints() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getRenderingHints returns the
RenderingHints currently being used by the
Graphics2D instances of delegate renderers.
- getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getRenderingHints() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- getRenderingHints() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getRenderingHints returns the
RenderingHints currently being used by the
Graphics2D instances of delegate renderers.
- getReplace() - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Returns the current expenses of a single replace operation.
- getReplaced(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
if ChemComp is replacing another one, get the old version
otherwise return the same ChemComp again.
- getReplaced(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplacer(ChemComp) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
if ChemComp is replaced by another one, get the newer version
otherwise return the same ChemComp again.
- getReplacer(String) - Method in class org.biojava.bio.structure.io.mmcif.ChemicalComponentDictionary
-
- getReplaces() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getRepository(String) - Static method in class org.biojava.bio.seq.FeatureTypes
-
Fetch a repository by name.
- getRepositoryNames() - Static method in class org.biojava.bio.seq.FeatureTypes
-
Find the names of all known repositories.
- getResidue() - Method in interface org.biojava.bio.symbol.WobbleDistribution
-
returns the residue encoded by this WobbleDistribution
- getResidueType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getResidueTypeFromString(String) - Static method in enum org.biojava.bio.structure.io.mmcif.chem.ResidueType
-
- getResNames() - Method in class org.biojava.bio.structure.Compound
-
- getResnum1() - Method in class org.biojava.bio.structure.SSBond
-
get residue number for first CYS.
- getResnum2() - Method in class org.biojava.bio.structure.SSBond
-
get residue number for second CYS.
- getResolution() - Method in class org.biojava.bio.structure.PDBHeader
-
- getResolver() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- getResolver() - Method in interface org.biojava.bio.seq.RemoteFeature
-
- getResolver() - Method in class org.biojava.bio.symbol.FuzzyLocation
-
Retrieve the Location that this decorates.
- getResolver() - Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getResultType(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getResultType(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getReturnCode() - Method in exception org.biojava.utils.ProcessTimeoutException
-
Get the return code from the dying child process.
- getReturnFormat() - Method in class org.biojava.bio.seq.db.FetchURL
-
- getReverseRegex() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getReverseRegex returns a regular expression which
matches the reverse strand of the recognition site.
- getReverter() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
-
- getReverter() - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getReverter() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- getRevisionId() - Method in class org.biojava.utils.lsid.LifeScienceIdentifier
-
Return the revision id of this identifier.
- getRichAnnotation() - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Return the associated annotation object.
- getRichAnnotation() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Return the associated annotation object.
- getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Return the associated annotation object.
- getRichAnnotation() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Return the associated annotation object.
- getRichAnnotation() - Method in class org.biojavax.bio.SimpleBioEntry
-
Return the associated annotation object.
- getRichAnnotation() - Method in interface org.biojavax.RichAnnotatable
-
Return the associated annotation object.
- getRichAnnotation() - Method in class org.biojavax.SimpleCrossRef
-
Return the associated annotation object.
- getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ContainedByRichLocation
-
- getRichLocation() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.OverlapsRichLocation
-
- getRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getRichSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String, Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Given the appropriate Genbank ID, return the matching RichSequence object.
- getRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
-
Retrieve a single RichSequence by its id.
- getRichSequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getRichSequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB
-
Returns a RichSequenceIterator over all sequences in the database.
- getRichSequences(Set) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- getRichSequences(Set) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Retrieve rich sequences from a Genbank
- getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Retrieve rich sequences from a Genbank
- getRichSequences(Set) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Retrieve rich sequences from a Genbank
- getRichSequences(Set, RichSequenceDB) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Retrieve rich sequences from a Genbank
- getRichSequences(Set) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
-
Retrieve multiple RichSequence by its id.
- getRichSequences(Set, RichSequenceDB) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
-
Retrieve multiple RichSequence into a specific sequence database.
- getRightValue() - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Gets the right value.
- getRightValue() - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Gets the right value.
- getRms() - Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- getRMS(Atom[], Atom[], JointFragments) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
get the RMS of the JointFragments pair frag
- getRms() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getRMS(Atom[], Atom[]) - Static method in class org.biojava.bio.structure.SVDSuperimposer
-
Calculate the RMS (root mean square) deviation of two sets of atoms.
- getRmsd() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- getRNA() - Static method in class org.biojava.bio.seq.RNATools
-
Return the RNA alphabet.
- getRNAParser() - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Creates a RNA symbol tokenizer.
- getRole() - Method in class org.biojava.bio.program.das.DASLink
-
- getRoot() - Method in class org.biojava.bio.symbol.SuffixTree
-
Return the node object which is the root of this suffix tree.
- getRoot() - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- getRoot() - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- getRoot() - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.
Retrieve the root upon which all rooted Taxon that this
factory knows about are rooted.
- getRoot() - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- getRot() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getRotation() - Method in class org.biojava.bio.structure.SVDSuperimposer
-
Get the Rotation matrix that is required to superimpose the two atom sets.
- getRotationMatrix() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1
- getRow() - Method in class org.biojava.bio.structure.align.helper.IndexPair
-
- getRowDimension() - Method in class org.biojava.bio.structure.jama.Matrix
-
Get row dimension.
- getRowPackedCopy() - Method in class org.biojava.bio.structure.jama.Matrix
-
Make a one-dimensional row packed copy of the internal array.
- getRows() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getRows() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getS() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getS() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Return the diagonal matrix of singular values
- getSaturation() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getSBFactory() - Method in class org.biojava.bio.seq.db.BioIndex
-
- getSBFactory() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getSBFactory() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Retrieve the SequenceBuilderFactory used to build Sequence instances.
- getSBFactory() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getScale() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getScale() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getScale returns the scale in pixels per
Symbol.
- getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Retrieve the current scale.
- getScale() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getScale() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the current scale.
- getScale() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Gets the scale as pixels per Symbol
- getScale() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getScale() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getScale() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getScale returns the scale in pixels per
Symbol.
- getScale() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getScale() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- getScale() - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- getScale(int) - Method in interface org.biojava.stats.svm.tools.SuffixTreeKernel.DepthScaler
-
Retrieve the scaling factor at a given depth
- getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
-
- getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
-
- getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
-
- getScale(int) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
-
- getScalevalue() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getSchema() - Method in interface org.biojava.bio.annodb.AnnotationDB
-
Get an AnnotationType that accepts all Annotation instances in this DB.
- getSchema() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
- getSchema() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
-
- getSchema() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
-
- getSchema() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
- getSchema() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
-
- getSchema() - Method in class org.biojava.bio.program.das.DASSequence
-
- getSchema() - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
-
- getSchema() - Method in interface org.biojava.bio.seq.FeatureHolder
-
Return a schema-filter for this FeatureHolder.
- getSchema() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
-
Get the schema for this type.
- getSchema() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- getSchema() - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- getSchema() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSchema() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getSchema() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getSchema() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getSchema() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getSchema() - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- getSchema() - Method in class org.biojava.bio.seq.MergeFeatureHolder
-
- getSchema() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getSchema() - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- getSchema(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getSchema() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- getSchema() - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
- getSchema(Name) - Method in class org.biojava.naming.ObdaContext
-
- getSchema(String) - Method in class org.biojava.naming.ObdaContext
-
- getSchema() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Return a schema-filter for this FeatureHolder.
- getSchema() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Return a schema-filter for this FeatureHolder.
- getSchemaClassDefinition(Name) - Method in class org.biojava.naming.ObdaContext
-
- getSchemaClassDefinition(String) - Method in class org.biojava.naming.ObdaContext
-
- getScientificName() - Method in class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- getScientificName() - Method in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
The scientific name of this taxon.
- getScope() - Method in class org.biojava.ontology.Synonym
-
- getScore() - Method in interface org.biojava.bio.dp.DPMatrix
-
- getScore() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- getScore() - Method in class org.biojava.bio.dp.SimpleStatePath
-
- getScore() - Method in interface org.biojava.bio.dp.StatePath
-
Return the overall score for this state-path and it's emissions.
- getScore() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
-
- getScore() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The score of the feature.
- getScore() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getScore() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getScore() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the overall score of this hit in the units defined by the
search algorithm.
- getScore() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the score of this sub-hit in the units defined by the
search algorithm.
- getScore() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getScore() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getScore() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getScore() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
-
getScore returns the alignment score.
- getScore() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
-
getScore returns the alignment score.
- getScore() - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- getScore() - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- getScore() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
the alignment score
- getScore() - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- getScoreAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
-
define the alignment Score Annotation Type.
- getScores() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
get all "Score" Annotations.
- getSearchableDBs() - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
-
Return a set of all databases that can be searched with this
sequence similarity searcher.
- getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
getSearchContentHandler gets the handler which
will recieve the method calls generated by the adapter.
- getSearchContentHandler() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
-
getSearchContentHandler gets the handler which
will receive the method calls generated by the adapter.
- getSearchParameters() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
-
Returns the search parameters used in the search that produced
this search result.
- getSearchParameters() - Method in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- getSearchParameters() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getSearchProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
-
- getSearchProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- getSecondaryDirection() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
getSecondaryDirection returns the direction in
which the secondary sequence is rendered.
- getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSecondaryDirection returns the direction in
which this context expects the secondary sequence to be
rendered - HORIZONTAL or VERTICAL.
- getSecondaryDirection() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondaryFeatures() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
getSecondaryFeatures returns the features on the
secondary sequence.
- getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSecondaryFeatures returns all of the
Features belonging to the currently rendered
secondary Sequence.
- getSecondaryFeatures() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondaryRange() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
getSecondaryRange returns the range of the
secondary sequence currently rendered.
- getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSecondaryRange returns a
RangeLocation representing the region of the
secondary sequence currently being rendered.
- getSecondaryRange() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondarySequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSecondarySequence returns the entire secondary
Sequence currently being rendered.
- getSecondarySymbols() - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
getSecondarySymbols returns the symbols of the
secondary sequence.
- getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSecondarySymbols returns all of the
Symbols belonging to the currently rendered
secondary Sequence.
- getSecondarySymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSecondarySymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSecondarySymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
- getSecondIntActID() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Getter for property secondIntActID.
- getSecondOrthologue() - Method in interface org.biojava.bio.program.homologene.OrthoPair
-
gets the first orthologue in the orthology
relationship.
- getSecondOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getSecretion() - Method in class org.biojava.bio.structure.Compound
-
- getSecStruc() - Method in interface org.biojava.bio.structure.AminoAcid
-
get secondary structure data .
- getSecStruc() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
get secondary structure data .
- getSeedFragmentLength() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getSeedRmsdCutoff() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getSegmentAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
-
define the alignment Segment Annotation Type.
- getSelectedAlignmentPos() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- getSelectionFunction() - Method in interface org.biojavax.ga.GeneticAlgorithm
-
- getSelectionFunction() - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- getSeq_align_beg() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_align_end() - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- getSeq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- getSeq_id() - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- getSeqBegin() - Method in class org.biojava.bio.structure.DBRef
-
Initial sequence number of the PDB sequence segment.
- getSeqCautions() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property seqCautions.
- getSeqDB() - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
-
- getSeqDBs() - Method in interface org.biojava.bio.seq.homol.HomologyDB
-
Retrieve the SeqDBs that have been searched against each other.
- getSeqEnd() - Method in class org.biojava.bio.structure.DBRef
-
Ending sequence number of the PDB sequence segment.
- getSeqID() - Method in class org.biojava.bio.seq.RemoteFeature.Region
-
Return the remote Sequence ID if this Region is on another Sequence
(isRemote will return true), null otherwise.
- getSeqIDs() - Method in class org.biojava.bio.program.Meme
-
- getSeqIOEvents(Sequence, SeqIOListener) - Method in class org.biojava.bio.seq.io.SeqIOEventEmitter
-
Deprecated.
getSeqIOEvents scans a Sequence
object and sends events describing its data to the
SeqIOListener.
- getSeqName() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The sequence name field.
- getSeqName() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
Retrieve the current sequence name.
- getSeqName() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getSeqPos(int) - Method in class org.biojava.bio.structure.gui.util.CoordManager
-
start counting at 0...
- getSeqResGroup(int) - Method in interface org.biojava.bio.structure.Chain
-
return the Group at position X.
- getSeqResGroup(int) - Method in class org.biojava.bio.structure.ChainImpl
-
return the Group at position X.
- getSeqResGroups(String) - Method in interface org.biojava.bio.structure.Chain
-
Return a List of all groups of a special type (e.g.
- getSeqResGroups() - Method in interface org.biojava.bio.structure.Chain
-
Return all groups of this chain.
- getSeqResGroups(String) - Method in class org.biojava.bio.structure.ChainImpl
-
Return a List of all groups of a special type (e.g.
- getSeqResGroups() - Method in class org.biojava.bio.structure.ChainImpl
-
Return all groups of this chain.
- getSeqResLength() - Method in interface org.biojava.bio.structure.Chain
-
Returns the number of groups in the SEQRES records of the chain.
- getSeqResLength() - Method in class org.biojava.bio.structure.ChainImpl
-
- getSeqResSequence() - Method in interface org.biojava.bio.structure.Chain
-
Get the sequence for all amino acids as it is specified in the SEQRES residues.
- getSeqResSequence() - Method in class org.biojava.bio.structure.ChainImpl
-
Get the sequence for all amino acids as it is specified in the SEQRES residues.
- getSequence() - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- getSequence() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSequence returns the entire
Sequence currently being rendered.
- getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getSequence() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- getSequence() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getSequence returns the entire
Sequence currently being rendered.
- getSequence() - Method in class org.biojava.bio.program.abi.ABITrace
-
Returns the original programatically determined (unedited) sequence as a SymbolList.
- getSequence(String) - Method in class org.biojava.bio.program.das.DASSequenceDB
-
- getSequence() - Method in class org.biojava.bio.program.fastq.Fastq
-
Return the sequence for this FASTQ formatted sequence.
- getSequence() - Method in class org.biojava.bio.proteomics.Digest
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- getSequence(int) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- getSequence(String) - Method in class org.biojava.bio.seq.db.CachingSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
- getSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
-
Retrieve a single sequence by its id.
- getSequence(String) - Method in class org.biojava.bio.seq.db.SubSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.ViewingSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
- getSequence(String) - Method in interface org.biojava.bio.seq.distributed.DistDataSource
-
Get a Sequence object for an ID.
- getSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- getSequence(String) - Method in class org.biojava.bio.seq.distributed.GFFDataSource
-
- getSequence(String) - Method in class org.biojava.bio.seq.distributed.SequenceDBDataSource
-
- getSequence() - Method in interface org.biojava.bio.seq.Feature
-
Return the Sequence object to which this feature
is (ultimately) attached.
- getSequence() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSequence() - Method in class org.biojava.bio.seq.impl.SubSequence
-
Return the parent sequence of which this is a partial view
- getSequence() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getSequence(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Get the sequence for a feature.
- getSequence(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getSequence() - Method in interface org.biojava.bio.structure.Chain
-
Deprecated.
use getAtomSequence instead
- getSequence() - Method in class org.biojava.bio.structure.ChainImpl
-
Deprecated.
use getAtomSequence instead
- getSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- getSequence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getSequence() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Return the Sequence object to which this feature
is (ultimately) attached.
- getSequenceDB(Map) - Method in class org.biojava.bio.program.das.DASSequenceDBProvider
-
- getSequenceDB() - Method in interface org.biojava.bio.search.SeqSimilaritySearchResult
-
Returns the sequence database against which the search was
performed.
- getSequenceDB() - Method in class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
- getSequenceDB() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
- getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDBProvider
-
- getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDBProvider
-
Deprecated.
- getSequenceDB(String) - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
-
- getSequenceDB(Map) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDBProvider
-
- getSequenceDB(String) - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
-
Return the SequenceDB for the given identifier.
- getSequenceDB(String) - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
If the given identifier is known to this sequence db installation
because it has been used in a call to addSequenceDB(), then this
method returns the SequenceDB associated with this
identifier.
- getSequenceDB(Map) - Method in interface org.biojava.directory.SequenceDBProvider
-
Get a sequence database.
- getSequenceDBs() - Method in class org.biojava.bio.seq.db.DummySequenceDBInstallation
-
- getSequenceDBs() - Method in interface org.biojava.bio.seq.db.SequenceDBInstallation
-
Return all sequence dbs available in this sequence db
installation.
- getSequenceDBs() - Method in class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
Return a newly created set of the SequenceDB objects that were
already created through method addSequenceDB().
- getSequenceFormat() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
getSequenceFormat returns the current sequence
format name.
- getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
- getSequenceFormat() - Method in class org.biojava.bio.seq.db.GenpeptSequenceDB
-
- getSequenceFormat() - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- getSequenceFormat() - Method in class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- getSequenceFormat() - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
- getSequenceFormat(int) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
getSequenceFormat accepts a value which represents
a sequence format and returns the relevant
SequenceFormat object.
- getSequenceID() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getSequenceID() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getSequenceId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getSequenceId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getSequenceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Return the sequence length.
- getSequenceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Returns the number of bases called by whatever base-calling software
analyzed the chromatogram as loaded.
- getSequenceLength() - Method in class org.biojava.bio.program.abi.ABITrace
-
Returns the length of the sequence (number of bases) in this trace.
- getSequenceLength() - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
-
Gets the sequenceLength attribute of the GAMESeqHandler object
- getSequenceLength() - Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- getSequenceLength() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
- getSequenceName() - Method in class org.biojava.bio.seq.FeatureFilter.BySequenceName
-
- getSequenceName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySequenceName
-
- getSequenceOffset() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getSequenceRef() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Getter for property sequenceRef.
- getSequences(Set) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
Retrieve sequences from a Genbank
- getSequences(Set, SequenceDB) - Method in class org.biojava.bio.seq.db.GenbankSequenceDB
-
Retrieve sequences from a Genbank
- getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
-
- getSequences() - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
-
get all the top level sequences
bio_sequence --> SimpleSequence
contig --> SimpleAssembly
--> SimpleSequence( if only one sequence )
chromosome -> SimpleAssembly
-> SimpleSequence( if only one sequence)
- getSequenceType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Getter for property sequenceType.
- getSeqVersion() - Method in interface org.biojavax.bio.seq.RichSequence
-
The version of the associated symbol list.
- getSeqVersion() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
The version of the associated symbol list.
- getSerNum() - Method in class org.biojava.bio.structure.SSBond
-
set serial number of this SSBOND in PDB file
- getServerurl() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
-
get url of alignment service.
- getServerurl() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
-
get url of structure service.
- getShape(List, List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
-
- getShape(List) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
-
- getShape(int[], int[]) - Static method in class org.biojava.bio.gui.glyph.GlyphUtils
-
- getShatter() - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Determine if features with non-contiguous locations will be broken into
multiple GFF records.
- getShift() - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
returns the shift vector that has to be applied on structure to to shift on structure one
- getShort(long) - Method in class org.biojava.utils.io.LargeBuffer
-
- getShort() - Method in class org.biojava.utils.io.LargeBuffer
-
- getSibling() - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
-
getSibling returns the sibling
Feature, query for subject and vice versa.
- getSibling() - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
-
getSibling returns the sibling feature of the
pair.
- getSignificantBits() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Return the number of significant bits.
- getSignificantBits() - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Returns the number of bits of the traces which are significant.
- getSimilarity() - Method in interface org.biojava.bio.program.homologene.OrthoPair
-
gets the second orthologue in the
orthology relationship.
- getSimilarity() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPair
-
- getSingularValues() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Return the one-dimensional array of singular values
- getSize() - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
-
- getSize() - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
-
Deprecated.
- getSize() - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
-
Gets the current size of the border in pixels.
- getSleepTime() - Method in class org.biojava.utils.process.ExternalProcess
-
- getSolvent_model_details() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_bsol() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getSolvent_model_param_ksol() - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- getSource() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The source, or creator of this feature.
- getSource() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
Retrieve the current source.
- getSource() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getSource() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getSource() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getSource() - Method in interface org.biojava.bio.seq.Feature
-
The source of the feature.
- getSource() - Method in class org.biojava.bio.seq.FeatureFilter.BySource
-
- getSource() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSource() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getSource() - Method in class org.biojava.utils.ChangeForwarder
-
Retrieve the 'source' object for ChangeEvents fired by this forwarder.
- getSource() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
The source of the feature.
- getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
-
- getSourceAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
-
- getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
-
- getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
-
- getSourceAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
-
- getSourceAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
-
The alphabet of Symbols that can be translated.
- getSourceHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getSourceSymbolList() - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Return the underlying (ungapped) SymbolList.
- getSourceSymbolList() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- getSourceTerm() - Method in interface org.biojava.bio.seq.Feature
-
An ontology term defining the source of this feature.
- getSourceTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSourceTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTerm
-
- getSourceTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
An ontology term defining the source of this feature.
- getSourceTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.BySourceTermName
-
- getSpacer() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the current spacer value
- getSpeciesForShortName(String) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
-
Converts short species names (like Hs) to long species names (like Homo
Sapiens).
- getSpeciesTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Species term
- getSplitOffset() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Get the current offset at which lines are split.
- getSplitter(Object) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
-
Get the Splitter currently registered to handle a tag.
- getSrc_method() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getSSBonds() - Method in interface org.biojava.bio.structure.Structure
-
get the list of SSBonds as they have been defined in the PDB files
- getSSBonds() - Method in class org.biojava.bio.structure.StructureImpl
-
get the list of SSBonds as they have been defined in the PDB files
- getStandardFillPaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- getStandardOutlinePaints(Alphabet) - Static method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- getStart() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The start of this feature within the source sequence.
- getStart() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getStart() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getStart() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getStart() - Method in interface org.biojava.bio.seq.db.Index
-
Skipping this number of bytes through the file should put the file pointer
to the first byte of the sequence.
- getStart() - Method in class org.biojava.bio.seq.db.SimpleIndex
-
- getStart() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- getStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- getStart() - Method in class org.biojava.utils.automata.FiniteAutomaton
-
- getStart() - Method in interface org.biojava.utils.automata.NfaBuilder
-
- getStart() - Method in class org.biojava.utils.automata.NfaSubModel
-
- getStart() - Method in interface org.biojava.utils.automata.StateMachineInstance
-
- getStart() - Method in interface org.biojavax.bio.seq.Position
-
Returns the beginning of the range of bases this base could lie in.
- getStart() - Method in class org.biojavax.bio.seq.SimplePosition
-
Returns the beginning of the range of bases this base could lie in.
- getStart() - Method in interface org.biojavax.RankedDocRef
-
The start position in the sequence that this reference is referred to from.
- getStart() - Method in class org.biojavax.SimpleRankedDocRef
-
The start position in the sequence that this reference is referred to from.
- getStartPage() - Method in class org.biojava.bio.structure.JournalArticle
-
- getState(String) - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- getStates() - Method in class org.biojava.bio.dp.DP
-
- getStatus() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- getStatusDateTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the StatusDate term
- getStatusTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the Status term
- getStAXContentHandler() - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
-
Return a StAXContentHandler which can deal with any FilterXML construct known to this class.
- getStoreLocation() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
getStoreLocation returns the directory of the bew
index.
- getStoreName() - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
getStoreName returns the name to be given to the
new index.
- getStrain() - Method in class org.biojava.bio.structure.Compound
-
- getStrainTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Strain term
- getStrand() - Method in interface org.biojava.bio.program.gff.GFFRecord
-
The strand of the feature.
- getStrand() - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- getStrand() - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
- getStrand() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getStrand() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getStrand() - Method in class org.biojava.bio.seq.FeatureFilter.StrandFilter
-
Retrieve the strand this matches.
- getStrand() - Method in interface org.biojava.bio.seq.FramedFeature
-
- getStrand() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
-
- getStrand() - Method in interface org.biojava.bio.seq.StrandedFeature
-
Retrieve the strand that this feature lies upon.
- getStrand() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByStrand
-
- getStrand() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the strand associated with this location.
- getStrand() - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
Retrieves the strand associated with this location.
- getStrand() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the strand associated with this location.
- getStrand() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Retrieve the strand that this feature lies upon.
- getStrand() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the strand associated with this location.
- getStrandedFeatureTemplate() - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
-
- getStrandedTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Strand term; legal values are "single", "double", and
"mixed".
- getStringSequence() - Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- getStructure(String) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
-
connect to a DAS structure service and retreive 3D data.
- getStructure() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getStructure() - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
This method will return the parsed protein structure, once the parsing has been finished
- getStructure(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
Opens filename, parses it and returns
a Structure object .
- getStructure(File) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
Opens filename, parses it and returns a Structure object.
- getStructure(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
opens filename, parses it and returns
aStructure object .
- getStructure(File) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
opens filename, parses it and returns a Structure object
- getStructure(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
open filename and returns
a Structure object.
- getStructure(File) - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
read file from File and returns
a Structure object.
- getStructure(String) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- getStructure(String) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
- getStructure(String) - Method in interface org.biojava.bio.structure.server.PDBInstallation
-
request a structure by its PDB identifier
- getStructure() - Method in interface org.biojava.bio.structure.server.StructureEvent
-
- getStructure() - Method in class org.biojava.bio.structure.server.StructureEventImpl
-
- getStructure1() - Method in class org.biojava.bio.structure.gui.util.PDBDirPanel
-
- getStructure1() - Method in class org.biojava.bio.structure.gui.util.PDBServerPanel
-
- getStructure1() - Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
-
- getStructure1() - Method in interface org.biojava.bio.structure.gui.util.StructurePairSelector
-
- getStructure2() - Method in class org.biojava.bio.structure.gui.util.PDBDirPanel
-
- getStructure2() - Method in class org.biojava.bio.structure.gui.util.PDBServerPanel
-
- getStructure2() - Method in class org.biojava.bio.structure.gui.util.PDBUploadPanel
-
- getStructure2() - Method in interface org.biojava.bio.structure.gui.util.StructurePairSelector
-
- getStructureById(String) - Method in class org.biojava.bio.structure.io.DASStructureClient
-
if pdb code is set (setId):
connect to a DAS-structure service and retreive data.
- getStructureById(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
Get a structure by PDB code.
- getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
load a structure from local file system and return a PDBStructure object
- getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBMSDReader
-
Get a structure by providing a PDB code.
- getStructureById(String) - Method in class org.biojava.bio.structure.io.PDBSRSReader
-
load a structure from from SRS installation using wgetz
returns null if no structure found
- getStructureById(String) - Method in interface org.biojava.bio.structure.io.StructureIO
-
Get a structure by providing a PDB code.
- getStructureListeners() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
- getStructurePairAligner() - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- getStyle() - Method in class org.biojava.bio.gui.DistributionLogo
-
Retrieve the current style.
- getStyle() - Method in interface org.biojava.bio.gui.LogoContext
-
- getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.AbstractAlignmentStyler
-
Return the styles for the two aligned characters.
- getStyle(String, String, String[]) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
Returns the styles for the two aligned characters in the form
of predefined font classes.
- getSubAlphabet(double, double) - Static method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getSubAlphabet(int, int) - Static method in class org.biojava.bio.symbol.IntegerAlphabet
-
Construct a finite contiguous subset of the IntegerAlphabet.
- getSubContext(PairwiseRenderContext) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
getSubContext creates a new context which has
FeatureHolders filtered using the current filter.
- getSubHitProperty(Object) - Method in interface org.biojava.bio.search.BlastLikeSearchFilter.Node
-
- getSubHitProperty(Object) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- getSubHits() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return all sub-hits for this sequence similarity search
hit.
- getSubHits() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getSubHits() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubject() - Method in interface org.biojava.ontology.Triple
-
Return the subject term of this triple
- getSubject() - Method in class org.biojava.ontology.Triple.Impl
-
- getSubject() - Method in interface org.biojavax.bio.BioEntryRelationship
-
Returns the subject of this relationship (ie.
- getSubject() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
-
Gets the feature that this relationship refers to.
- getSubject() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Gets the feature that this relationship refers to.
- getSubject() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Returns the subject of this relationship (ie.
- getSubject() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return the subject term of this triple
- getSubjectDBInstallation() - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
getSubjectDBInstallation returns the installation
in which all the databases searched may be
found.
- getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the end position of the last sub-hit in the subject
sequence.
- getSubjectEnd() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the start position of the sub-hit in the subject
sequence.
- getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getSubjectEnd() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectEnd() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getSubjectID() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
The sequence identifier of this hit within the sequence
database against which the search was performed.
- getSubjectID() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getSubjectID() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the start position of the first sub-hit in the subject
sequence.
- getSubjectStart() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the start position of the sub-hit in the subject
sequence.
- getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getSubjectStart() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectStart() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchHit
-
Return the strand of the sub-hit with respect to the subject
sequence.
- getSubjectStrand() - Method in interface org.biojava.bio.search.SeqSimilaritySearchSubHit
-
Return the strand of the sub-hit with respect to the subject
sequence.
- getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
- getSubjectStrand() - Method in class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
- getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
- getSubjectStrand() - Method in class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
- getSubmitterAccessionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the SubmitterAccession term
- getSubmitterVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the SubmitterVersion term
- getSubmitterWgsVersionTerm() - Static method in class org.biojavax.bio.seq.io.EMBLxmlFormat.Terms
-
Getter for the SubmitterWgsVersion term
- getSubSeqStart() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getSubstitutionMatrix(BufferedReader) - Static method in class org.biojava.bio.alignment.SubstitutionMatrix
-
This constructor can be used to guess the alphabet of this substitution
matrix.
- getSubstitutionMatrix(FiniteAlphabet) - Static method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- getSuppliers(RestrictionEnzyme) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
getSuppliers returns a string describing the suppliers
of this enzyme according to REBASE encoding for commercial sources
or an empty String if the enzyme is not commecially available.
- getSupportedCriteria() - Method in interface org.biojava.bibliography.BibRefSupport
-
It returns all supported searching and sorting criteria for the
whole bibliographic repository.
- getSupportedCriteria(String) - Method in interface org.biojava.bibliography.BibRefSupport
-
It returns all supported searching and sorting criteria in the given
repository subset.
- getSupportedValues(String, String) - Method in interface org.biojava.bibliography.BibRefSupport
-
It returns a controlled vocabulary containing all possible
values of the attribute given in attrName in the
context given in resourceType.
- getSurname() - Method in class org.biojava.bio.structure.Author
-
- getSwissprotBuilderFactory() - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Get a default SequenceBuilderFactory for handling Swissprot
files.
- getSwissprotId() - Method in interface org.biojava.bio.structure.Chain
-
Get the Swissprot id of this chain.
- getSwissprotId() - Method in class org.biojava.bio.structure.ChainImpl
-
get the Swissprot id of this chains .
- getSymbol(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getSymbol(List) - Method in interface org.biojava.bio.symbol.Alphabet
-
Get a symbol from the Alphabet which corresponds
to the specified ordered list of symbols.
- getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
Retrieve the Symbol for a double.
- getSymbol(double, double) - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
Retrieve the symbol for a range of doubles.
- getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getSymbol(List) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getSymbol(double) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getSymbol() - Method in exception org.biojava.bio.symbol.IllegalSymbolException
-
Retrieve the symbol that caused this exception, or null.
- getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
Retrieve the Symbol for an int.
- getSymbol(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
- getSymbol(int) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getSymbol(List) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
Gets the compound symbol composed of the Symbols in the List.
- getSymbolArray() - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
Return the Java Symbol[] array that backs this object.
- getSymbolImpl(List) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getSymbolImpl(List) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- getSymbolImpl(List) - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getSymbolList() - Method in interface org.biojava.bio.alignment.AlignmentElement
-
- getSymbolList() - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
-
- getSymbolParser() - Method in class org.biojava.bio.seq.db.BioIndex
-
- getSymbolParser() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
- getSymbolParser() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Retrieve the symbol parser used to turn the sequence characters
into Symobl objects.
- getSymbolParser() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- getSymbolPropertyTable(String) - Static method in class org.biojava.bio.seq.ProteinTools
-
- getSymbols() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getSymbols() - Method in interface org.biojava.bio.gui.sequence.CircularRendererContext
-
The SymbolList that is currently rendered by this context.
- getSymbols() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getSymbols() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSymbols returns all of the Symbols
belonging to the currently rendered Sequence.
- getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Retrieve the currently rendered SymbolList
- getSymbols() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the currently rendered SymbolList
- getSymbols() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
The SymbolList that is currently rendered by this SequenceRenderContext.
- getSymbols() - Method in class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
- getSymbols() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getSymbols() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getSymbols() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getSymbols returns all of the Symbols
belonging to the currently rendered Sequence.
- getSymbols() - Method in class org.biojava.bio.program.das.DASSequence
-
- getSymbols() - Method in interface org.biojava.bio.seq.Feature
-
Return a list of symbols that are contained in this feature.
- getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getSymbols() - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
-
- getSymbols() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getSymbols() - Method in interface org.biojava.bio.seq.StrandedFeature
-
Return a list of symbols that are contained in this feature.
- getSymbols() - Method in interface org.biojava.bio.symbol.BasisSymbol
-
The list of symbols that this symbol is composed from.
- getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleRange
-
- getSymbols() - Method in class org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol
-
- getSymbols() - Method in class org.biojava.bio.symbol.FundamentalAtomicSymbol
-
- getSymbols() - Method in class org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol
-
- getSymbols() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Return a list of symbols that are contained in this feature.
- getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getSymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
- getSymbolTranslation() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getSymbolTranslation returns the current
translation in Symbols which will be applied when
rendering.
- getSyms() - Method in class org.biojava.bio.symbol.PackedSymbolList
-
Return the long array within which the symbols are bit-packed.
- getSynonyms() - Method in class org.biojava.bio.structure.Compound
-
- getSynonyms() - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- getSynonyms() - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getSynonyms() - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- getSynonyms() - Method in interface org.biojava.ontology.Term
-
Return the synonyms for this term.
- getSynonyms() - Method in class org.biojava.ontology.Term.Impl
-
- getSynonyms() - Method in class org.biojava.ontology.Triple.Impl
-
- getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Return the synonyms for this term.
- getSynonyms() - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Return the synonyms for this term.
- getSynthetic() - Method in class org.biojava.bio.structure.Compound
-
- getT() - Method in class org.biojava.bio.molbio.DNAComposition
-
Get the relative compositon of 'T'.
- getT() - Method in class org.biojava.bio.proteomics.StructureTools
-
- getTable() - Method in class org.biojava.bio.dist.TranslatedDistribution
-
Retrieve the translation table encapsulating the map from this emission
spectrum to the underlying one.
- getTableNumber() - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
-
- getTag() - Method in class org.biojava.bio.program.tagvalue.TagValue
-
- getTagGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Get the group number that matches the tag.
- getTags() - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- getTags() - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
Get the complete set of tags that are currently recognized.
- getTAlphabet() - Static method in class org.biojava.bio.seq.ProteinTools
-
Gets the protein alphabet including the translation termination symbols
- getTarget() - Method in class org.biojava.bio.gui.sequence.SequenceViewerEvent
-
Get the Object that was the target of the mouse gesture or null if the
mouse is not gesturing over any recognizable rendered object.
- getTarget(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- getTarget(Object) - Method in interface org.biojava.stats.svm.SVMTarget
-
- getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractManyToOneTranslationTable
-
- getTargetAlphabet() - Method in class org.biojava.bio.symbol.AbstractReversibleTranslationTable
-
- getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
-
- getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
-
- getTargetAlphabet() - Method in class org.biojava.bio.symbol.SimpleTranslationTable
-
- getTargetAlphabet() - Method in interface org.biojava.bio.symbol.TranslationTable
-
The alphabet of Symbols that will be produced.
- getTargetOntology() - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- getTaxa() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
get the taxa represented in this group
- getTaxa() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- getTaxon(int) - Static method in class org.biojava.bio.program.homologene.HomologeneTools
-
get the Taxon corresponding to this Taxon ID
- getTaxon() - Method in interface org.biojava.bio.program.homologene.Orthologue
-
return the Taxon associated with this orthologue
- getTaxon() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getTaxon(Connection, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Attempts to get a Taxon object corresponding to the specified
NCBI taxon ID.
- getTaxon(Connection, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Attempts to get a Taxon object corresponding to the specified
name.
- getTaxon() - Method in interface org.biojavax.bio.BioEntry
-
Gets the taxon associated with this bioentry.
- getTaxon() - Method in class org.biojavax.bio.SimpleBioEntry
-
Gets the taxon associated with this bioentry.
- getTaxonID() - Method in interface org.biojava.bio.program.homologene.Orthologue
-
a convenience method to return the TaxonID for thsi orhtologue.
- getTaxonID() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getTaxonID() - Method in interface org.biojava.bio.program.homologene.Taxon
-
returns the taxon ID
- getTaxonID() - Method in class org.biojava.bio.program.homologene.Taxon.TaxonStub
-
- getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getTaxonId(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getTaxonId(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getTechnique() - Method in class org.biojava.bio.structure.PDBHeader
-
- getTempBuffer() - Method in class org.biojava.ontology.obo.OboFileParser
-
- getTemperatureDependence() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property temperatureDependence.
- getTempFactor() - Method in interface org.biojava.bio.structure.Atom
-
get set temp factor.
- getTempFactor() - Method in class org.biojava.bio.structure.AtomImpl
-
- getTerm(String) - Method in class org.biojava.ontology.IntegerOntology
-
- getTerm(String) - Method in interface org.biojava.ontology.Ontology
-
Fetch the term with the specified name.
- getTerm(String) - Method in class org.biojava.ontology.Ontology.Impl
-
- getTerm() - Method in interface org.biojavax.bio.BioEntryRelationship
-
Returns the term describing the relationship.
- getTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByNoteTermOnly
-
- getTerm() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Retrieves the term associated with this location.
- getTerm() - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
-
Gets the term that describes this relationship.
- getTerm() - Method in interface org.biojavax.bio.seq.RichLocation
-
Retrieves the term associated with this location.
- getTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Gets the term that describes this relationship.
- getTerm() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Retrieves the term associated with this location.
- getTerm() - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Returns the term describing the relationship.
- getTerm() - Method in interface org.biojavax.Note
-
Gets the term that defines this note.
- getTerm(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Fetch the term with the specified name.
- getTerm() - Method in class org.biojavax.SimpleNote
-
Gets the term that defines this note.
- getTermMass() - Method in class org.biojava.bio.proteomics.MassCalc
-
getTermMass returns the terminal mass being used
by the instance methods.
- getTerms() - Method in class org.biojava.ontology.IntegerOntology
-
- getTerms() - Method in interface org.biojava.ontology.Ontology
-
Return all the terms in this ontology
- getTerms() - Method in class org.biojava.ontology.Ontology.Impl
-
- getTerms() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Return all the terms in this ontology
- getTermSet() - Method in interface org.biojavax.ontology.ComparableOntology
-
Returns the set of terms in this ontology.
- getTermSet() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Returns the set of terms in this ontology.
- getTestClass() - Method in class org.biojava.bio.seq.FeatureFilter.ByClass
-
- getText() - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
-
- getText() - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- getText() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property text.
- getTextColor() - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Get the color of the label text
- getThreadFetches() - Static method in class org.biojava.bio.program.das.DAS
-
- getThree_letter_code() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getThreshold() - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- getThreshold() - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- getThreshold() - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getTickDirection() - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- getTimeStamp() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
-
Returns a time stamp .
- getTimeStamp() - Method in class org.biojava.bio.structure.io.PDBFileParser
-
Returns a time stamp.
- getTissue() - Method in class org.biojava.bio.structure.Compound
-
- getTissueTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Tissue term
- getTitle() - Method in interface org.biojava.bio.program.homologene.Orthologue
-
return the title used by Genbank for this protein
- getTitle() - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- getTitle() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
-
The cluster title.
- getTitle() - Method in class org.biojava.bio.structure.Compound
-
- getTitle() - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- getTitle() - Method in class org.biojava.bio.structure.JournalArticle
-
Get the value of title
- getTitle() - Method in class org.biojava.bio.structure.PDBHeader
-
- getTitle() - Method in interface org.biojavax.DocRef
-
Returns the title of the document reference.
- getTitle() - Method in class org.biojavax.SimpleDocRef
-
Returns the title of the document reference.
- getTo() - Method in exception org.biojava.bio.dp.IllegalTransitionException
-
- getToken() - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- getToken() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
-
Returns the token for strandedness.
- getTokenization(String) - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
- getTokenization(String) - Method in interface org.biojava.bio.symbol.Alphabet
-
Get a SymbolTokenization by name.
- getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet
-
- getTokenization(String) - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
- getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet
-
Creates a new parser (Mark Schreiber 3 May 2001).
- getTokenization(String) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- getTokenization(String) - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- getTokenization(String) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
- getTokenTable() - Method in class org.biojava.bio.seq.io.CharacterTokenization
-
- getTokenType() - Method in class org.biojava.bio.seq.io.AlternateTokenization
-
Tokens have fixed size.
- getTokenType() - Method in class org.biojava.bio.seq.io.CharacterTokenization
-
- getTokenType() - Method in interface org.biojava.bio.seq.io.SymbolTokenization
-
Determine the style of tokenization represented by this object.
- getTokenType() - Method in class org.biojava.bio.seq.io.WordTokenization
-
- getTokenType() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization
-
- getTotalDepth() - Method in class org.biojava.bio.gui.sequence.LineInfo
-
- getTotalWeight() - Method in class org.biojavax.ga.util.WeightedSet
-
The total weight that has been added to this Set.
- getTrace(AtomicSymbol) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getTrace(AtomicSymbol) - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Returns an array containing the intensities of the sampled waveform
representing the chromatogram trace for base nucleotide.
- getTrace() - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- getTrace(AtomicSymbol) - Method in class org.biojava.bio.program.abi.ABITrace
-
Returns one of the four traces - all of the y-coordinate values,
each of which correspond to a single x-coordinate relative to the
position in the array, so that if element 4 in the array is 972, then
x is 4 and y is 972 for that point.
- getTraceLength() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- getTraceLength() - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Returns the length of the trace of the Chromatogram.
- getTraceLength() - Method in class org.biojava.bio.program.abi.ABITrace
-
Returns the length of the trace (number of x-coordinate points in the graph).
- getTraceOffset(Chromatogram, int) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
-
Get a specific value from the trace offset sequence in the given
chromatogram and extract its int value.
- getTraceOffsetArray(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
-
Converts the peak offsets list of the given chromatogram
into a new int array.
- getTraceOffsets(Chromatogram) - Static method in class org.biojava.bio.chromatogram.ChromatogramTools
-
Get the peak offsets for the called bases of a chromatogram.
- getTrackLayout() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getTrailer() - Method in class org.biojava.utils.ListTools.SeriesList
-
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getTrailingBorder returns the trailing border of
the primary sequence.
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Retrieve the object that encapsulates the trailing border area - the space
after sequence information is rendered.
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Retrieve the object that encapsulates the trailing border area - the space
after sequence information is rendered.
- getTrailingBorder() - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Gets the TrailingBorder attribute of the SequenceRenderContext object.
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- getTrailingBorder() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getTrailingBorder returns the trailing border.
- getTrailingPixles() - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- getTrainer(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Return the Distribution trainer object from the current context.
- getTrainer(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- getTrans() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getTransform() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns a new AffineTransform describing the transformation
from chromatogram coordinates to output coordinates.
- getTransformAndConcat(AffineTransform) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Concatenates the chromatogram-to-output transform to the
provided given AffineTransform.
- getTransformer() - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
-
- getTransformer() - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getTransformer() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- getTransitions() - Method in class org.biojava.utils.automata.FiniteAutomaton
-
retrieve Set of all transitions in instance.
- getTransitions() - Method in interface org.biojava.utils.automata.NfaBuilder
-
- getTransitions() - Method in class org.biojava.utils.automata.NfaSubModel
-
- getTransitionTable() - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
retrieve the TransitionTable for this State.
- getTranslation() - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- getTranslation() - Method in class org.biojava.bio.structure.SVDSuperimposer
-
Get the shift vector.
- getTransposonTerm() - Static method in class org.biojavax.bio.seq.RichSequence.Terms
-
Getter for the Transposon term
- getTrimTag() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
See if tag trimming is enabled.
- getTrimTag() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
See if trimming of tags is enabled.
- getTrimValue() - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
See if value trimming is enabled.
- getTrimValue() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
See if trimming of values is enabled.
- getTriples(Term, Term, Term) - Method in class org.biojava.ontology.IntegerOntology
-
- getTriples(Term, Term, Term) - Method in interface org.biojava.ontology.Ontology
-
Return all triples from this ontology which match the supplied
pattern.
- getTriples(Term, Term, Term) - Method in class org.biojava.ontology.Ontology.Impl
-
- getTriples(Term, Term, Term) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Return all triples from this ontology which match the supplied
pattern.
- getTripleSet() - Method in interface org.biojavax.ontology.ComparableOntology
-
Returns the set of triples in this ontology.
- getTripleSet() - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Returns the set of triples in this ontology.
- getTrypsin() - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
- getType() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
-
getType returns the type of hotspot.
- getType() - Method in class org.biojava.bio.program.formats.Embl
-
- getType() - Method in class org.biojava.bio.program.formats.Enzyme
-
- getType() - Method in interface org.biojava.bio.program.formats.Format
-
Get the AnnotationType that constrains the events that will be fired.
- getType() - Method in class org.biojava.bio.program.formats.Ligand.Compound
-
- getType() - Method in class org.biojava.bio.program.formats.Ligand.Enzyme
-
- getType() - Method in class org.biojava.bio.program.formats.Ligand.Reaction
-
- getType() - Method in class org.biojava.bio.program.formats.Swissprot
-
- getType() - Method in interface org.biojava.bio.program.gff3.GFF3Record
-
- getType() - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- getType() - Method in interface org.biojava.bio.seq.Feature
-
The type of the feature.
- getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
-
- getType() - Method in class org.biojava.bio.seq.FeatureFilter.ByType
-
- getType(String) - Static method in class org.biojava.bio.seq.FeatureTypes
-
Get a Type by URI.
- getType(String) - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
-
Find the type for a name.
- getType(String) - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getType() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getType() - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAlias
-
- getType() - Method in class org.biojava.bio.structure.AminoAcidImpl
-
- getType() - Method in interface org.biojava.bio.structure.Group
-
get Type of group, e.g.
- getType() - Method in class org.biojava.bio.structure.HetatomImpl
-
Returns the type value.
- getType() - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- getType() - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- getType() - Method in class org.biojava.bio.structure.NucleotideImpl
-
- getType() - Method in class org.biojava.utils.ChangeEvent
-
Find the type of this event.
- getType() - Method in class org.biojava.utils.ChangeForwarder.Retyper
-
- getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
-
Getter for property type.
- getType() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- getType() - Method in interface org.biojavax.bio.seq.Position
-
Returns the type of this position if it is not a point/single position.
- getType() - Method in class org.biojavax.bio.seq.SimplePosition
-
Returns the type of this position if it is not a point/single position.
- getType() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
The type of the feature.
- getType_symbol() - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- getTypeClass() - Method in class org.biojava.utils.walker.WalkerFactory
-
- getTypeHandler() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
- getTypes(URL) - Static method in class org.biojava.bio.program.das.DAS
-
- getTypes() - Method in interface org.biojava.bio.seq.FeatureTypes.Repository
-
Get a set of all type names defined in this repository.
- getTypes() - Method in class org.biojava.bio.seq.FeatureTypes.RepositoryImpl
-
- getTypeTerm() - Method in interface org.biojava.bio.seq.Feature
-
An ontology term defining the type of feature.
- getTypeTerm() - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- getTypeTerm() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTerm
-
- getTypeTerm() - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
An ontology term defining the type of feature.
- getTypeTermName() - Method in class org.biojavax.bio.db.biosql.BioSQLFeatureFilter.ByTypeTermName
-
- getU() - Method in class org.biojava.bio.structure.jama.LUDecomposition
-
Return upper triangular factor
- getU() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Return the left singular vectors
- getUngappedLocation() - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Get a Location that contains exactly those positions that are not gaps.
- getUngappedLocation() - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- getUniProtDBNameTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
-
Getter for the UniProt combined database term
- getUniprotKWOnto() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the private uniprot ontology.
- getUniProtTerm() - Static method in class org.biojavax.bio.seq.io.UniProtFormat.Terms
-
Getter for the UniProt term
- getUniProtXMLTerm() - Static method in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
Getter for the UniProtXML term
- getUnique() - Method in interface org.biojava.bio.program.unigene.UnigeneCluster
-
The unique sequence that is used as a representative for this cluster.
- getUnits() - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- getUnitv() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getUnprojectedFeatures() - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Get the features before projection.
- getUnprojectedFeatures() - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getUpdateDate(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getUpdateDate(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getUpstreamCut() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getUpstreamCut returns the cut site upstream of
the recognition site.
- getUpstreamEndType() - Method in class org.biojava.bio.molbio.RestrictionEnzyme
-
getUpstreamEndType returns the double-stranded end
type produced by the secondary (upstream) cut.
- getURI() - Method in interface org.biojava.bio.seq.FeatureTypes.Type
-
Get the URI for this type.
- getUri() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property uri.
- getURI() - Method in interface org.biojavax.Namespace
-
If the namespace has a URI, this will return it.
- getURI() - Method in class org.biojavax.SimpleNamespace
-
If the namespace has a URI, this will return it.
- getURL() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
-
getURL returns the hotspot URL.
- getURL() - Method in class org.biojava.bio.program.das.DASSequenceDB
-
Return the URL of the reference server for this database.
- getURL() - Method in class org.biojava.bio.program.das.DataSource
-
- getURN() - Method in class org.biojava.bio.program.das.DASSequence
-
- getURN() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- getURN() - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- getURN() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- getURN() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- getURN() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- getURN() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- getURN() - Method in interface org.biojava.bio.seq.Sequence
-
- getURN() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- getURN() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
- getUsed() - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- getUsedAtomNames() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- getUserObject() - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
-
getUserObject returns the current user object
(or null).
- getV() - Method in class org.biojava.bio.structure.jama.EigenvalueDecomposition
-
Return the eigenvector matrix
- getV() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Return the right singular vectors
- getValue() - Method in class org.biojava.bio.program.tagvalue.TagValue
-
- getValue() - Method in class org.biojava.bio.PropertyConstraint.ExactValue
-
Get the value that all properties must match.
- getValue() - Method in class org.biojava.bio.seq.FeatureFilter.AnnotationContains
-
- getValue() - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotation
-
- getValue() - Method in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- getValue() - Method in class org.biojava.bio.seq.StrandedFeature.Strand
-
Returns the integer label for strandedness.
- getValue() - Method in class org.biojava.bio.structure.align.helper.AligMatEl
-
- getValue() - Method in class org.biojava.bio.structure.align.helper.GapArray
-
- getValue() - Method in interface org.biojava.stats.svm.ItemValue
-
- getValue() - Method in class org.biojava.stats.svm.SimpleItemValue
-
- getValue() - Method in interface org.biojava.utils.walker.Walker
-
If the visitor has a return value, then the result of applying the visitor
to the tree can be obtained using this method, otherwise the result will
be null.
- getValue() - Method in interface org.biojavax.Note
-
Gets the value that defines this note.
- getValue() - Method in class org.biojavax.SimpleNote
-
Gets the value that defines this note.
- getValue() - Method in class org.biojavax.utils.CRC64Checksum
-
- getValueAt(Symbol, Symbol) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
There are some substitution matrices containing more columns than lines.
- getValueAtIndex(int) - Method in class org.biojava.stats.svm.SparseVector
-
Retrieve the value at a specific index.
- getValueGroup() - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Get the group number that matches the value.
- getValues() - Method in class org.biojava.bio.PropertyConstraint.Enumeration
-
getValues returns the set of values which
constrain the property.
- getVariableMasses(SymbolList) - Method in class org.biojava.bio.proteomics.MassCalc
-
Get all masses including the variable mass.
- getVariant() - Method in class org.biojava.bio.program.fastq.Fastq
-
Return the FASTQ sequence format variant for this FASTQ formatted sequence.
- getVariant() - Method in class org.biojava.bio.program.fastq.IlluminaFastqReader
-
Return the FASTQ sequence format variant for this reader.
- getVariant() - Method in class org.biojava.bio.program.fastq.SangerFastqReader
-
Return the FASTQ sequence format variant for this reader.
- getVariant() - Method in class org.biojava.bio.program.fastq.SolexaFastqReader
-
Return the FASTQ sequence format variant for this reader.
- getVariant() - Method in class org.biojava.bio.structure.Compound
-
- getVector(int) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- getVector() - Method in class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
-
- getVectorAnnotationType() - Static method in class org.biojava.bio.program.das.dasalignment.Alignment
-
define the shift vector annotation type
- getVectorNTISupport() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
Is VectorNTI compatable output being produced?
- getVectors() - Method in class org.biojava.bio.program.das.dasalignment.Alignment
-
Returns the shift vectors.
- getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getVersion(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getVersion() - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.Embl2AgaveAnnotFilter
-
- getVersion(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getVersion() - Method in interface org.biojava.utils.candy.CandyVocabulary
-
It returns a vesrion of this vocabulary.
- getVersion() - Method in interface org.biojavax.bio.BioEntry
-
Gets the version of this bioentry.
- getVersion() - Method in class org.biojavax.bio.SimpleBioEntry
-
Gets the version of this bioentry.
- getVersion() - Method in interface org.biojavax.CrossRef
-
Returns the version of the object that the crossref refers to.
- getVersion() - Method in class org.biojavax.SimpleCrossRef
-
Returns the version of the object that the crossref refers to.
- getVersionLineTerm() - Static method in class org.biojavax.bio.seq.io.EMBLFormat.Terms
-
Getter for the Ensembl-specific 'versionLine' term
- getVerticalScale() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the in use vertical scale factor.
- getViewedFeature() - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- getViewedFeature() - Method in interface org.biojava.bio.seq.projection.Projection
-
- getVisibleRange(SequenceRenderContext, Graphics2D) - Static method in class org.biojava.bio.gui.sequence.GUITools
-
- getVisibleRange() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- getVisibleSecondarySymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getVisibleSecondarySymbolCount returns the
maximum number of secondary
Symbols which can be rendered in the visible area
(excluding all borders) of the
PairwiseSequencePanel at the current scale.
- getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
getVisibleSymbolCount returns the
maximum number of Symbols which
can be rendered in the visible area (excluding all borders) of
the PairwiseSequencePanel at the current
scale.
- getVisibleSymbolCount() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
getVisibleSymbolCount returns the
maximum number of Symbols which
can be rendered in the visible area (excluding all borders) of
the TranslatedSequencePanel at the current
scale.
- getVMaxes() - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Getter for property VMaxes.
- getVocabularyByName(String) - Method in interface org.biojava.utils.candy.CandyFinder
-
It returns a selected vocabulary.
- getVocabularyFinder() - Method in interface org.biojava.bibliography.BibRefSupport
-
It returns an object representing a central place where all
controlled vocabularies can be received from and shared by all
users.
- getVolume() - Method in class org.biojava.bio.structure.JournalArticle
-
- getWalker(Visitor) - Method in class org.biojava.utils.walker.WalkerFactory
-
Get a Walker that is customosed to a particular visitor.
- getWeight(Symbol) - Method in class org.biojava.bio.dist.AbstractDistribution
-
Retrieve the weight for this distribution.
- getWeight(Symbol) - Method in interface org.biojava.bio.dist.Distribution
-
Return the probability that Symbol s is emitted by this spectrum.
- getWeight(Symbol) - Method in class org.biojava.bio.dist.GapDistribution
-
- getWeight(Symbol) - Method in class org.biojava.bio.dist.PairDistribution
-
- getWeight(Symbol) - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- getWeight(Object) - Method in class org.biojavax.ga.util.WeightedSet
-
Determines the normalized weight for o
- getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractDistribution
-
Override this method to implement getting the weight for an atomic
symbol.
- getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
Get a weight from one of the sub-distributions, conditioned
on the first part of the symbol.
- getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.SimpleDistribution
-
- getWeightImpl(AtomicSymbol) - Method in class org.biojava.bio.dist.UniformDistribution
-
- getWeightMatrixID() - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
-
Get the value of the weight matrix id.
- getWeights() - Method in class org.biojava.bio.dist.SimpleDistribution
-
Get the underlying array that stores the weights.
- getWeights(State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Get a probability Distribution over the transition from 'source'.
- getWeights(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- getWeights(State) - Method in class org.biojava.bio.dp.WMAsMM
-
- getWidth() - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Returns the width of the whole graphic (in pixels).
- getWidth() - Method in class org.biojava.bio.seq.io.AlternateTokenization
-
Get the width of the tokens.
- getWidth() - Method in class org.biojava.stats.svm.RadialBaseKernel
-
- getWobbleDistributionForSynonyms(Symbol) - Method in interface org.biojava.bio.symbol.CodonPref
-
returns a WobbleDistribution for
a specified residue.
- getWobbleDistributionForSynonyms(Symbol) - Method in class org.biojava.bio.symbol.SimpleCodonPref
-
- getWobbleFrequency(Symbol) - Method in interface org.biojava.bio.symbol.WobbleDistribution
-
returns the frequency of a specific
wobble base in a set of synonymous
codons that start with the same two
bases.
- getWorkingDirectory() - Method in class org.biojava.utils.process.ExternalProcess
-
Gets the working directory for the external process.
- getWrap() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- getWrap() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- getWrap() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- getWrapIncrement() - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- getWrapIncrement() - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- getWrapped() - Method in class org.biojava.bio.AnnotationChanger
-
getWrapped returns the Annotation
being remapped.
- getWrapped() - Method in class org.biojava.bio.AnnotationRenamer
-
getWrapped returns the Annotation
being remapped.
- getWrapped() - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- getWrappedKernel() - Method in class org.biojava.stats.svm.SigmoidKernel
-
- getWriter() - Method in class org.biojava.utils.process.ReaderWriterPipe
-
Gets the writer.
- getX() - Method in interface org.biojava.bio.structure.Atom
-
Get coordinate X.
- getX() - Method in class org.biojava.bio.structure.AtomImpl
-
Get the X coordinate.
- getXFFEnvironment() - Method in class org.biojava.bio.program.xff.FeatureHandler
-
Return the XFF processing environment passed in when this handler was
created.
- getXrefDb() - Method in class org.biojava.bio.seq.io.game.GAMEDbxrefPropHandler.DbXrefElement
-
- getXrefProps() - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.Agave2AgaveAnnotFilter
-
- getXrefs(Annotation) - Method in interface org.biojava.bio.seq.io.agave.AGAVEAnnotFilter
-
- getXrefs() - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefs
-
return a set of AGAVEXref
- getXrefs(Annotation) - Method in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- getXYZEuler(Matrix) - Static method in class org.biojava.bio.structure.Calc
-
Convert a rotation Matrix to Euler angles.
- getY() - Method in interface org.biojava.bio.structure.Atom
-
Get coordinate Y.
- getY() - Method in class org.biojava.bio.structure.AtomImpl
-
Get the Y coordinate.
- getZ() - Method in interface org.biojava.bio.structure.Atom
-
Get coordinate Z.
- getZ() - Method in class org.biojava.bio.structure.AtomImpl
-
Get the Z coordinate.
- getZYZEuler(Matrix) - Static method in class org.biojava.bio.structure.Calc
-
Gget euler angles for a matrix given in ZYZ convention.
- GFF - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
GFF indicates that the sequence format is GFF.
- GFF3DocumentHandler - Interface in org.biojava.bio.program.gff3
-
The interface for things that listen to GFF event streams.
- GFF3Parser - Class in org.biojava.bio.program.gff3
-
Parse a stream of GFF text into a stream of records and comments.
- GFF3Parser() - Constructor for class org.biojava.bio.program.gff3.GFF3Parser
-
- GFF3Record - Interface in org.biojava.bio.program.gff3
-
A record in a GFF3 formatted file.
- GFF3Record.Impl - Class in org.biojava.bio.program.gff3
-
- GFF3Record.Impl() - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- GFF3Record.Impl(GFF3Record) - Constructor for class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- GFFDataSource - Class in org.biojava.bio.seq.distributed
-
Use a GFFEntrySet as a DataSource for adding annotation to sequences.
- GFFDataSource(GFFEntrySet) - Constructor for class org.biojava.bio.seq.distributed.GFFDataSource
-
- GFFDocumentHandler - Interface in org.biojava.bio.program.gff
-
The interface for things that listen to GFF event streams.
- GFFEntrySet - Class in org.biojava.bio.program.gff
-
A set of entries and comments as a representation of a GFF file.
- GFFEntrySet() - Constructor for class org.biojava.bio.program.gff.GFFEntrySet
-
Make an empty GFFEntrySet.
- GFFErrorHandler - Interface in org.biojava.bio.program.gff
-
Interface which captures any errors which occur when parsing
a GFF stream.
- GFFErrorHandler.AbortErrorHandler - Class in org.biojava.bio.program.gff
-
- GFFErrorHandler.AbortErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.AbortErrorHandler
-
- GFFErrorHandler.SkipRecordErrorHandler - Class in org.biojava.bio.program.gff
-
- GFFErrorHandler.SkipRecordErrorHandler() - Constructor for class org.biojava.bio.program.gff.GFFErrorHandler.SkipRecordErrorHandler
-
- GFFFilterer - Class in org.biojava.bio.program.gff
-
An object that filters a stream of GFF, forwarding some
GFFRecords to a
listening GFFDocumentHandler, and dropping others.
- GFFFilterer(GFFDocumentHandler, GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFFilterer
-
Create a new GFFFilterer that will forward
to handler everything that
filter accepts.
- gffFromSeqDB(SequenceDB) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Creates a GFFEntrySet containing one entry for each feature on each
sequence of a SequenceDB.
- gffFromSequence(Sequence) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Creates a GFFEntrySet containing one entry for each feature on a sequence.
- GFFParser - Class in org.biojava.bio.program.gff
-
Parse a stream of GFF text into a stream of records and comments.
- GFFParser() - Constructor for class org.biojava.bio.program.gff.GFFParser
-
- GFFRecord - Interface in org.biojava.bio.program.gff
-
A single GFF record.
- GFFRecordFilter - Interface in org.biojava.bio.program.gff
-
A filter that will accept or reject a GFFEntry.
- GFFRecordFilter.AcceptAll - Class in org.biojava.bio.program.gff
-
Implementation of GFFRecordFilter that accepts everything.
- GFFRecordFilter.AcceptAll() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.AcceptAll
-
- GFFRecordFilter.FeatureFilter - Class in org.biojava.bio.program.gff
-
Implementation of GFFRecordFilter that accepts
records based upon the feature field.
- GFFRecordFilter.FeatureFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
- GFFRecordFilter.FeatureFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
- GFFRecordFilter.FrameFilter - Class in org.biojava.bio.program.gff
-
- GFFRecordFilter.FrameFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- GFFRecordFilter.FrameFilter(int) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- GFFRecordFilter.NotFilter - Class in org.biojava.bio.program.gff
-
- GFFRecordFilter.NotFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- GFFRecordFilter.NotFilter(GFFRecordFilter) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- GFFRecordFilter.SequenceFilter - Class in org.biojava.bio.program.gff
-
Implementation of GFFRecordFilter that accepts
records based upon the sequence name.
- GFFRecordFilter.SequenceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
- GFFRecordFilter.SequenceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
- GFFRecordFilter.SourceFilter - Class in org.biojava.bio.program.gff
-
Implementation of GFFRecordFilter that accepts
records based upon the source field.
- GFFRecordFilter.SourceFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
- GFFRecordFilter.SourceFilter(String) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
- GFFRecordFilter.StrandFilter - Class in org.biojava.bio.program.gff
-
- GFFRecordFilter.StrandFilter() - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- GFFRecordFilter.StrandFilter(StrandedFeature.Strand) - Constructor for class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- GFFTools - Class in org.biojava.bio.program.gff
-
- GFFTools() - Constructor for class org.biojava.bio.program.gff.GFFTools
-
- GFFWriter - Class in org.biojava.bio.program.gff
-
Listens to a stream of GFF events and writes the lines to a
PrintWriter.
- GFFWriter(PrintWriter) - Constructor for class org.biojava.bio.program.gff.GFFWriter
-
Create a new GFFWriter that will write to
out.
- GI_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- gList - Variable in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- gln() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Glutamine (Q)
- GLOBAL - Static variable in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
The TaxonFactory that the biojava system should use for storing
the taxonomy used by swissprot and embl as in-memory objects.
- GLOBAL - Static variable in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
The TaxonFactory that the biojava system should use for storing
the taxonomy used by swissprot and embl as in-memory objects.
- glu() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Glutamic Acid (E)
- GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.Protease
-
- GLU_C_BICARB - Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.Protease
-
- GLU_C_PHOS - Static variable in class org.biojava.bio.proteomics.ProteaseManager
-
- gly() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Glycine (G)
- Glyph - Interface in org.biojava.bio.gui.glyph
-
The Glyph interface for painting a shape within bounds
- GlyphFeatureRenderer - Class in org.biojava.bio.gui.sequence
-
A FeatureRenderer that renders a particular Glyph for Features accepted by a
particular FeatureFilter
- GlyphFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- GlyphUtils - Class in org.biojava.bio.gui.glyph
-
Utils class used by Glyph implementors.
- GOParser - Class in org.biojava.ontology.io
-
Simple parser for the Gene Ontology (GO) flatfile format.
- GOParser() - Constructor for class org.biojava.ontology.io.GOParser
-
- Gotoh - Class in org.biojava.bio.structure.align.pairwise
-
a class to perform Gotoh algorithm
- Gotoh(Alignable) - Constructor for class org.biojava.bio.structure.align.pairwise.Gotoh
-
- graphicsToSecondarySequence(double) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
graphicsToSecondarySequence converts a graphical
position to a sequence coordinate on the secondary sequence.
- graphicsToSecondarySequence(Point) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
- graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
- graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
graphicsToSecondarySequence converts a graphical
position to a secondary sequence index.
- graphicsToSecondarySequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSecondarySequence(Point) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
graphicsToSequence converts a graphical position
to a sequence index.
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
graphicsToSequence converts a graphical position
to a sequence index.
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- graphicsToSequence(double) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Converts a graphical position into a sequence coordinate.
- graphicsToSequence(Point2D) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Converts a graphical position into a sequence coordinate.
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- graphicsToSequence(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
graphicsToSequence converts a graphical position
to a sequence index.
- graphicsToSequence(Point2D) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
graphicsToSequence converts a graphical position
to a sequence index.
- greater(int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- group() - Method in interface org.biojava.bio.search.BioMatcher
-
Get the matching region as a SymbolList.
- group() - Method in class org.biojava.bio.search.MaxMismatchMatcher
-
- Group - Interface in org.biojava.bio.structure
-
This is the data structure for a single Group of atoms.
- group() - Method in class org.biojava.utils.regex.Matcher
-
Returns the input subsequence matched by the previous match.
- group(int) - Method in class org.biojava.utils.regex.Matcher
-
Returns the input subsequence captured by the given group during the previous match operation.
- groupCount() - Method in class org.biojava.utils.regex.Matcher
-
Returns the number of capturing groups in this matcher's pattern.
- GroupIterator - Class in org.biojava.bio.structure
-
An iterator over all groups of a structure.
- GroupIterator(Structure) - Constructor for class org.biojava.bio.structure.GroupIterator
-
Constructs a GroupIterator object.
- groups - Variable in class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
-
- GroupType - Class in org.biojava.bio.structure
-
contains only the static declaration of which types of Groups are available
- GroupType() - Constructor for class org.biojava.bio.structure.GroupType
-
- growIfNecessary() - Method in class org.biojava.utils.ChangeSupport
-
Grows the internal resources if by adding one more listener they would be
full.
- guessFileType(File) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
because there is no standard file naming convention
and guessing by file name is inherantly error prone and bad.
- guessRecLen(RandomAccessFile) - Method in class org.biojava.bio.seq.db.BioIndex
-
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(File) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
On the assumption that the file is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- guessSymbolTokenization(BufferedInputStream) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
On the assumption that the stream is readable by this format (not checked),
attempt to guess which symbol tokenization we should use to read it.
- GUITools - Class in org.biojava.bio.gui.sequence
-
- GZIP_MAGIC - Static variable in class org.biojava.utils.io.InputStreamProvider
-
The magic number found at the start of a GZIP stream.
- r() - Static method in class org.biojava.bio.seq.DNATools
-
- r() - Static method in class org.biojava.bio.seq.NucleotideTools
-
- r() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Arginine
- R_NORVEGICUS - Static variable in interface org.biojava.bio.program.homologene.Taxon
-
- RadialBaseKernel - Class in org.biojava.stats.svm
-
This kernel computes the radial base kernel that corresponds to a gausian
distribution.
- RadialBaseKernel() - Constructor for class org.biojava.stats.svm.RadialBaseKernel
-
- RadialBaseKernel(SVMKernel, double) - Constructor for class org.biojava.stats.svm.RadialBaseKernel
-
- radiansPerDegree - Static variable in class org.biojava.bio.structure.Calc
-
Radians per degree.
- RAF - Class in org.biojava.utils.io
-
- RAF(File, String) - Constructor for class org.biojava.utils.io.RAF
-
- RAF(String, String) - Constructor for class org.biojava.utils.io.RAF
-
- raIndexFile - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
- random(int, int) - Static method in class org.biojava.bio.structure.jama.Matrix
-
Generate matrix with random elements
- RandomAccessReader - Class in org.biojava.utils.io
-
RandomAccessReader extends Reader to
provide a means to create buffered Readers from
RandomAccessFiles.
- RandomAccessReader(RandomAccessFile) - Constructor for class org.biojava.utils.io.RandomAccessReader
-
Creates a new RandomAccessReader wrapping the
RandomAccessFile and using a default-sized buffer
(8192 bytes).
- RandomAccessReader(RandomAccessFile, int) - Constructor for class org.biojava.utils.io.RandomAccessReader
-
Creates a new RandomAccessReader wrapping the
RandomAccessFile and using a buffer of the
specified size.
- randomizeDistribution(Distribution) - Static method in class org.biojava.bio.dist.DistributionTools
-
Randomizes the weights of a Distribution.
- RangeLocation - Class in org.biojava.bio.symbol
-
A simple implementation of Location that contains all points between
getMin and getMax inclusive.
- RangeLocation(int, int) - Constructor for class org.biojava.bio.symbol.RangeLocation
-
Construct a new RangeLocation from min to max.
- rangeSelected(AlignedPosition, AlignedPosition) - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
-
- rangeSelected(AlignedPosition, AlignedPosition) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
-
- rank() - Method in class org.biojava.bio.structure.jama.Matrix
-
Matrix rank
- rank() - Method in class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Effective numerical matrix rank
- RANK - Static variable in interface org.biojavax.bio.BioEntryRelationship
-
- RANK - Static variable in interface org.biojavax.bio.seq.RichFeature
-
- RANK - Static variable in interface org.biojavax.bio.seq.RichFeatureRelationship
-
- RANK - Static variable in interface org.biojavax.bio.seq.RichLocation
-
- RANK - Static variable in interface org.biojavax.Comment
-
- RANK - Static variable in interface org.biojavax.Note
-
- RANK - Static variable in interface org.biojavax.RankedCrossRef
-
- RANK - Static variable in interface org.biojavax.RankedDocRef
-
- RANKEDCROSSREF - Static variable in interface org.biojavax.bio.BioEntry
-
- RANKEDCROSSREF - Static variable in interface org.biojavax.ontology.ComparableTerm
-
- RankedCrossRef - Interface in org.biojavax
-
Allows cross-references to other databases to be ranked.
- RankedCrossRefable - Interface in org.biojavax
-
Defines an object as being able to have ranked cross references associated
with it.
- rankedCrossRefs - Variable in class org.biojavax.bio.seq.RichFeature.Template
-
- RANKEDDOCREF - Static variable in interface org.biojavax.bio.BioEntry
-
- RankedDocRef - Interface in org.biojavax
-
Represents a documentary reference.
- RasmolCommandListener - Class in org.biojava.bio.structure.gui
-
a utility class that listens to Ramsol script commands in the @link
BiojavaJmol class
- RasmolCommandListener(BiojavaJmol.JmolPanel, JTextField) - Constructor for class org.biojava.bio.structure.gui.RasmolCommandListener
-
- RAT_NUCLEAR - Static variable in class org.biojava.bio.symbol.CodonPrefTools
-
Rattus norvegicus codon preferences
- RATIO - Static variable in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
-
Constant RATIO indicating a change to the minimum
allowed ratio of long axis to short axis of the features.
- RAW - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
RAW indicates that the alignment format is raw
(symbols only).
- RAW - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
RAW indicates that the sequence format is raw
(symbols only).
- RAW_AA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
RAW_AA premade RAW | AA.
- RAW_DNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
RAW_DNA premade RAW | DNA.
- RAW_RNA - Static variable in class org.biojava.bio.seq.io.AlignIOConstants
-
RAW_RNA premade RAW | RNA.
- rawGet(int) - Method in class org.biojava.utils.FileAsList
-
rawGet reads the record at the specified index as
a raw byte array.
- rbfKernel - Static variable in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
- RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- RC_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- RC_PLASMID_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- RC_SPECIES_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- RC_STRAIN_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- RC_TISSUE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- RC_TRANSP_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- read(File) - Method in interface org.biojava.bio.program.fastq.FastqReader
-
Read zero or more FASTQ formatted sequences from the specified file.
- read(URL) - Method in interface org.biojava.bio.program.fastq.FastqReader
-
Read zero or more FASTQ formatted sequences from the specified url.
- read(InputStream) - Method in interface org.biojava.bio.program.fastq.FastqReader
-
Read zero or more FASTQ formatted sequences from the specified input stream.
- read(BufferedReader, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.Parser
-
- read(BufferedReader) - Method in interface org.biojava.bio.seq.io.AlignmentFormat
-
Read in an alignment from a buffered reader object
- read(BufferedReader) - Method in class org.biojava.bio.seq.io.FastaAlignmentFormat
-
Reads an alignment in FASTA format.
- read(BufferedReader) - Method in class org.biojava.bio.seq.io.MSFAlignmentFormat
-
Reads an MSF Alignment File
- read(BufferedReader) - Static method in class org.biojava.bio.structure.jama.Matrix
-
Read a matrix from a stream.
- read() - Method in class org.biojava.utils.io.CachingInputStream
-
- read(byte[], int, int) - Method in class org.biojava.utils.io.CachingInputStream
-
- read() - Method in class org.biojava.utils.io.CountedBufferedReader
-
- read(char[]) - Method in class org.biojava.utils.io.CountedBufferedReader
-
- read(char[], int, int) - Method in class org.biojava.utils.io.CountedBufferedReader
-
- read() - Method in class org.biojava.utils.io.RandomAccessReader
-
read reads one byte from the underlying
RandomAccessFile.
- read(char[], int, int) - Method in class org.biojava.utils.io.RandomAccessReader
-
read reads from the underlying
RandomAccessFile into an array.
- read() - Method in class org.biojava.utils.io.UncompressInputStream
-
- read(byte[], int, int) - Method in class org.biojava.utils.io.UncompressInputStream
-
- read() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
- readableFileNames - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- readableFiles - Static variable in class org.biojavax.bio.seq.io.FastaFormat
-
- readableFiles - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- readColourMap() - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
Read the the properties file that specifies the character/colour mapping.
- readColourMapFromProperties(String) - Method in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
Setup styles from java property file.
- readDBDate() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readDBDate reads the date from the index
header.
- readDBName() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readDBName returns the database name from the
index header.
- readDBRelease() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readDBRelease returns the database release from
the index header.
- readEmbl(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an EMBL-format stream.
- readEMBL(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a EMBL file using a custom type of SymbolList.
- readEMBLDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an EMBL-format stream of DNA sequences.
- readEmblNucleotide(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an EMBL-format stream.
- readEMBLProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an EMBL-format stream of Protein
sequences.
- readEmblRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an EMBL-format stream, but for RNA.
- readEMBLRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an EMBL-format stream of RNA sequences.
- readEMBLxml(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a EMBLxml file using a custom type of SymbolList.
- readEMBLxmlDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an EMBLxml-format stream of DNA
sequences.
- readEMBLxmlProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an EMBLxml-format stream of Protein
sequences.
- readEMBLxmlRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an EMBLxml-format stream of RNA
sequences.
- ReaderInputHandler - Class in org.biojava.utils.process
-
- ReaderInputHandler(Reader, String) - Constructor for class org.biojava.utils.process.ReaderInputHandler
-
Initializes the reader input handler.
- ReaderWriterPipe - Class in org.biojava.utils.process
-
A multi threaded class
which pipes the contents of an input reader to an output
writer.
- ReaderWriterPipe(Reader, Writer, String) - Constructor for class org.biojava.utils.process.ReaderWriterPipe
-
Initializes the reader writer pipe.
- readFasta(BufferedReader, SymbolTokenization) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Read a fasta file.
- readFasta(BufferedReader, SymbolTokenization, SequenceBuilderFactory) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Read a fasta file using a custom type of SymbolList.
- readFasta(InputStream, Alphabet) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Create a sequence database from a fasta file provided as an
input stream.
- readFasta(BufferedReader, SymbolTokenization, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a fasta file.
- readFasta(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a fasta file building a custom type of RichSequence
.
- readFastaDNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an FASTA-format stream of DNA sequences.
- readFastaDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an FASTA-format stream of DNA
sequences.
- readFastaProtein(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an FASTA-format stream of Protein sequences.
- readFastaProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an FASTA-format stream of Protein
sequences.
- readFastaRNA(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an FASTA-format stream of RNA sequences.
- readFastaRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an FASTA-format stream of RNA
sequences.
- readFile(File, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Guess which format a file is then attempt to read it.
- readFile(File, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Guess which format a file is then attempt to read it.
- readFileLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readFileLength returns the file length in bytes
(stored within the file's header by the indexing program).
- readFromXML(InputStream) - Static method in class org.biojava.bio.dist.DistributionTools
-
Read a distribution from XML.
- readFromXML(InputStream, String) - Static method in class org.biojava.bio.symbol.CodonPrefTools
-
reads a specified CodonPref from an file.
- readFromXML(InputStream) - Static method in class org.biojava.bio.symbol.CodonPrefTools
-
- readFromXML(InputStream, CodonPrefFilter) - Static method in class org.biojava.bio.symbol.CodonPrefTools
-
read an CodonPref XML stream and handle it with a CodonPrefFilter object.
- readGenbank(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an Genbank-format stream.
- readGenbank(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a GenBank file using a custom type of SymbolList.
- readGenbankDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an GenBank-format stream of DNA
sequences.
- readGenbankProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an GenBank-format stream of Protein
sequences.
- readGenbankRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an GenBank-format stream of RNA
sequences.
- readGenbankXml(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an GenbankXML-format stream.
- readGenpept(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an Genpept-format stream.
- readGFF(String) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Deprecated.
use: readGff(File)
- readGFF(String, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Deprecated.
use: readGff(File,GFFRecordFilter)
- readGFF(File) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Reads a GFFEntrySet from a file with no filtering.
- readGFF(File, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Reads a GFFEntrySet from a file with the specified filter.
- readGFF(BufferedReader) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Read all GFF entries from a buffered reader.
- readGFF(BufferedReader, GFFRecordFilter) - Static method in class org.biojava.bio.program.gff.GFFTools
-
Read all GFF entries matching a filter from a buffered reader.
- readHashedFastaDNA(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an FASTA-format stream of DNA
sequences.
- readingFrame - Variable in class org.biojava.bio.seq.FramedFeature.Template
-
- readINSDseq(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a INSDseq file using a custom type of SymbolList.
- readINSDseqDNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an INSDseq-format stream of DNA
sequences.
- readINSDseqProtein(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an INSDseq-format stream of Protein
sequences.
- readINSDseqRNA(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an INSDseq-format stream of RNA
sequences.
- readLine() - Method in class org.biojava.utils.io.CountedBufferedReader
-
- readMatrix(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
-
- readModel(Element) - Static method in class org.biojava.bio.dp.XmlMarkovModel
-
- readModelFile(String) - Static method in class org.biojava.stats.svm.tools.SVM_Light
-
- readName(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader
-
Reads the next entry from the names.dmp file and returns the corresponding
NCBITaxon object with the name added in already.
- readName(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
-
Reads the next entry from the names.dmp file and returns the corresponding
NCBITaxon object with the name added in already.
- readNode(BufferedReader) - Method in interface org.biojavax.bio.taxa.io.NCBITaxonomyLoader
-
Reads the next entry from the nodes.dmp file and returns the corresponding
NCBITaxon object.
- readNode(BufferedReader) - Method in class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
-
Reads the next entry from the nodes.dmp file and returns the corresponding
NCBITaxon object.
- readPhredQuality(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools
-
Constructs a StreamReader to read in Phred quality data in FASTA format.
- readPhredSequence(BufferedReader) - Static method in class org.biojava.bio.program.phred.PhredTools
-
Calls SeqIOTools.readFastaDNA(br), added here for convinience.
- readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.ontology.obo.OboFileParser
-
- readRawRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readRawRecord returns the raw bytes of a single
record from the index.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumHitReader
-
readRecord creates an array of Objects from the
raw byte array of a single record.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.AcnumTrgReader
-
readRecord creates an array of Objects from the
raw byte array of a single record.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.DivisionLkpReader
-
readRecord creates an array of Objects from the
raw byte array of a single record.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readRecord returns an array of objects parsed from
a single record.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
readRecord returns an array of objects parsed from
a single record.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamIdxReader
-
readRecord creates an array of Objects from the
raw byte array of a single record.
- readRecord() - Method in class org.biojava.bio.seq.db.emblcd.EntryNamRandomAccess
-
readRecord creates an array of Objects from the
raw byte array of a single record.
- readRecordCount() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readRecordCount returns the number of records in
the file.
- readRecordLength() - Method in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
readRecordLength returns the record length
(bytes).
- readResolve() - Method in class org.biojava.bio.proteomics.Protease
-
Prevent duplication of the object during Serialization
- readResolve() - Method in class org.biojava.bio.symbol.AbstractAlphabet
-
To prevent duplication of a what should be a
single instance of an existing alphabet.
- readResolve() - Method in class org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet
-
To prevent duplication of a what should be a
single instance of an existing alphabet.
- readResolve() - Method in class org.biojava.utils.StaticMemberPlaceHolder
-
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readRichSequence(BufferedReader, SymbolTokenization, RichSeqIOListener, Namespace) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.program.phred.PhredFormat
-
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
Reads information from a flatfile to a SeqIOListener
using a SymbolTokenizer to convert sequence strings
to Symbol objects.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GAMEFormat
-
this version only reads annotations (no symbols)
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
Reads a sequence from the specified reader using the Symbol
parser and Sequence Factory provided.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojava.bio.seq.io.GenbankXmlFormat
-
Deprecated.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in interface org.biojava.bio.seq.io.SequenceFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.GenbankFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.INSDseqFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readSequence(BufferedReader, SymbolTokenization, SeqIOListener) - Method in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
Read a sequence and pass data on to a SeqIOListener.
- readStream(BufferedInputStream, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Guess which format a stream is then attempt to read it.
- readStream(BufferedInputStream, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Guess which format a stream is then attempt to read it.
- readSwissprot(BufferedReader) - Static method in class org.biojava.bio.seq.io.SeqIOTools
-
Deprecated.
Iterate over the sequences in an Swissprot-format stream.
- readSymbol() - Method in interface org.biojava.bio.seq.io.SymbolReader
-
Return a single symbol from the stream.
- readSymbols(Symbol[], int, int) - Method in interface org.biojava.bio.seq.io.SymbolReader
-
Read one or more symbols from the stream.
- readUniProt(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a UniProt file using a custom type of SymbolList.
- readUniProt(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an UniProt-format stream of RNA
sequences.
- readUniProtXML(BufferedReader, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Read a UniProt XML file using a custom type of SymbolList.
- readUniProtXML(BufferedReader, Namespace) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Iterate over the sequences in an UniProt XML-format stream of RNA
sequences.
- readXFF(File, String, FiniteAlphabet) - Static method in class org.biojava.bio.program.xff.XFFTools
-
- readXFF(File, String) - Static method in class org.biojava.bio.program.xff.XFFTools
-
- readXMLChunk(BufferedReader, DefaultHandler, String) - Static method in class org.biojavax.utils.XMLTools
-
Attempts to read XML file in chunks, passing each chunk to a SAX parser.
- ready() - Method in class org.biojava.utils.io.CountedBufferedReader
-
- realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.program.das.DASSequence
-
- realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.FeatureRealizer
-
Install a feature on the specified sequence.
- realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- realizeFeature(FeatureHolder, Feature.Template) - Method in interface org.biojava.bio.seq.RealizingFeatureHolder
-
Realize a feature template.
- realizeFeature(FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- realizeFeature(Sequence, FeatureHolder, Feature.Template) - Method in class org.biojava.bio.seq.SimpleFeatureRealizer
-
- realizeSubFeatures(Feature) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
recursively attach children features to parent
- RealizingFeatureHolder - Interface in org.biojava.bio.seq
-
Interface for FeatureHolder objects which know how to
instantiate new child Features.
- reapGarbageListeners() - Method in class org.biojava.utils.ChangeSupport
-
Remove all references to listeners which have been cleared by the
garbage collector.
- REBASE_DATA_KEY - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_DATA_KEY the ResourceBundle key which
specifies the location of the REBASE flat file.
- REBASE_TAG_COMM - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_COMM the REBASE tag containing the
commercial suppliers.
- REBASE_TAG_ISZR - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_ISZR the REBASE tag containing the
enzyme isoschizomers.
- REBASE_TAG_METH - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_METH the REBASE tag containing the
methylation site.
- REBASE_TAG_NAME - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_NAME the REBASE tag containing the
enzyme name.
- REBASE_TAG_ORGN - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_ORGN the REBASE tag containing the
organism.
- REBASE_TAG_REFS - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_REFS the REBASE tag containing the
references.
- REBASE_TAG_SITE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_SITE the REBASE tag containing the
enzyme site.
- REBASE_TAG_SRCE - Static variable in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
REBASE_TAG_SRCE the REBASE tag containing the
source.
- rebind(Name, Object) - Method in class org.biojava.naming.ObdaContext
-
- rebind(Name, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
-
- rebind(String, Object) - Method in class org.biojava.naming.ObdaContext
-
- rebind(String, Object, Attributes) - Method in class org.biojava.naming.ObdaContext
-
- recBytes - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
- receiveSequence(String) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
-
- receiveSequence(String) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
-
Receive sequence data for the current sequence.
- Record - Interface in org.biojava.bio.program.indexdb
-
Record represents a record within an indexed flat file
databank as defined by the OBDA standard.
- Record.Impl - Class in org.biojava.bio.program.indexdb
-
Impl is the default implementation of Record.
- Record.Impl(String, RAF, long, int) - Constructor for class org.biojava.bio.program.indexdb.Record.Impl
-
Creates a new Impl record.
- recordEmittedSymbol(State, Symbol, double) - Method in interface org.biojava.bio.dp.HMMTrainer
-
record that the specified symbol was emitted from the specified state.
- recordEmittedSymbol(State, Symbol, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
-
- recordLength - Variable in class org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord
-
- recordLine(GFFRecord) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
-
A record line has been encountered.
- recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFFilterer
-
Only forward the GFFRecords that match a filter.
- recordLine(GFFRecord) - Method in class org.biojava.bio.program.gff.GFFWriter
-
Prints record to the PrintWriter.
- recordLine(GFF3Record) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
-
A record line has been encountered.
- recordTransition(State, State, double) - Method in interface org.biojava.bio.dp.HMMTrainer
-
record that a transition was observed between the specified states.
- recordTransition(State, State, double) - Method in class org.biojava.bio.dp.SimpleHMMTrainer
-
- recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
- recParser - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMRandomAccess
-
A recParser for implementing
readRecord() specific to each concrete subclass.
- RECT - Static variable in interface org.biojava.bio.gui.sequence.ImageMap
-
RECT indicates a rectangular image map hotspot.
- rect - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
- rect - Variable in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
- RectangleGlyph - Class in org.biojava.bio.gui.glyph
-
A Glyph that paints a rectangle shape within the bounds.
- RectangleGlyph() - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
-
- RectangleGlyph(Rectangle2D.Float) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
-
- RectangleGlyph(Paint) - Constructor for class org.biojava.bio.gui.glyph.RectangleGlyph
-
- RectangularBeadRenderer - Class in org.biojava.bio.gui.sequence
-
RectangularBeadRenderer renders features as simple
rectangles.
- RectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
Creates a new RectangularBeadRenderer with the
default settings.
- RectangularBeadRenderer(double, double, Paint, Paint, Stroke) - Constructor for class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
Creates a new RectangularBeadRenderer.
- RectangularImapRenderer - Class in org.biojava.bio.gui.sequence
-
RectangularImapRenderer is a decorator for
RectangularBeadRenderer which adds the ability to
create HTML image map coordinates which correspond to the feature
rendering produced by the RectangularBeadRenderer.
- RectangularImapRenderer(RectangularBeadRenderer, ImageMap, URLFactory) - Constructor for class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
Creates a new RectangularImapRenderer.
- RECURSE - Static variable in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- recurse - Variable in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- RECURSE - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
Constant RECURSE indicating a change to the
renderer's filter recursion flag.
- recurse - Variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
recurse indicates whether the filter should
recurse through any subfeatures.
- reduceFragments(List<FragmentPair>, FragmentPair, Matrix) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
In helices often many similar fragments can be found.
- reduceInitialFragments() - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
if this is set to false, the time spent to joint the initial fragments (step 2)
is increased.
- REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- REF_ACCESSION_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- REF_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- REF_POS_BEGIN_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- REF_POS_END_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- REF_XREF_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- REFERENCE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
- REFERENCE_LOCATION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- REFERENCE_POSITION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- REFERENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- REFERENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- REFERENCE_XREF_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- ReferenceAnnotation - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- ReferenceAnnotation() - Constructor for class org.biojava.bio.seq.io.ReferenceAnnotation
-
Deprecated.
- REFERENCES_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- ReferenceServer - Class in org.biojava.bio.program.das
-
Reflects a reference server on the DAS network.
- refine(StrucAligParameters, Atom[], Atom[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
Refinement procedure based on superposition and dynamic programming.
- Refine - Class in org.biojava.bio.structure.io.mmcif.model
-
- Refine() - Constructor for class org.biojava.bio.structure.io.mmcif.model.Refine
-
- REFLEXIVE - Static variable in class org.biojava.ontology.OntoTools
-
- refp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- refRange - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- refreshSequencePanels() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- REFSEQ - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
REFSEQ indicates that the sequence format is
REFSEQ.
- REFSEQ_AA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
REFSEQ_AA premade REFSEQ | AA.
- REFSEQ_DNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
REFSEQ_DNA premade REFSEQ | DNA.
- REFSEQ_RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
REFSEQ_RNA premade REFSEQ | RNA.
- RegexChanger - Class in org.biojava.bio.program.tagvalue
-
A ValueChanger.Changer that returns a specific match value using a regex
Pattern.
- RegexChanger(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexChanger
-
Create a new RegexChanger with a pattern.
- RegexException - Exception in org.biojava.utils.regex
-
An exception thrown by classes of this package.
- RegexException(String) - Constructor for exception org.biojava.utils.regex.RegexException
-
- RegexException(Throwable) - Constructor for exception org.biojava.utils.regex.RegexException
-
- RegexException(Throwable, String) - Constructor for exception org.biojava.utils.regex.RegexException
-
- RegexFieldFinder - Class in org.biojava.bio.program.tagvalue
-
- RegexFieldFinder(TagValueListener, Pattern, String[], boolean) - Constructor for class org.biojava.bio.program.tagvalue.RegexFieldFinder
-
Creates a new RegexFiledFinder.
- RegexParser - Class in org.biojava.bio.program.tagvalue
-
A TagValueParser that splits a line based upon a regular expression.
- RegexParser() - Constructor for class org.biojava.bio.program.tagvalue.RegexParser
-
Create a new RegexParser with all boolean values set to false.
- RegexSplitter - Class in org.biojava.bio.program.tagvalue
-
A ValueChanger.Splitter that splits a line of text using a regular
expression, returning one value per match.
- RegexSplitter(Pattern, int) - Constructor for class org.biojava.bio.program.tagvalue.RegexSplitter
-
Create a new RegexSplitter with a pattern.
- regions - Variable in class org.biojava.bio.seq.RemoteFeature.Template
-
- register(RestrictionEnzyme, Set) - Static method in class org.biojava.bio.molbio.RestrictionEnzymeManager
-
register regisiters a new
RestrictionEnzyme with the manager.
- registerAlphabet(String, Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Register an alphabet by name.
- registerAlphabet(String[], Alphabet) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Register and Alphabet by more than one name.
- registerCollectionHandlerFactory(String, String, XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
-
Register a factory used to create handlers for the specified tag in an
XML AnnotationType
- registerDistribution(Distribution) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Register a distribution object with this context.
- registerDistribution(Distribution) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- registered(String) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
Has a Protease been registered with that name?
- registered(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Has an Alphabet been registered by that name
- registerFactory(UnigeneFactory) - Static method in class org.biojava.bio.program.unigene.UnigeneTools
-
Register a UnigeneFactory.
- registerFormat(Class) - Static method in class org.biojavax.bio.seq.RichSequence.IOTools
-
Register a new format with IOTools for auto-guessing.
- registerHandlerFactory(String, String, XMLFilterHandler.FilterHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterHandler
-
Register a factory used to create handlers for the specified tag name
- registerModel(MarkovModel) - Method in interface org.biojava.bio.dp.ModelTrainer
-
Registers an HMM with this trainer.
- registerModel(MarkovModel) - Method in class org.biojava.bio.dp.SimpleModelTrainer
-
- registerPropertyHandlerFactory(String, String, XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
-
Register a factory used to create handlers for the specified tag in an
XML AnnotationType
- registerProtease(Protease) - Static method in class org.biojava.bio.proteomics.ProteaseManager
-
Registers a protease and ensures its flyweight status
- registerTrainer(Distribution, DistributionTrainer) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Register a Distribution and an associated DistributionTrainer object.
- registerTrainer(Distribution, DistributionTrainer) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractDistribution
-
Register an IgnoreCountsTrainer instance as the trainer for this
distribution.
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
- registerWithTrainer(DistributionTrainerContext) - Method in interface org.biojava.bio.dist.Distribution
-
Register this distribution with a training context.
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.GapDistribution
-
- registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dist.PairDistribution
-
Register this paired distribution with a model trainer.
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.PairDistribution
-
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.SimpleDistribution
-
Register an SimpleDistribution.Trainer instance as the trainer for this distribution.
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UniformDistribution
-
- registerWithTrainer(DistributionTrainerContext) - Method in class org.biojava.bio.dist.UntrainableDistribution
-
- registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- registerWithTrainer(ModelTrainer) - Method in interface org.biojava.bio.dp.Trainable
-
Perform any registration that is necessary with mt.
- registerWithTrainer(ModelTrainer) - Method in class org.biojava.bio.dp.WMAsMM
-
- registrations() - Static method in class org.biojava.bio.symbol.AlphabetManager
-
A set of names under which Alphabets have been registered.
- Registry - Class in org.biojava.directory
-
Registry is a factory which gets implementations of
the BioJava SequenceDBLite interface.
- Registry(RegistryConfiguration) - Constructor for class org.biojava.directory.Registry
-
Creates a new OBDA Registry with the specified
configuration.
- RegistryConfiguration - Interface in org.biojava.directory
-
The BioDirectory Registry is a simple system for specifying
where to find services which provide sequence databases.
- RegistryConfiguration.Composite - Class in org.biojava.directory
-
A RegistryConfiguration that allows you to treat other
configurations as providing important or default configuration
information.
- RegistryConfiguration.Composite() - Constructor for class org.biojava.directory.RegistryConfiguration.Composite
-
- RegistryConfiguration.Impl - Class in org.biojava.directory
-
A simple implementation of RegistryConfiguration backed by a Map.
- RegistryConfiguration.Impl(String, Map) - Constructor for class org.biojava.directory.RegistryConfiguration.Impl
-
- RegistryException - Exception in org.biojava.directory
-
A RegistryException thrown when the registry cannot
find an implementation of a requested SequenceDB.
- RegistryException() - Constructor for exception org.biojava.directory.RegistryException
-
Creates a new RegistryException with no detail
message.
- RegistryException(String) - Constructor for exception org.biojava.directory.RegistryException
-
Creates a new RegistryException with the specified
detail message.
- RegistryException(Throwable) - Constructor for exception org.biojava.directory.RegistryException
-
Creates a new RegistryException with no detail
message, wrapping another Throwable.
- RegistryException(Throwable, String) - Constructor for exception org.biojava.directory.RegistryException
-
Deprecated.
use new RegistryException(message, cause)
- RegistryException(String, Throwable) - Constructor for exception org.biojava.directory.RegistryException
-
- REL_SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
-
- RelabeledAlignment - Class in org.biojava.bio.symbol
-
An alignment that relabels another alignment.
- RelabeledAlignment(Alignment) - Constructor for class org.biojava.bio.symbol.RelabeledAlignment
-
- RELATED_SYNONYM - Static variable in class org.biojava.ontology.Synonym
-
- RELATION - Static variable in class org.biojava.ontology.OntoTools
-
- RELATION - Static variable in interface org.biojavax.bio.seq.RichFeature
-
- RELATIONS - Static variable in interface org.biojavax.bio.BioEntry
-
- RELATIONSHIP - Static variable in class org.biojava.ontology.obo.OboFileHandler
-
- REMARK - Static variable in interface org.biojavax.DocRef
-
- REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- REMARK_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- RemoteFeature - Interface in org.biojava.bio.seq
-
A feature that indicates that there is some remote feature that can't be
represented entirely on a single Sequence.
- RemoteFeature.Region - Class in org.biojava.bio.seq
-
A tuple of Location and sequence ID.
- RemoteFeature.Region(Location, String, boolean) - Constructor for class org.biojava.bio.seq.RemoteFeature.Region
-
Create a new Region.
- RemoteFeature.Resolver - Interface in org.biojava.bio.seq
-
The interface for objects that actually can take a RemoteFeature and
return a Sequence object with the feature resolved into a real feature.
- RemoteFeature.Template - Class in org.biojava.bio.seq
-
- RemoteFeature.Template() - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
-
- RemoteFeature.Template(Feature.Template) - Constructor for class org.biojava.bio.seq.RemoteFeature.Template
-
Creates a RemoteFeature.Template that has the same values as the
template passed in.
- RemoteTerm - Interface in org.biojava.ontology
-
A term in another ontology.
- RemoteTerm.Impl - Class in org.biojava.ontology
-
Simple in-memory implementation of a remote ontology term.
- RemoteTerm.Impl(Ontology, Term, String) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
-
- RemoteTerm.Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.ontology.RemoteTerm.Impl
-
- remove() - Method in class org.biojava.bio.dp.DP.ReverseIterator
-
- remove() - Method in class org.biojava.bio.structure.AtomIterator
-
does nothing.
- remove() - Method in class org.biojava.bio.structure.GroupIterator
-
does nothing .
- remove() - Method in class org.biojava.bio.symbol.Alignment.SymbolListIterator
-
- remove(Object) - Method in interface org.biojava.utils.cache.CacheMap
-
Explicitly remove an object.
- remove(Object) - Method in class org.biojava.utils.cache.FixedSizeMap
-
- remove(Object) - Method in class org.biojava.utils.cache.WeakCacheMap
-
- remove() - Method in class org.biojava.utils.MergingIterator
-
- remove(Object) - Method in class org.biojava.utils.MergingSet
-
- remove(Object) - Method in class org.biojavax.ga.util.WeightedSet
-
- REMOVE_LABEL - Static variable in interface org.biojava.bio.alignment.ARAlignment
-
- removeActivityListener(ActivityListener) - Static method in class org.biojava.bio.program.das.DAS
-
- removeAllOrganisms() - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- removeAllOrganisms() - Method in interface org.biojavax.ga.Population
-
Removes all the Organisms in this Population
- removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- removeAllOrganismsImpl() - Method in class org.biojavax.ga.impl.SimplePopulation
-
- removeAnnotation(Annotation) - Method in class org.biojava.bio.MergeAnnotation
-
Remove an Annotation from the list.
- removeAnnotationDB(AnnotationDB) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
Remove a DB from this view.
- removeAnnotationSource(URL) - Method in class org.biojava.bio.program.das.DASSequence
-
- removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractBioEntryDB
-
- removeBioEntry(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- removeBioEntry(String) - Method in interface org.biojavax.bio.db.BioEntryDBLite
-
Remove the BioEntry associated with an ID from the database.
- removeBioEntry(String) - Method in class org.biojavax.bio.db.biosql.BioSQLBioEntryDB
-
- removeBioEntry(String) - Method in class org.biojavax.bio.db.HashBioEntryDB
-
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
removeChangeListener removes a listener.
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
removeChangeListener removes a listener.
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
removeChangeListener removes a listener.
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
removeChangeListener removes a listener.
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.program.das.ReferenceServer
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.program.das.ReferenceServer
-
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- removeChangeListener(ChangeListener) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- removeChangeListener(Feature, ChangeListener, ChangeType) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Remove a ChangeListener from a projected feature.
- removeChangeListener(Feature, ChangeListener, ChangeType) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- removeChangeListener(ChangeListener) - Method in class org.biojava.utils.AbstractChangeable
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.AbstractChangeable
-
- removeChangeListener(ChangeListener) - Method in interface org.biojava.utils.Changeable
-
Deprecated.
use removeChangeListener(cl, ChangeType.UNKNOWN)
- removeChangeListener(ChangeListener, ChangeType) - Method in interface org.biojava.utils.Changeable
-
Remove a listener that was interested in a specific types of changes.
- removeChangeListener(ChangeListener) - Method in class org.biojava.utils.ChangeSupport
-
Remove a listener that was interested in all types of changes.
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.ChangeSupport
-
Remove a listener that was interested in a specific types of changes.
- removeChangeListener(ChangeListener) - Method in class org.biojava.utils.Unchangeable
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojava.utils.Unchangeable
-
- removeChangeListener(ChangeListener) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Remove a listener that was interested in all types of changes.
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Remove a listener that was interested in a specific types of changes.
- removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- removeChangeListener(ChangeListener) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- removeChangeListener(ChangeListener, ChangeType) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- removeChild(Taxon, Taxon) - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.
Remove a Taxon as a child to this one.
- removeChild(Taxon, Taxon) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- removeComment(Comment) - Method in interface org.biojavax.bio.BioEntry
-
Removes a comment instance from this bioentry.
- removeComment(Comment) - Method in class org.biojavax.bio.SimpleBioEntry
-
Removes a comment instance from this bioentry.
- removeComponent(Location) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- removeComponent(ComponentFeature) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
-
- removeDataSource(DistDataSource) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
Remove a distributed data source.
- removeDelegateRenderer(OptimizableFilter) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
removeDelegateRenderer removes any association
of the given OptimizableFilter with a
BeadFeatureRenderer.
- removeDescriptor(ComparableTerm) - Method in interface org.biojavax.ontology.ComparableTriple
-
Removes a descriptor.
- removeDescriptor(ComparableTerm) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Removes a descriptor.
- removeEnzyme(RestrictionEnzyme) - Method in class org.biojava.bio.molbio.RestrictionMapper
-
removeEnzyme removes an enzyme from those to be
searched for in the Sequence.
- removeFeature(Feature) - Method in class org.biojava.bio.program.das.DASSequence
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.AbstractFeatureHolder
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.FeatureHolder.EmptyFeatureHolder
-
- removeFeature(Feature) - Method in interface org.biojava.bio.seq.FeatureHolder
-
Remove a feature from this FeatureHolder.
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.DummySequence
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.LazyFilterFeatureHolder
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.RevCompSequence
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
Remove a feature attached to this sequence.
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
Remove a feature from this sequence.
- removeFeature(Feature) - Method in class org.biojava.bio.seq.LazyFeatureHolder
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeature
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ProjectedFeatureHolder
-
- removeFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Remove the dying child.
- removeFeature(Feature, Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Remove the dying child.
- removeFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- removeFeature(Feature, Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- removeFeature(Feature) - Method in class org.biojava.bio.seq.SimpleFeatureHolder
-
- removeFeature(Feature) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Remove a feature from this FeatureHolder.
- removeFeature(Feature) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Remove a feature from this FeatureHolder.
- removeFeatureHolder(FeatureHolder) - Method in class org.biojava.bio.seq.MergeFeatureHolder
-
Remove a FeatureHolder from the set of FeatureHolders which
are merged.
- removeFeatureRelationship(RichFeatureRelationship) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
-
Removes a relationship from this feature holder.
- removeFeatureRelationship(RichFeatureRelationship) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Removes a relationship from this feature holder.
- removeFilterWithGlyph(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- removeForwarder(ChangeForwarder, ChangeType) - Method in class org.biojava.utils.Unchangeable
-
- removeFromEnvironment(String) - Method in class org.biojava.naming.ObdaContext
-
- removeGap(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Remove a single gap at position pos in this GappedSymbolList.
- removeGap(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- removeGaps(GappedSymbolList, int, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
because there is a bug in GappedSymbolList
- removeGaps(int, int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Remove some gaps at position pos in this GappedSymbolList.
- removeGaps(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- removeGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes the genetic code annotation from the taxon in the database.
- removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- removeItem(Object) - Method in class org.biojava.stats.svm.AbstractSVMTarget
-
- removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- removeItem(Object) - Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- removeItem(Object) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- removeItem(Object) - Method in interface org.biojava.stats.svm.SVMTarget
-
- removeKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
removeKey removes the specified
key.
- removeKeyPath(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
Remove a key.
- removeLabelString(String) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Remove a piece of text from the label
- removeLeftValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes the left value from the specified taxon in the database.
- removeListener(Object, ChangeListener, ChangeType) - Method in interface org.biojava.utils.ChangeHub
-
remove a ChangeListener associated with given key.
- removeListener(Object, ChangeListener, ChangeType) - Method in class org.biojava.utils.IndexedChangeHub
-
- removeMitochondrialGeneticCodeID(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes the so called mitochondrial genetic code annotation from the given taxon.
- removeMMcifConsumer(MMcifConsumer) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifParser
-
remove a single consumer from the parser
- removeMMcifConsumer(MMcifConsumer) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- removeName(Connection, DBHelper, Taxon, String, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes the specified name from of the taxon from the database.
- removeName(String, String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Removes the name from the given name class.
- removeName(String, String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Removes the name from the given name class.
- removeNote(Note) - Method in class org.biojavax.EmptyRichAnnotation
-
Removes a note from this annotation.
- removeNote(Note) - Method in interface org.biojavax.RichAnnotation
-
Removes a note from this annotation.
- removeNote(Note) - Method in class org.biojavax.SimpleRichAnnotation
-
Removes a note from this annotation.
- removeOrganism(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- removeOrganism(Organism) - Method in interface org.biojavax.ga.Population
-
Kills off the organism
- removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- removeOrganismImpl(Organism) - Method in class org.biojavax.ga.impl.SimplePopulation
-
- removeOrganisms(Organism[]) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- removeOrganisms(Set) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- removeOrganisms(Organism[]) - Method in interface org.biojavax.ga.Population
-
Removes all the Organisms in orgs
- removeOrganisms(Set) - Method in interface org.biojavax.ga.Population
-
Removes all the Organisms in orgs
- removeOrthologue(Orthologue) - Method in interface org.biojava.bio.program.homologene.OrthologueSet
-
Remove an orthologue from the set.
- removeOrthologue(Orthologue) - Method in class org.biojava.bio.program.homologene.SimpleOrthologueSet
-
- removeOrthoPair(OrthoPair) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
removes a specified OrthoPair relationship
from this group.
- removeOrthoPair(OrthoPair) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.program.phred.PhredFormat
-
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.EmblProcessor
-
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.GenbankProcessor
-
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
- removeParseErrorListener(ParseErrorListener) - Method in interface org.biojava.utils.ParseErrorSource
-
Removes a parse error listener from the list of listeners.
- removeProperty(Object) - Method in class org.biojava.bio.AbstractAnnotation
-
- removeProperty(Object) - Method in interface org.biojava.bio.Annotation
-
Delete a property.
- removeProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- removeProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
-
Remove a value from the specified property slot.
- removeProperty(Object) - Method in class org.biojava.bio.MergeAnnotation
-
- removeProperty(Object) - Method in class org.biojava.bio.OverlayAnnotation
-
- removeProperty(Object) - Method in class org.biojavax.EmptyRichAnnotation
-
Delete a property.
- removeProperty(Object) - Method in class org.biojavax.SimpleRichAnnotation
-
Deprecated.
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
-
Deprecated.
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
-
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.StackedLogoPainter
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
-
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class org.biojava.bio.gui.TextLogoPainter
-
- removeRank(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Removes the rank persistently from the taxon in the database.
- removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Removes a ranked cross reference from the existing set.
- removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.SimpleBioEntry
-
Removes a ranked cross reference from the existing set.
- removeRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Removes a ranked cross reference from the existing set.
- removeRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.RankedCrossRefable
-
Removes a ranked cross reference from the existing set.
- removeRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.BioEntry
-
Removes a ranked docref instance from this bioentry.
- removeRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.SimpleBioEntry
-
Removes a ranked docref instance from this bioentry.
- removeRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.BioEntry
-
Removes a relation instance from this bioentry.
- removeRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.SimpleBioEntry
-
Removes a relation instance from this bioentry.
- removeRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularMLR
-
- removeRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
removeRenderer removes a renderer.
- removeRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
removeRenderer removes a renderer.
- removeRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
-
- removeRepository(FeatureTypes.Repository) - Static method in class org.biojava.bio.seq.FeatureTypes
-
Remove a repository from FeaturTypes.
- removeRichSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- removeRichSequence(String) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceDB
-
- removeRichSequence(String) - Method in interface org.biojavax.bio.db.RichSequenceDBLite
-
Remove the RichSequence associated with an ID from the database.
- removeRightValue(Connection, DBHelper, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes the right value from the specified taxon in the database.
- removeSecondaryKey(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
-
Remove a secondary key.
- removeSequence(Object) - Method in interface org.biojava.bio.alignment.ARAlignment
-
- removeSequence(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- removeSequence(String) - Method in class org.biojava.bio.program.das.DASSequenceDB
-
- removeSequence(String) - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
-
- removeSequence(String) - Method in class org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB
-
- removeSequence(String) - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- removeSequence(String) - Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- removeSequence(String) - Method in class org.biojava.bio.seq.db.flat.FlatSequenceDB
-
removeSequence always throws a
ChangeVetoException as this implementation is
immutable.
- removeSequence(String) - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- removeSequence(String) - Method in interface org.biojava.bio.seq.db.SequenceDBLite
-
Remove the sequence associated with an ID from the database.
- removeSequence(String) - Method in class org.biojava.bio.seq.db.WebSequenceDB
-
Not supported, you can't remove a sequence from a WebDB!
- removeSequence(String) - Method in class org.biojava.bio.seq.distributed.DistributedSequenceDB
-
- removeSequence(String) - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- removeSequence(String) - Method in class org.biojavax.bio.db.HashRichSequenceDB
-
- removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
removeSequenceViewerListener removes a listener
for mouse click SequenceViewerEvents.
- removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerSupport
-
- removeSequenceViewerListener(SequenceViewerListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
removeSequenceViewerListener removes a listener
for mouse click SequenceViewerEvents.
- removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
addSequenceViewerMotionListener removes a listener for
mouse motion SequenceViewerEvents.
- removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
-
- removeSequenceViewerMotionListener(SequenceViewerMotionListener) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
addSequenceViewerMotionListener removes a listener for
mouse motion SequenceViewerEvents.
- removeSet(Set) - Method in class org.biojava.utils.MergingSet
-
- removeState(State) - Method in interface org.biojava.bio.dp.MarkovModel
-
Remove a state from the model.
- removeState(State) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- removeState(State) - Method in class org.biojava.bio.dp.WMAsMM
-
- removeSymbol(Symbol) - Method in interface org.biojava.bio.symbol.FiniteAlphabet
-
Remove a symbol from this alphabet.
- removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- removeSymbol(Symbol) - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
SoftMaskedAlphabets cannot remove Symbols.
- removeSynonym(Object) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- removeSynonym(Object) - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- removeSynonym(Object) - Method in class org.biojava.ontology.RemoteTerm.Impl
-
- removeSynonym(Object) - Method in class org.biojava.ontology.Term.Impl
-
- removeSynonym(Object) - Method in interface org.biojava.ontology.Term
-
Remove a synonym for this term.
- removeSynonym(Object) - Method in class org.biojava.ontology.Triple.Impl
-
- removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Remove a synonym for this term.
- removeSynonym(Object) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Remove a synonym for this term.
- removeTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
Remove a tag so that it will not be retained.
- removeTaxon(Connection, DBHelper, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes a taxon specified by one of it's names with all it's different
names, annotations and sequences from the database.
- removeTaxon(Connection, int, DBHelper) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Deletes the taxon given by it's NCBI-Taxon-ID from the database and returns the
removed taxon.
- removeVariableModifications(char) - Method in class org.biojava.bio.proteomics.MassCalc
-
Remove all variable modifications assocaited with this residue.
- removeVariableModifications(Symbol) - Method in class org.biojava.bio.proteomics.MassCalc
-
Remove all variable modifications assocaited with this residue.
- rename(Name, Name) - Method in class org.biojava.naming.ObdaContext
-
- rename(String, String) - Method in class org.biojava.naming.ObdaContext
-
- render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
- render(Graphics2D) - Method in interface org.biojava.bio.gui.glyph.Glyph
-
- render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.HelixGlyph
-
- render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
-
- render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
-
- render(Graphics2D) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
-
- RENDER_NOTHING - Static variable in interface org.biojava.bio.gui.sequence.LabelRenderer
-
- renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
renderBead should be overridden by the concrete
BeadRenderer.
- renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
-
renderBead should implement rendering for this
bead type only.
- renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
-
renderBead renders features as simple ellipse.
- renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
renderBead renders features as simple rectangle.
- renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
- renderBead(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
renderBead renders features as a rectangle with
rounded corners.
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
Constant RENDERER indicating a change to the
renderer.
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
Constant RENDERER is a ChangeType
which indicates a change to the renderer, requiring a layout
update.
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePanel
-
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- RENDERER - Static variable in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
Constant RENDERER is a ChangeType
which indicates a change to the renderer, requiring a layout
update.
- RENDERERS - Static variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- renderers - Variable in class org.biojava.bio.gui.sequence.MultiLineRenderer
-
- RENDERERS - Static variable in class org.biojava.bio.gui.sequence.PairwiseOverlayRenderer
-
Constant RENDERERS indicating a change to the
renderers handled by the overlay.
- RENDERERS - Static variable in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
renderFeature draws a feature using the supplied
graphics context.
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
-
- renderFeature(Graphics2D, Feature, CircularRendererContext) - Method in interface org.biojava.bio.gui.sequence.CircularFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.FeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.StackedFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- renderFeature(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
-
- renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
-
renderImageMap writes a set of image map
coordinates corresponding to the rectangle sections drawn by
the renderer.
- renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in interface org.biojava.bio.gui.sequence.ImageMapRenderer
-
renderImageMap renders the Feature as
set of image map hotspots.
- renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
renderImageMap writes a set of image map
coordinates corresponding to the rectangle drawn by the
renderer.
- renderImageMap(Graphics2D, Feature, SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
-
renderImageMap writes a set of image map
coordinates corresponding to the rectangle sections drawn by
the renderer.
- renderLocation(Graphics2D, SequenceRenderContext, Location) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
Render another "exon" in the correct translation frame.
- renumber(int, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Renumber the view indexes from block, adding delta to each offset.
- REPAINT - Static variable in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
- ReparentContext - Class in org.biojava.bio.seq.projection
-
A good base class to implement ProjectionContext from.
- ReparentContext(FeatureHolder, FeatureHolder) - Constructor for class org.biojava.bio.seq.projection.ReparentContext
-
- RepeatedCharSequence - Class in org.biojava.utils
-
- RepeatedCharSequence(int, char) - Constructor for class org.biojava.utils.RepeatedCharSequence
-
- RepeatedCharSequence() - Constructor for class org.biojava.utils.RepeatedCharSequence
-
- replacement - Variable in class org.biojava.bio.symbol.Edit
-
- replicate(String) - Method in class org.biojavax.ga.impl.SimpleOrganism
-
- replicate(String) - Method in interface org.biojavax.ga.Organism
-
Creates a replica of this Organism with a new name.
- reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
-
- reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
-
- reportDna(String) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
-
- reportDna(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
-
- reportExon(RangeLocation, StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
-
- reportExon(RangeLocation, StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMETranscriptCallbackItf
-
Allows nesting class that manages a transcript template
to gain information about its extent from nested
elements that represent exons.
- reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
-
Allows nesting class that manages a gene template
to gain information about its extent from nested
elements.
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
-
- reportFeature(Location) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
-
- reportFeature(Location) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
-
- reportFeature(Location) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
-
Allows nesting class that manages a gene template
to gain information about its extent from nested
elements.
- reportMatch(SymbolList, Pattern, int, int) - Method in interface org.biojava.utils.regex.Search.Listener
-
- reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVECallbackItf
-
- reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEChromosomeCallbackItf
-
- reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
-
- reportSequence(Sequence) - Method in interface org.biojava.bio.seq.io.agave.AGAVEContigCallbackItf
-
- reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
-
- reportSequence(Sequence) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
-
- reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEBioSeqCallbackItf
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
-
- reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.agave.AGAVEFeatureCallbackItf
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
-
- reportStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
-
- reportStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.io.game.GAMEFeatureCallbackItf
-
- REPOSITORY_SUBSETS - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name.
- repositorySubset - Variable in class org.biojava.bibliography.BiblioEntryStatus
-
Some bibliographic repositories consist of several, or even
many, databases.
- requestNextStructure(StructureListener) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- requestNextStructure(StructureListener) - Method in interface org.biojava.bio.structure.server.StructureServer
-
- requestsQueued() - Method in class org.biojava.utils.SimpleThreadPool
-
requestsQueued returns the number of
Runnables currently queued.
- reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
-
- reset() - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
-
- reset() - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
-
- reset() - Method in class org.biojava.bio.search.BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
-
- reset() - Method in interface org.biojava.bio.search.BlastLikeSearchFilter
-
resets the internal state of this filter including
any cached evaluations.
- reset() - Method in class org.biojava.utils.io.CountedBufferedReader
-
- reset() - Method in class org.biojava.utils.regex.Matcher
-
Resets this matcher.
- reset(SymbolList) - Method in class org.biojava.utils.regex.Matcher
-
Resets this matcher with a new input SymbolList.
- reset() - Method in class org.biojavax.utils.CRC64Checksum
-
- resetRange() - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
check that begining is at 1 otherwise shift everything over
- ResidueType - Enum in org.biojava.bio.structure.io.mmcif.chem
-
Enumerates the possible classifications of residues.
- resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
resizeAndValidate sets the minimum, preferred and
maximum sizes of the component according to the current visible
symbol count.
- resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- resizeAndValidate() - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
resizeAndValidate sets the minimum, preferred and
maximum sizes of the component according to the current leading
and trailing borders, renderer depth and visible symbol count.
- resizeArray(Object, int) - Static method in class org.biojava.bio.structure.align.pairwise.FragmentJoiner
-
Reallocates an array with a new size, and copies the contents
of the old array to the new array.
- resolve(RemoteFeature) - Method in class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
-
- resolve(RemoteFeature) - Method in interface org.biojava.bio.seq.RemoteFeature.Resolver
-
Resolve rFeat.
- resolve(FuzzyPointLocation) - Method in interface org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
-
Return the actual point that the specified location should claim to
occupy.
- RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyLocation
-
Use the arithmetic mean of the `inner' and `outer' values, unless the
outer value is unbounded.
- RESOLVE_AVERAGE - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
-
- RESOLVE_INNER - Static variable in class org.biojava.bio.symbol.FuzzyLocation
-
Always use the `inner' values.
- RESOLVE_MAX - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
-
- RESOLVE_MIN - Static variable in class org.biojava.bio.symbol.FuzzyPointLocation
-
- RESOLVE_OUTER - Static variable in class org.biojava.bio.symbol.FuzzyLocation
-
Use the `outer' values, unless they are unbounded in which case the
`inner' values are used.
- resolveAlphabet(String) - Static method in class org.biojava.bio.program.ssbind.AlphabetResolver
-
resolveAlphabet returns an appropriate
Alphabet for an arbitrary identifier.
- resolveCommands(String, Properties) - Static method in class org.biojava.utils.process.ExternalProcess
-
Resolves the given command line by replacing all placeholder of the
format %NAME% with the values from the given properties
for the corresponding keys of the format NAME.
- resolveEntity(String, String) - Method in class org.biojava.utils.xml.ResourceEntityResolver
-
- resolveInt(int) - Method in class org.biojava.ontology.IntegerOntology
-
- resolveMax(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
-
Delegate for the getMax() method.
- resolveMin(FuzzyLocation) - Method in interface org.biojava.bio.symbol.FuzzyLocation.RangeResolver
-
Delegate for the getMin() method.
- resolver - Variable in class org.biojava.bio.seq.RemoteFeature.Template
-
- RESOURCE_TYPES - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name.
- ResourceEntityResolver - Class in org.biojava.utils.xml
-
SAX EntityResolve which looks up system IDs as resources
from a Java ClassLoader.
- ResourceEntityResolver(String) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
-
Construct a resolver which searches for resources in the specified
path relative to the current classloader.
- ResourceEntityResolver(String[]) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
-
Construct a resolver which searches for resources in the specified
list of directories relative to the current classloader.
- ResourceEntityResolver(String[], ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
-
Construct a resolver which searches for resources in the specified
list of directories relative to the supplied classloader.
- ResourceEntityResolver(String, ClassLoader) - Constructor for class org.biojava.utils.xml.ResourceEntityResolver
-
Construct a resolver which searches for resources in the specified
path relative to the supplied classloader.
- RestrictionEnzyme - Class in org.biojava.bio.molbio
-
RestrictionEnzyme represents a restriction enzyme
according to the REBASE standard.
- RestrictionEnzyme(String, SymbolList, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme
-
Creates a new RestrictionEnzyme which cuts within
or downstream of the recognition site.
- RestrictionEnzyme(String, SymbolList, int, int, int, int) - Constructor for class org.biojava.bio.molbio.RestrictionEnzyme
-
Creates a new RestrictionEnzyme of the unusual
type which cuts both upstream and downstream of its recognition
site.
- RestrictionEnzymeManager - Class in org.biojava.bio.molbio
-
RestrictionEnzymeManager manages collections of
static RestrictionEnzyme instances.
- RestrictionMapper - Class in org.biojava.bio.molbio
-
RestrictionMapper is a class for annotating
Sequences with Features which represent
restriction sites.
- RestrictionMapper(ThreadPool) - Constructor for class org.biojava.bio.molbio.RestrictionMapper
-
Creates a new RestrictionMapper which will use
the specified ThreadPool.
- RestrictionSite - Interface in org.biojava.bio.molbio
-
RestrictionSite represents the recognition site of a
restriction enzyme.
- RestrictionSite.Template - Class in org.biojava.bio.molbio
-
Template for construction of
RestrictionSites.
- RestrictionSite.Template() - Constructor for class org.biojava.bio.molbio.RestrictionSite.Template
-
- RESULT_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- retainAll(Collection) - Method in class org.biojavax.ga.util.WeightedSet
-
- returnData(Object) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
-
provides a standardised way of returning an
object that represents the result of parsing the
child element
- RevCompSequence - Class in org.biojava.bio.seq.impl
-
A reverse complement view onto Sequence interface.
- RevCompSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
-
URN, Name and Annotation are copied as is from the original Sequence, unless you use the
the other contructor that sets these.
- RevCompSequence(Sequence, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.RevCompSequence
-
- reverse(int[]) - Static method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Utility method for reversing an int[] array.
- reverse(SymbolList) - Static method in class org.biojava.bio.symbol.SymbolListViews
-
A reversed view onto a SymbolList.
- reverseComplement() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- reverseComplement() - Method in interface org.biojava.bio.chromatogram.Chromatogram
-
Returns a new Chromatogram representing the reverse
complement of this one.
- reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.DNATools
-
Retrieve a reverse-complement view of list.
- reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.NucleotideTools
-
Retrieve a reverse-complement view of list.
- reverseComplement(SymbolList) - Static method in class org.biojava.bio.seq.RNATools
-
Retrieve a reverse-complement view of list.
- reverseComplement(Sequence) - Static method in class org.biojava.bio.seq.SequenceTools
-
Reverse-complement a sequence, and flip all of its features.
- reverseComplementBaseCallList(Object) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Return a symbol list containing the reverse complement of the base call
data for the given label.
- reverseComplementBaseCallList(Object) - Method in class org.biojava.bio.program.scf.SCF
-
- reverseComplementBaseCalls() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Returns a new base call alignment that is the reverse complement of
one in this chromatogram.
- reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
- reverseComplementInstance() - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
-
- reverseComplementInstance() - Method in class org.biojava.bio.program.abi.ABIFChromatogram
-
- reverseComplementInstance() - Method in class org.biojava.bio.program.scf.SCF
-
- reverseRegex - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
- ReversibleTranslationTable - Interface in org.biojava.bio.symbol
-
A translation table that can also translate from the target to source
alphabet.
- revertFeature(Feature) - Method in class org.biojava.bio.seq.impl.SubSequence.SubProjectedFeatureContext
-
- revertFeature(Feature) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Unproject a feature.
- revertFeature(Feature) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- revertFilter(FeatureFilter) - Method in interface org.biojava.bio.seq.projection.ProjectionContext
-
Transform a filter on projected features so that it applies to unprojected
features.
- revertFilter(FeatureFilter) - Method in class org.biojava.bio.seq.projection.ReparentContext
-
- revertLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
-
- revertLocation(Location, int, boolean) - Static method in class org.biojava.bio.seq.projection.ProjectionUtils
-
Revert a location, translating and flipping as required.
- revertLocation(Location) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- revertStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.projection.TranslateFlipContext
-
- revertTemplate(Feature.Template, ProjectionContext) - Method in class org.biojava.bio.seq.projection.ProjectionEngine
-
Revert a template so that it can be used on the original feature-space.
- revertTemplate(ProjectionContext, Feature.Template) - Method in interface org.biojava.bio.seq.projection.ProjectionEngine.TemplateProjector
-
- RichAnnotatable - Interface in org.biojavax
-
Annotatable objects that can have rich annotations.
- RichAnnotation - Interface in org.biojavax
-
An annotation collection which stores annotations as Note objects.
- RichFeature - Interface in org.biojavax.bio.seq
-
Represents a feature that can be given name and rank and be
moved from one sequence to another.
- RichFeature.Template - Class in org.biojavax.bio.seq
-
Added-value extension of Feature.Template including bits we're
interested in, eg.
- RichFeature.Template() - Constructor for class org.biojavax.bio.seq.RichFeature.Template
-
- RichFeature.Tools - Class in org.biojavax.bio.seq
-
Some useful tools for working with features.
- RichFeatureRelationship - Interface in org.biojavax.bio.seq
-
Represents the relation between two features.
- RichFeatureRelationshipHolder - Interface in org.biojavax.bio.seq
-
Holds feature relationships.
- RichLocation - Interface in org.biojavax.bio.seq
-
Describes locations, and adds the concepts of circularity, fuzziness,
annotations, and cross-references to other databases.
- RichLocation.Strand - Class in org.biojavax.bio.seq
-
This class represents a strand on which a location may lie.
- RichLocation.Tools - Class in org.biojavax.bio.seq
-
Some useful tools for working with Locations.
- RichObjectBuilder - Interface in org.biojavax
-
This interface allows a class to generate Rich objects based on a class
name and some parameters.
- RichObjectFactory - Class in org.biojavax
-
Runs a service that builds rich objects, and provides some default values
for things like default ontology, default namespace, etc.
- RichSeqIOAdapter - Class in org.biojavax.bio.seq.io
-
This class implements all methods of RichSeqIOListener and takes no action.
- RichSeqIOAdapter() - Constructor for class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
Creates a new instance of RichSeqIOAdapter
- RichSeqIOListener - Interface in org.biojavax.bio.seq.io
-
An interface for classes that listen to BioEntry or
RichSequence I/O streams.
- RichSequence - Interface in org.biojavax.bio.seq
-
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a
Sequence.
- RichSequence.IOTools - Class in org.biojavax.bio.seq
-
A set of convenience methods for handling common file formats.
- RichSequence.IOTools.SingleRichSeqIterator - Class in org.biojavax.bio.seq
-
Used to iterate over a single rich sequence
- RichSequence.IOTools.SingleRichSeqIterator(Sequence) - Constructor for class org.biojavax.bio.seq.RichSequence.IOTools.SingleRichSeqIterator
-
Creates an iterator over a single sequence.
- RichSequence.Terms - Class in org.biojavax.bio.seq
-
Stores a number of useful terms used across many sequence formats for
consistency's sake.
- RichSequence.Terms() - Constructor for class org.biojavax.bio.seq.RichSequence.Terms
-
- RichSequence.Tools - Class in org.biojavax.bio.seq
-
Some useful tools for working with RichSequence objects.
- RichSequenceBuilder - Interface in org.biojavax.bio.seq.io
-
An interface for objects that can build RichSequences.
- RichSequenceBuilderFactory - Interface in org.biojavax.bio.seq.io
-
Simple factory for constructing new RichSequenceBuilder objects.
- RichSequenceDB - Interface in org.biojavax.bio.db
-
A database of RichSequences with accessible keys and iterators over all
sequences.
- RichSequenceDBLite - Interface in org.biojavax.bio.db
-
A database of RichSequences.
- RichSequenceFormat - Interface in org.biojavax.bio.seq.io
-
Allows a file format to be read/written as RichSequences.
- RichSequenceFormat.BasicFormat - Class in org.biojavax.bio.seq.io
-
Provides a basic format with simple things like line-widths precoded.
- RichSequenceFormat.BasicFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
- RichSequenceFormat.HeaderlessFormat - Class in org.biojavax.bio.seq.io
-
Provides the basic implementation required for simple header/footer-less files such as Genbank.
- RichSequenceFormat.HeaderlessFormat() - Constructor for class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
-
- RichSequenceHandler - Interface in org.biojavax.bio.seq
-
An interface for classes that know how to handle subsequence operations.
- RichSequenceIterator - Interface in org.biojavax.bio.seq
-
Essentially the same as SequenceIterator.
- RichStreamReader - Class in org.biojavax.bio.seq.io
-
Parses a stream into sequences.
- RichStreamReader(InputStream, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader
-
Creates a new stream reader on the given input stream, which will attempt to read
sequences in the given format, having symbols from the given tokenization, and
pass them to the given factory to be transformed into RichSequence objects in
the given namespace.
- RichStreamReader(BufferedReader, RichSequenceFormat, SymbolTokenization, RichSequenceBuilderFactory, Namespace) - Constructor for class org.biojavax.bio.seq.io.RichStreamReader
-
Creates a new stream reader on the given reader, which will attempt to read
sequences in the given format, having symbols from the given tokenization, and
pass them to the given factory to be transformed into RichSequence objects in
the given namespace.
- RichStreamWriter - Class in org.biojavax.bio.seq.io
-
Writes all of the sequences from a SequenceIterator to a stream with a
particular format.
- RichStreamWriter(OutputStream, RichSequenceFormat) - Constructor for class org.biojavax.bio.seq.io.RichStreamWriter
-
Generate a new RichStreamWriter to the stream os and using format.
- rightMost() - Method in class org.biojava.bio.alignment.AbstractULAlignment
-
- rightPad(String, int) - Static method in class org.biojavax.utils.StringTools
-
Pads a string to be a certain width by appending spaces.
- rightPad(String, char, int) - Static method in class org.biojavax.utils.StringTools
-
Pads a string to be a certain width by appending given symbols.
- rights - Variable in class org.biojava.bibliography.BibRef
-
It specifies information about rights over the cited resource.
- RIGHTVALUE - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
- rms_dk_diag(double[], double[], int, int, int, int) - Static method in class org.biojava.bio.structure.align.helper.AlignTools
-
Given distance matrix diagonals dk1, dk2, get the rmsd of a fpair.
- RNA - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
RNA indicates that a sequence contains RNA
(ribonucleic acid) symbols.
- RNA_ONLY - Static variable in enum org.biojava.bio.structure.io.mmcif.chem.PolymerType
-
Convenience Set of polymer types classified as RNA.
- RNATools - Class in org.biojava.bio.seq
-
Useful functionality for processing DNA and RNA sequences.
- ROLE_ATTR_QUERYABLE - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A role of an attribute.
- ROLE_ATTR_RETRIEVABLE - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A role of an attribute.
- rollback() - Method in class org.biojava.bio.seq.db.BioIndex
-
- rollback() - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
rollback rolls back changes made since the last
commit.
- rollback() - Method in interface org.biojava.bio.seq.db.IndexStore
-
Discard all uncommited changes.
- rollback() - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- rollback() - Method in interface org.biojava.utils.Commitable
-
rollback reverses pending changes to restore
initial (or prior commit) state.
- rollback() - Method in class org.biojava.utils.FileAsList
-
- rotate(Atom, double[][]) - Static method in class org.biojava.bio.structure.Calc
-
rotate a single atom aroud a rotation matrix.
- rotate(Structure, double[][]) - Static method in class org.biojava.bio.structure.Calc
-
Rotate a structure.
- rotate(Group, double[][]) - Static method in class org.biojava.bio.structure.Calc
-
rotate a structure .
- rotate(Atom, Matrix) - Static method in class org.biojava.bio.structure.Calc
-
Rotate an atom around a Matrix object.
- rotate(Group, Matrix) - Static method in class org.biojava.bio.structure.Calc
-
Rotate a group object.
- rotate(Structure, Matrix) - Static method in class org.biojava.bio.structure.Calc
-
Rotate a structure object.
- RoundRectangularBeadRenderer - Class in org.biojava.bio.gui.sequence
-
RoundRectangularBeadRenderer renders features
as rectangles with rounded corners.
- RoundRectangularBeadRenderer() - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
Creates a new RoundRectangularBeadRenderer
object with the default settings.
- RoundRectangularBeadRenderer(double, double, Paint, Paint, Stroke, double, double) - Constructor for class org.biojava.bio.gui.sequence.RoundRectangularBeadRenderer
-
Creates a new RoundRectangularBeadRenderer.
- rowSymbols - Variable in class org.biojava.bio.alignment.SubstitutionMatrix
-
- RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- RP_LINE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- rpp - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- rppat - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- rppat - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- RulerRenderer - Class in org.biojava.bio.gui.sequence
-
RulerRenderer renders numerical scales in sequence
coordinates.
- RulerRenderer() - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer
-
Creates a new RulerRenderer with the default
setting of ticks pointing downwards.
- RulerRenderer(int) - Constructor for class org.biojava.bio.gui.sequence.RulerRenderer
-
Creates a new RulerRenderer with the specified
tick direction.
- run() - Method in class org.biojava.bio.structure.gui.util.AlignmentCalc
-
- run() - Method in class org.biojava.bio.structure.server.DemoStructureServer
-
- run() - Method in class org.biojava.bio.structure.server.StructureFetcherRunnable
-
- run() - Method in class org.biojava.utils.process.ReaderInputHandler
- run() - Method in class org.biojava.utils.process.ReaderWriterPipe
- run() - Method in class org.biojava.utils.process.SimpleInputHandler
- run() - Method in class org.biojava.utils.process.StreamPipe
- run(GAStoppingCriteria) - Method in interface org.biojavax.ga.GeneticAlgorithm
-
Iterates the Algorithm until the stopping criteria are met.
- run(GAStoppingCriteria) - Method in class org.biojavax.ga.impl.SimpleGeneticAlgorithm
-
- s() - Static method in class org.biojava.bio.seq.DNATools
-
- s() - Static method in class org.biojava.bio.seq.NucleotideTools
-
- s() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Serine
- S_SCROFA - Static variable in interface org.biojava.bio.program.homologene.Taxon
-
- sample() - Method in class org.biojavax.ga.util.WeightedSet
-
Randomly samples an Object from the Set according
to its weight.
- sampleSymbol() - Method in class org.biojava.bio.dist.AbstractDistribution
-
- sampleSymbol() - Method in interface org.biojava.bio.dist.Distribution
-
Sample a symbol from this state's probability distribution.
- sampleSymbol() - Method in class org.biojava.bio.dist.GapDistribution
-
- sampleSymbol() - Method in class org.biojava.bio.dist.PairDistribution
-
- sampleSymbol() - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- SangerFastqReader - Class in org.biojava.bio.program.fastq
-
- SangerFastqReader() - Constructor for class org.biojava.bio.program.fastq.SangerFastqReader
-
- SangerFastqWriter - Class in org.biojava.bio.program.fastq
-
- SangerFastqWriter() - Constructor for class org.biojava.bio.program.fastq.SangerFastqWriter
-
- SAX2StAXAdaptor - Class in org.biojava.bio.seq.io.agave
-
Lightweight adaptor which translates SAX content events into
StAX form, and provides delegation services.
- SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
Construct a new SAX Content handler which wraps a StAX
handler.
- SAX2StAXAdaptor - Class in org.biojava.utils.stax
-
Lightweight adaptor which translates SAX content events into
StAX form, and provides delegation services.
- SAX2StAXAdaptor(StAXContentHandler) - Constructor for class org.biojava.utils.stax.SAX2StAXAdaptor
-
Construct a new SAX Content handler which wraps a StAX
handler.
- sb - Variable in class org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader
-
- scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity
-
- scale(Chromatogram, int) - Method in interface org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler
-
Returns the remapped coordinate for the provided trace sample index of the
given chromatogram.
- scale(Chromatogram, int) - Method in class org.biojava.bio.chromatogram.graphic.FixedBaseWidthScaler
-
- SCALE_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- ScaleableMatrixPanel - Class in org.biojava.bio.structure.gui
-
A JPanel that can display the underlying distance matrix
data of the protein structure alignment algorithm.
- ScaleableMatrixPanel() - Constructor for class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- scaleHeight - Variable in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
- SCENE_MITO - Static variable in interface org.biojava.bio.symbol.TranslationTable
-
Translation table name for the scenedesmus obliquus mitochondrial genetic
code.
- SCF - Class in org.biojava.bio.program.scf
-
- SCF() - Constructor for class org.biojava.bio.program.scf.SCF
-
Creates a new, completely empty SCF.
- SCF_MAGIC - Static variable in class org.biojava.bio.chromatogram.ChromatogramFactory
-
The magic number for SCF files.
- SCHEMA - Static variable in interface org.biojava.bio.seq.FeatureHolder
-
Signals that the schema of this FeatureHolder has changed.
- SCI_PROPERTY - Static variable in class org.biojava.bio.seq.io.agave.AGAVEProperty
-
- SCIENTIFIC - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
Use this to define scientific names for things.
- SCIENTIFIC_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- SCINAME_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SCOOP - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- score - Variable in class org.biojava.bio.dp.BackPointer
-
The score of this element of the DP matrix.
- score - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- score - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
-
score of the search which produced the
alignment.
- scores - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- SCORES - Static variable in interface org.biojava.bio.dp.StatePath
-
Alignment label for the likelyhood at each step.
- scores - Variable in class org.biojava.bio.dp.twohead.Cell
-
- ScoreType - Interface in org.biojava.bio.dp
-
This class computes the score that is used to be used
in a DP optimisation.
- ScoreType.NullModel - Class in org.biojava.bio.dp
-
In this class, calculateScore returns the probability of
a Symbol being emitted by the null model.
- ScoreType.NullModel() - Constructor for class org.biojava.bio.dp.ScoreType.NullModel
-
- ScoreType.Odds - Class in org.biojava.bio.dp
-
In this class, calculateScore returns the odds ratio
of a symbol being emitted.
- ScoreType.Odds() - Constructor for class org.biojava.bio.dp.ScoreType.Odds
-
- ScoreType.Probability - Class in org.biojava.bio.dp
-
In this class, calculateScore returns the probability
of a Symbol being emitted.
- ScoreType.Probability() - Constructor for class org.biojava.bio.dp.ScoreType.Probability
-
- scoreWeightMatrix(WeightMatrix, SymbolList, int) - Static method in class org.biojava.bio.dp.DP
-
Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix.
- scoreWeightMatrix(WeightMatrix, SymbolList, ScoreType, int) - Static method in class org.biojava.bio.dp.DP
-
Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix using a particular ScoreType.
- search(AnnotationType) - Method in interface org.biojava.bio.annodb.AnnotationDB
-
Find all Annotation instances in this DB and any Annotations that are child
properties of these that match an AnnotationType.
- search(AnnotationType) - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
- search(AnnotationType) - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
-
- search(AnnotationType) - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
-
- search(AnnotationType) - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
- search(AnnotationType) - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
-
- search(String, SymbolList, SearchListener) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
-
- search(String, SymbolList, SearchListener) - Method in interface org.biojava.bio.program.ssaha.DataStore
-
Search the DataStore with a symbol list.
- search(SymbolList, SequenceDB, Map) - Method in interface org.biojava.bio.search.SeqSimilaritySearcher
-
Using this sequence similarity searcher, search with the given
sequence against the given sequence database.
- search(Object) - Method in class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- search(Object) - Method in interface org.biojava.bio.taxa.TaxonFactory
-
Deprecated.
Retrieve a Taxon that matches some ID.
- search(Object) - Method in class org.biojava.bio.taxa.WeakTaxonFactory
-
Deprecated.
- search(Name, Attributes) - Method in class org.biojava.naming.ObdaContext
-
- search(Name, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
-
- search(Name, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
-
- search(Name, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
-
- search(String, Attributes, String[]) - Method in class org.biojava.naming.ObdaContext
-
- search(String, Attributes) - Method in class org.biojava.naming.ObdaContext
-
- search(String, String, SearchControls) - Method in class org.biojava.naming.ObdaContext
-
- search(String, String, Object[], SearchControls) - Method in class org.biojava.naming.ObdaContext
-
- search(SymbolList) - Method in class org.biojava.utils.automata.PatternBlitz
-
- Search - Class in org.biojava.utils.regex
-
A utility class to make searching a Sequence with many regex patterns
easier.
- Search(FiniteAlphabet) - Constructor for class org.biojava.utils.regex.Search
-
- search(SymbolList) - Method in class org.biojava.utils.regex.Search
-
search the Sequence with the patterns already registered with this object.
- search(SymbolList, int, int) - Method in class org.biojava.utils.regex.Search
-
search part of the SymbolList with the patterns already registered with this object.
- Search.Listener - Interface in org.biojava.utils.regex
-
Interface for a class that will recieve match information
from this class.
- searchAnnotation(Annotation, AnnotationType) - Static method in class org.biojava.bio.AnnotationTools
-
Scans an Annotation with an AnnotationType and returns all Annotation
instances matching a Type.
- SearchBuilder - Interface in org.biojava.bio.search
-
The SearchBuilder interface is to be used by objects
which accumulate state via a SearchContentHandler and
then construct a SeqSimilaritySearchResult object.
- SearchContentAdapter - Class in org.biojava.bio.search
-
An adapter for SearchContentHandler.
- SearchContentAdapter() - Constructor for class org.biojava.bio.search.SearchContentAdapter
-
- SearchContentFilter - Class in org.biojava.bio.search
-
Filtering implementation of SearchContentHandler that by default passes
all messages on to the next delegate in the chain.
- SearchContentFilter(SearchContentHandler) - Constructor for class org.biojava.bio.search.SearchContentFilter
-
- SearchContentHandler - Interface in org.biojava.bio.search
-
SearchContentHandler is a notification interface for
objects which listen to search stream parsers.
- SearchContentHandlerDebugger - Class in org.biojava.bio.search
-
This class prints to a PrintStream
calls to the SearchContentHandler interface
in human readable form.
- SearchContentHandlerDebugger() - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
-
Create an instance that dumps to System.out.
- SearchContentHandlerDebugger(PrintStream) - Constructor for class org.biojava.bio.search.SearchContentHandlerDebugger
-
- SearchException - Exception in org.biojava.bio.program.ssaha
-
There has been some failure that prevents a search from completing.
- SearchException(String) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
-
- SearchException(Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
-
- SearchException(String, Throwable) - Constructor for exception org.biojava.bio.program.ssaha.SearchException
-
- SearchListener - Interface in org.biojava.bio.program.ssaha
-
The interface used to inform interested parties that some sequence has
been searched and something found.
- SearchListener.Echo - Class in org.biojava.bio.program.ssaha
-
A SearchListener that prints events out to a PrintStream.
- SearchListener.Echo(PrintStream) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Echo
-
- SearchListener.FilterByLength - Class in org.biojava.bio.program.ssaha
-
A simple listener that filters out all hits that are too short.
- SearchListener.FilterByLength(SearchListener, int) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.FilterByLength
-
- SearchListener.Tee - Class in org.biojava.bio.program.ssaha
-
A SearchListener that passes events on to two delegate listeners.
- SearchListener.Tee(SearchListener, SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Tee
-
- SearchListener.Wrapper - Class in org.biojava.bio.program.ssaha
-
A simple wrapper implementation.
- SearchListener.Wrapper(SearchListener) - Constructor for class org.biojava.bio.program.ssaha.SearchListener.Wrapper
-
- sec() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Selenocysteine (U)
- SEC_ACC_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SECONDARY_ACCESSION_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- SECONDARY_ACCESSIONS_GROUP_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- secondarySequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.PairwiseRenderContext
-
secondarySequenceToGraphics converts a sequence
coordinate on the secondary sequence to a graphical position.
- secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
secondarySequenceToGraphics converts a sequence
index to a graphical position.
- secondarySequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- SecondaryStructureFeatureRenderer - Class in org.biojava.bio.gui.sequence
-
A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure
(Helices, Turns and Strands).
- SecondaryStructureFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.SecondaryStructureFeatureRenderer
-
- sectp - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- seek(long) - Method in class org.biojava.utils.io.CachingInputStream
-
- seek(long) - Method in class org.biojava.utils.io.RandomAccessReader
-
seek moves the pointer to the specified position.
- seek(long) - Method in interface org.biojava.utils.io.Seekable
-
Moves the pointer in the inputstream such that the byte starting at
pos are returned by the next read.
- Seekable - Interface in org.biojava.utils.io
-
This interface provides a collective name for IO classes that implement a
seek function (e.g., RandomAccessFile).
- select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.ProportionalSelection
-
- select(Population, GeneticAlgorithm) - Method in interface org.biojavax.ga.functions.SelectionFunction
-
Selects a Population of Organisms for
replication based on their fitness.
- select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
-
- select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.SelectionFunction.Threshold
-
Selects individuals whose fitness (as determined by the
FitnessFunction) is more than the cutoff.
- select(Population, GeneticAlgorithm) - Method in class org.biojavax.ga.functions.TournamentSelection
-
Standard call to select organisms, will select a number of Organisms
corresponding to 75 % of the population.
- SELECTION_FUNCTION - Static variable in interface org.biojavax.ga.GeneticAlgorithm
-
- SelectionFunction - Interface in org.biojavax.ga.functions
-
Selects Organisms for Replication and returns the offspring.
- SelectionFunction.SelectAll - Class in org.biojavax.ga.functions
-
- SelectionFunction.SelectAll() - Constructor for class org.biojavax.ga.functions.SelectionFunction.SelectAll
-
- SelectionFunction.Threshold - Class in org.biojavax.ga.functions
-
Selects individuals who's fitness exceeds a threshold value.
- SelectionFunction.Threshold(double) - Constructor for class org.biojavax.ga.functions.SelectionFunction.Threshold
-
- selectionLocked() - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
-
- selectionLocked() - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
-
- selectionUnlocked() - Method in interface org.biojava.bio.structure.gui.events.AlignmentPositionListener
-
- selectionUnlocked() - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
-
- selectNIndividuals(Population, GeneticAlgorithm, int) - Method in class org.biojavax.ga.functions.TournamentSelection
-
This method selects n Organism from the population it is given, using the
tournament selection method
- SEPARATED - Static variable in interface org.biojava.bio.seq.io.SymbolTokenization
-
- SEPARATOR_COLOR - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option indicating the color that the call separators
should be.
- SEPARATOR_STROKE - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
Option providing the the stroke to use for drawing
call separators.
- SEPARATOR_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- seq - Variable in class org.biojava.bio.alignment.SimpleAlignmentElement
-
- seq - Variable in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- SeqContentPattern - Class in org.biojava.bio.search
-
A pattern that can be used to find regions with given sequence content.
- SeqContentPattern(FiniteAlphabet) - Constructor for class org.biojava.bio.search.SeqContentPattern
-
Create a new SeqContentPattern over an alphabet.
- SeqFileFormer - Interface in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- seqFont - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- SeqIOAdapter - Class in org.biojava.bio.seq.io
-
Adapter class for SeqIOListener that has empty methods.
- SeqIOAdapter() - Constructor for class org.biojava.bio.seq.io.SeqIOAdapter
-
- SeqIOConstants - Class in org.biojava.bio.seq.io
-
SeqIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing sequences.
- SeqIOConstants() - Constructor for class org.biojava.bio.seq.io.SeqIOConstants
-
- SeqIOEventEmitter - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- SeqIOEventEmitter(Comparator, Comparator) - Constructor for class org.biojava.bio.seq.io.SeqIOEventEmitter
-
Deprecated.
- SeqIOFilter - Class in org.biojava.bio.seq.io
-
Base-class for listeners that pass filtered events onto another listener.
- SeqIOFilter(SeqIOListener) - Constructor for class org.biojava.bio.seq.io.SeqIOFilter
-
Create a new SeqIOFilter that will forward events on to another listener.
- SeqIOListener - Interface in org.biojava.bio.seq.io
-
Notification interface for objects which listen to a sequence stream
parser.
- SeqIOTools - Class in org.biojava.bio.seq.io
-
Deprecated.
use org.biojavax.bio.seq.RichSequence.IOTools
- seqNameForID(int) - Method in class org.biojava.bio.program.ssaha.CompactedDataStore
-
- seqNameForID(int) - Method in interface org.biojava.bio.program.ssaha.DataStore
-
Resolve an ID to a sequence name.
- seqPanels - Variable in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- SeqRes2AtomAligner - Class in org.biojava.bio.structure.io
-
Aligns the SEQRES residues to the ATOM residues.
- SeqRes2AtomAligner() - Constructor for class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- SEQRESRECORD - Static variable in interface org.biojava.bio.structure.AminoAcid
-
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
- seqs - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
-
- SeqSimilarityAdapter - Class in org.biojava.bio.program.ssbind
-
A SeqSimilarityAdapter converts SAX events into method
calls on a SearchContentHandler implementation.
- SeqSimilarityAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- SeqSimilaritySearcher - Interface in org.biojava.bio.search
-
Objects of this type represent one particular installation (not
just implementation) of a sequence similarity searcher such as
BLASTP.
- SeqSimilaritySearchHit - Interface in org.biojava.bio.search
-
Objects of this type represent one particular hit (sequence and
associated information) from a sequence similarity search.
- SeqSimilaritySearchHit.ByScoreComparator - Class in org.biojava.bio.search
-
ByScoreComparator compares
SeqSimilaritySearchHits by their score.
- SeqSimilaritySearchHit.ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.ByScoreComparator
-
- SeqSimilaritySearchHit.BySubHitCountComparator - Class in org.biojava.bio.search
-
BySubHitCountComparator compares
SeqSimilaritySearchHits by their number of
sub-hits.
- SeqSimilaritySearchHit.BySubHitCountComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchHit.BySubHitCountComparator
-
- SeqSimilaritySearchResult - Interface in org.biojava.bio.search
-
Objects of this type represent one particular result of a sequence
similarity search.
- SeqSimilaritySearchSubHit - Interface in org.biojava.bio.search
-
Objects of this type represent one particular sub-hit (one concrete
sequence stretch within a sequence and associated information) from
a sequence similarity search hit.
- SeqSimilaritySearchSubHit.ByScoreComparator - Class in org.biojava.bio.search
-
ByScoreComparator compares
SeqSimilaritySearchSubHits by their score.
- SeqSimilaritySearchSubHit.ByScoreComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.ByScoreComparator
-
- SeqSimilaritySearchSubHit.BySubjectStartComparator - Class in org.biojava.bio.search
-
BySubjectStartComparator compares
SeqSimilaritySearchSubHits by their start position
on the subject sequence.
- SeqSimilaritySearchSubHit.BySubjectStartComparator() - Constructor for class org.biojava.bio.search.SeqSimilaritySearchSubHit.BySubjectStartComparator
-
- SeqSimilarityStAXAdapter - Class in org.biojava.bio.program.ssbind
-
SeqSimilarityStAXAdapter is a handler for XML
conforming to the BioJava BlastLike DTD.
- SeqSimilarityStAXAdapter() - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
-
- SeqSimilarityStAXHandler - Class in org.biojava.bio.program.ssbind
-
SeqSimilarityStAXHandler is a base class for creating
modular StAX handlers which send callbacks to a
SeqSimilarityStAXAdapter.
- SeqSimilarityStAXHandler(SeqSimilarityStAXAdapter) - Constructor for class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
-
Creates a new SeqSimilarityStAXHandler which
simply maintains a list of StAXHandlerBindings and
delegates to any suitable StAXContentHandler bound
by one of them.
- seqString() - Method in class org.biojava.bio.dp.SimpleStatePath
-
- seqString() - Method in class org.biojava.bio.program.das.DASSequence
-
- seqString() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- seqString() - Method in class org.biojava.bio.seq.impl.DummySequence
-
- seqString() - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- seqString() - Method in class org.biojava.bio.seq.impl.SubSequence
-
- seqString() - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- seqString() - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- seqString() - Method in class org.biojava.bio.seq.SimpleAssembly
-
- seqString() - Method in class org.biojava.bio.symbol.AbstractSymbolList
-
- seqString() - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- seqString() - Method in interface org.biojava.bio.symbol.SymbolList
-
Stringify this symbol list.
- seqString(RichSequence) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
-
Stringify this Sequences.
- seqString(RichSequence) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
-
Stringify this Sequences.
- seqString() - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Stringify this symbol list.
- seqString(RichSequence) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
-
Stringify this Sequences.
- seqString() - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Stringify this symbol list.
- SEQUENCE - Static variable in interface org.biojava.bio.dp.StatePath
-
Alignment label for the emitted sequence.
- SEQUENCE - Static variable in class org.biojava.bio.program.abi.ABITools
-
Alignment label for the DNA sequence row.
- sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
-
- sequence - Variable in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
-
- Sequence - Interface in org.biojava.bio.seq
-
A biological sequence.
- SEQUENCE_CAUTION - Static variable in class org.biojavax.bio.seq.io.UniProtCommentParser
-
A name for a comment type.
- SEQUENCE_CHECKSUM_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- SEQUENCE_COLOR - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- SEQUENCE_FORMAT - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
-
SEQUENCE_FORMAT is the key used to identify the
format of the indexed sequence files represented by the store
in the OBDA config.dat files.
- SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SEQUENCE_LENGTH_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- SEQUENCE_MASS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- SEQUENCE_MODIFIED_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- SEQUENCE_TOPOLOGY_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SEQUENCE_TYPE_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SEQUENCE_VER_ATTR - Static variable in class org.biojavax.bio.seq.io.EMBLxmlFormat
-
- SEQUENCE_VERSION_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- SequenceAlignment - Class in org.biojava.bio.alignment
-
This Interface provides methods for the alignment of bio-sequences.
- SequenceAlignment() - Constructor for class org.biojava.bio.alignment.SequenceAlignment
-
- SequenceAlignmentSAXParser - Class in org.biojava.bio.program.sax
-
A SAX2 parser for dealing with a sequence alignments.
- SequenceAlignmentSAXParser() - Constructor for class org.biojava.bio.program.sax.SequenceAlignmentSAXParser
-
Initialises internal state
Sets namespace prefix to "biojava"
- sequenceAndQualityLengthsMatch() - Method in class org.biojava.bio.program.fastq.FastqBuilder
-
Return true if the sequence and quality scores for this FASTQ formatted sequence builder are equal in length.
- SequenceAnnotator - Interface in org.biojava.bio.seq
-
An object which adds some additional information to a Sequence.
- SequenceBuilder - Interface in org.biojava.bio.seq.io
-
Interface for objects which accumulate state via SeqIOListener,
then construct a Sequence object.
- SequenceBuilderBase - Class in org.biojava.bio.seq.io
-
Basic SequenceBuilder implementation which accumulates all
notified information.
- SequenceBuilderBase() - Constructor for class org.biojava.bio.seq.io.SequenceBuilderBase
-
- SequenceBuilderFactory - Interface in org.biojava.bio.seq.io
-
Simple factory for constructing new SequenceBuilder objects.
- SequenceBuilderFilter - Class in org.biojava.bio.seq.io
-
Base-class for builders that pass filtered events onto another builder.
- SequenceBuilderFilter(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SequenceBuilderFilter
-
Create a new SeqIOFilter that will forward events on to another listener.
- SequenceContentHandlerBase - Class in org.biojava.bio.seq.io.game
-
StAX handler for elements containing sequence
- SequenceContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
-
- SequenceDB - Interface in org.biojava.bio.seq.db
-
A database of sequences with accessible keys and iterators over all
sequences.
- SequenceDBDataSource - Class in org.biojava.bio.seq.distributed
-
Turn an entire SequenceDB instance into a DistDataSource.
- SequenceDBDataSource(SequenceDB) - Constructor for class org.biojava.bio.seq.distributed.SequenceDBDataSource
-
- SequenceDBInstallation - Interface in org.biojava.bio.seq.db
-
A SequenceDBInstallation has the functionality of a factory for
SequenceDB objects and additionally manages the SequenceDB objects
created by itself such that the minimum number of SequenceDB
objects is created by a particular SequenceDBInstallation
object.
- SequenceDBLite - Interface in org.biojava.bio.seq.db
-
A database of sequences.
- SequenceDBProvider - Interface in org.biojava.directory
-
Interfaces for named resources that can provide sequences via a
database given some configuration information as defined by the
OBDA standard.
- SequenceDBSearchHit - Class in org.biojava.bio.search
-
Deprecated.
SimpleSeqSimilaritySearchHit has been made Annotatable
and is now functionally identical.
- SequenceDBSearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SequenceDBSearchHit
-
Deprecated.
Creates a new SequenceDBSearchHit object.
- SequenceDBSearchResult - Class in org.biojava.bio.search
-
Deprecated.
SimpleSeqSimilaritySearchResult has been made
Annotatable and is now functionally identical.
- SequenceDBSearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchResult
-
Deprecated.
Creates a new SequenceDBSearchResult.
- SequenceDBSearchSubHit - Class in org.biojava.bio.search
-
Deprecated.
SimpleSeqSimilaritySearchSubHit has been made
Annotatable and is now functionally identical.
- SequenceDBSearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SequenceDBSearchSubHit
-
Deprecated.
Creates a new SequenceDBSearchSubHit object.
- SequenceDBSequenceBuilder - Class in org.biojava.bio.seq.io
-
This SequenceBuilder has a variety of modes of operation.
- SequenceDBSequenceBuilder(SequenceDB, int) - Constructor for class org.biojava.bio.seq.io.SequenceDBSequenceBuilder
-
constructor
- SequenceDBWrapper - Class in org.biojava.bio.seq.db
-
An abstract implementation of SequenceDB that wraps up another database.
- SequenceDBWrapper(SequenceDB) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper
-
- SequenceDBWrapper.SequencesForwarder - Class in org.biojava.bio.seq.db
-
- SequenceDBWrapper.SequencesForwarder(Object, ChangeSupport) - Constructor for class org.biojava.bio.seq.db.SequenceDBWrapper.SequencesForwarder
-
- SequenceDisplay - Class in org.biojava.bio.structure.gui
-
A sequence display that can show the results of a protein structure alignment.
- SequenceDisplay(StructurePairAligner) - Constructor for class org.biojava.bio.structure.gui.SequenceDisplay
-
- sequenceExtentOfPixels(SequenceRenderContext) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- SequenceFactory - Interface in org.biojava.bio.seq
-
Deprecated.
use org.biojavax.bio.seq.io.RichSequenceBuilder or
use org.biojavax.bio.seq.io.SequenceBuilder
- SequenceFormat - Interface in org.biojava.bio.seq.io
-
Defines what a sequence format does.
- SequenceHandler - Interface in org.biojava.bio.seq.io.agave
-
mark interface
- sequenceIterator() - Method in class org.biojava.bio.program.das.DASSequenceDB
-
- sequenceIterator() - Method in class org.biojava.bio.seq.db.AbstractSequenceDB
-
- sequenceIterator() - Method in class org.biojava.bio.seq.db.AnnotatedSequenceDB
-
- sequenceIterator() - Method in class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
-
Deprecated.
- sequenceIterator() - Method in class org.biojava.bio.seq.db.DummySequenceDB
-
- sequenceIterator() - Method in class org.biojava.bio.seq.db.HashSequenceDB
-
- sequenceIterator() - Method in class org.biojava.bio.seq.db.IndexedSequenceDB
-
- sequenceIterator() - Method in interface org.biojava.bio.seq.db.SequenceDB
-
Returns a SequenceIterator over all sequences in the database.
- SequenceIterator - Interface in org.biojava.bio.seq
-
An iterator over a bag of sequences.
- sequenceIterator() - Method in class org.biojavax.bio.db.AbstractRichSequenceDB
-
- sequenceIterator() - Method in interface org.biojavax.bio.db.RichSequenceDB
-
Returns a SequenceIterator over all sequences in the database.
- SequenceMouseListener - Class in org.biojava.bio.structure.gui.util
-
a mouse listener for the AbstractChainRenderer class
it listens to all mouse events and triggeres appropriate
SequenceListener and FeatureListener events
- SequenceMouseListener(SequenceDisplay) - Constructor for class org.biojava.bio.structure.gui.util.SequenceMouseListener
-
- SequencePanel - Class in org.biojava.bio.gui.sequence
-
A panel that displays a Sequence.
- SequencePanel() - Constructor for class org.biojava.bio.gui.sequence.SequencePanel
-
Create a new SequencePanel.
- SequencePanel.Border - Class in org.biojava.bio.gui.sequence
-
- SequencePanelWrapper - Class in org.biojava.bio.gui.sequence
-
Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped
over more than one line on screen.
- SequencePanelWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
Creates a new instance of WrappedSequencePanel
- SequencePoster - Class in org.biojava.bio.gui.sequence
-
Deprecated.
This doesn't handle loads of stuff. Use SequencePoster.
- SequencePoster() - Constructor for class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Create a new SeqeuncePanel.
- SequencePoster.Border - Class in org.biojava.bio.gui.sequence
-
Deprecated.
- SequenceRenderContext - Interface in org.biojava.bio.gui.sequence
-
A context within which sequence information may be rendered.
- SequenceRenderContext.Border - Class in org.biojava.bio.gui.sequence
-
The metric object for the 'border' area - the area between the extent of
the rendered area and the beginning or end of the sequence.
- SequenceRenderContext.Border() - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
-
- SequenceRenderer - Interface in org.biojava.bio.gui.sequence
-
The interface for things that can render a line of information about a
sequence.
- SequenceRenderer.RendererForwarder - Class in org.biojava.bio.gui.sequence
-
- SequenceRenderer.RendererForwarder(SequenceRenderer, ChangeSupport) - Constructor for class org.biojava.bio.gui.sequence.SequenceRenderer.RendererForwarder
-
- SequenceRendererWrapper - Class in org.biojava.bio.gui.sequence
-
An implementation of SequenceRenderer that delegates rendering to another
renderer.
- SequenceRendererWrapper() - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
Create a new renderer with no wrapped renderer.
- SequenceRendererWrapper(SequenceRenderer) - Constructor for class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
Create a new wrapper with a wrapped renderer
- SEQUENCES - Static variable in interface org.biojava.bio.seq.db.SequenceDBLite
-
Signals that sequences are being added to or remove from the database.
- SequencesAsGFF - Class in org.biojava.bio.program.gff
-
Turns a sequence database into a GFF event stream.
- SequencesAsGFF() - Constructor for class org.biojava.bio.program.gff.SequencesAsGFF
-
- SequenceScalePanel - Class in org.biojava.bio.structure.gui.util
-
A class that draws a Sequence as a rectangle, a scale display over it.
- SequenceScalePanel(int) - Constructor for class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- SequenceStreamer - Interface in org.biojava.bio.program.ssaha
-
- SequenceStreamer.FileStreamer - Class in org.biojava.bio.program.ssaha
-
- SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, List) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
-
- SequenceStreamer.FileStreamer(SequenceFormat, SymbolTokenization, File) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
-
- SequenceStreamer.SequenceDBStreamer - Class in org.biojava.bio.program.ssaha
-
- SequenceStreamer.SequenceDBStreamer(SequenceDB) - Constructor for class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
-
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.HeadlessRenderContext
-
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
sequenceToGraphics converts a sequence index
to a graphical position.
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- sequenceToGraphics(int) - Method in interface org.biojava.bio.gui.sequence.SequenceRenderContext
-
Converts a sequence index into a graphical coordinate.
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- sequenceToGraphics(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
sequenceToGraphics converts a sequence index to a
graphical position.
- SequenceTools - Class in org.biojava.bio.seq
-
Methods for manipulating sequences.
- SequenceViewerEvent - Class in org.biojava.bio.gui.sequence
-
An event indicating that a mouse gesture was recognised within a widget that
renders sequences.
- SequenceViewerEvent(Object, Object, int, MouseEvent, List) - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerEvent
-
Construct a SequenceViewerEvent with the given source, target, mouseEvent
and path.
- SequenceViewerListener - Interface in org.biojava.bio.gui.sequence
-
- SequenceViewerMotionListener - Interface in org.biojava.bio.gui.sequence
-
- SequenceViewerMotionSupport - Class in org.biojava.bio.gui.sequence
-
- SequenceViewerMotionSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerMotionSupport
-
- SequenceViewerSupport - Class in org.biojava.bio.gui.sequence
-
- SequenceViewerSupport() - Constructor for class org.biojava.bio.gui.sequence.SequenceViewerSupport
-
- SEQVERSION - Static variable in interface org.biojavax.bio.BioEntry
-
- ser() - Static method in class org.biojava.bio.seq.ProteinTools
-
Returns the AtomicSymbol for the amino acid
Serine (S)
- serialize(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
-
Deprecated.
- serialize(Taxon) - Method in interface org.biojava.bio.taxa.TaxonParser
-
Deprecated.
Convert a Taxon into a stringified representation.
- serializeSource(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
-
Deprecated.
- serializeXRef(Taxon) - Method in class org.biojava.bio.taxa.EbiFormat
-
Deprecated.
- serialVersionUID - Static variable in class org.biojava.bio.dp.SimpleMarkovModel
-
- serialVersionUID - Static variable in exception org.biojava.bio.structure.io.PDBParseException
-
- serialVersionUID - Static variable in exception org.biojava.bio.structure.StructureException
-
- serialVersionUID - Static variable in class org.biojava.bio.symbol.AbstractAlphabet
-
- series - Variable in class org.biojava.bibliography.BiblioBook
-
Book series.
- server - Variable in class org.biojava.bio.structure.server.DemoStructureServer
-
- SERVERS - Static variable in class org.biojava.bio.program.das.DAS
-
- Services - Class in org.biojava.utils
-
Utility methods for handling META-INF/services files
- Services() - Constructor for class org.biojava.utils.Services
-
- set(int, int, double) - Method in class org.biojava.bio.structure.jama.Matrix
-
Set a single element.
- set(int, Object) - Method in class org.biojava.utils.FileAsList
-
This always returns null, not the previous object.
- set(Object, Object) - Method in class org.biojava.utils.ListTools.Doublet
-
- set(Object, Object, Object) - Method in class org.biojava.utils.ListTools.Triplet
-
- setA(Object) - Method in class org.biojava.utils.ListTools.Doublet
-
- setA(Object) - Method in class org.biojava.utils.ListTools.Triplet
-
- setAbsorpt_coefficient_mu(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_correction_T_max(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_correction_T_min(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_correction_type(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setAbsorpt_process_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setAbsorptionMax(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property absorptionMax.
- setAbsorptionNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property absorptionNote.
- setAccession(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setAccession(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setAccession(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the accession of the record being read.
- setAccession(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the accession of the record being read.
- setAcronym(String) - Method in interface org.biojavax.Namespace
-
Sets an optional acronym for the namespace.
- setAcronym(String) - Method in class org.biojavax.SimpleNamespace
-
Sets an optional acronym for the namespace.
- setAddPos(boolean) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Set a flag so that newly added points will be in the positive class or
negative class, depending on wether addPos is true or false respectively.
- setAdvance(int[]) - Method in interface org.biojava.bio.dp.EmissionState
-
Set the advance array.
- setAdvance(int[]) - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- setAligMap(List<AlignedPosition>) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- setAligMat(AligMatEl[][]) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setAligMat(int, int, AligMatEl) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setAligMat(AligMatEl[][]) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setAlign_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel.Border
-
- setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster.Border
-
Deprecated.
- setAlignment(int) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
-
Sets the Alignment attribute of the Border object.
- setAlignment(Alignment) - Method in class org.biojava.bio.seq.homol.SimpleHomology
-
setAlignment sets the alignment which describes
the homology.
- setAlignSeqRes(boolean) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
define if the SEQRES in the structure should be aligned with the ATOM records
if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
- setAlignSeqRes(boolean) - Method in class org.biojava.bio.structure.io.PDBFileParser
-
define if the SEQRES in the structure should be aligned with the ATOM records
if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.
- setAlignSeqRes(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
set the flag if the SEQRES and ATOM amino acids should be aligned and linked
- setAlpha(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- setAlpha(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- setAlpha(Object, double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- setAlpha(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- setAlphabetName(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- setAlphabetName(String) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
- setAlphaStar(int, double) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- setAltAligNumber(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- setAlternativeAlignment(AlternativeAlignment) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- setAlternativeAlignments(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
-
- setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setAlternativeAligs(AlternativeAlignment[]) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- setAltLoc(Character) - Method in interface org.biojava.bio.structure.Atom
-
get set alternate Location.
- setAltLoc(Character) - Method in class org.biojava.bio.structure.AtomImpl
-
set alternate Location.
- setAminoType(Character) - Method in interface org.biojava.bio.structure.AminoAcid
-
set the name of the AA, in single letter code .
- setAminoType(Character) - Method in class org.biojava.bio.structure.AminoAcidImpl
-
set the name of the AA, in single letter code .
- setAngleDiff(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setAniso_B(String[][]) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setAnnotation(Annotation) - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- setAnnotation(Annotation) - Method in interface org.biojava.bio.structure.Chain
-
get/set the Annotation of a Chain.
- setAnnotation(Annotation) - Method in class org.biojava.bio.structure.ChainImpl
-
get/set the Annotation of a Chain.
- setAnnotation(Annotation) - Method in class org.biojava.ontology.Term.Impl
-
- setApplicationClass(Class, Class) - Static method in class org.biojavax.RichObjectFactory
-
Allow application to override the default biojava class created in getObject - subclass restriction is checked in the builder.
- setArrowHeadSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- setArrowScoop(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- setArrowSize(double) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- setArticleAuthors(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Sets the names of the authors which first published an article about the
AAindex entry.
- setArticleTitle(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Sets the title of the article which describes the AAindex entry.
- setAsym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setAsym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setAtcc(String) - Method in class org.biojava.bio.structure.Compound
-
- setAtomGroups(List<Group>) - Method in interface org.biojava.bio.structure.Chain
-
Set all groups that have been specified in the ATOM section of this chain .
- setAtomGroups(List<Group>) - Method in class org.biojava.bio.structure.ChainImpl
-
Set all groups that have been specified in the ATOM section of this chain .
- setAtoms(List<Atom>) - Method in interface org.biojava.bio.structure.Group
-
Set the atoms of this group.
- setAtoms(List<Atom>) - Method in class org.biojava.bio.structure.HetatomImpl
-
set the atoms of this group
- setAuth_asym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setAuth_atom_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setAuth_comp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setAuth_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setAuth_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setAuth_seq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setAuth_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setAuth_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setAuthority(String) - Method in interface org.biojavax.Namespace
-
This method sets the authority that governs the namespace.
- setAuthority(String) - Method in class org.biojavax.SimpleNamespace
-
This method sets the authority that governs the namespace.
- setAuthorList(List<Author>) - Method in class org.biojava.bio.structure.JournalArticle
-
- setAutoFetch(boolean) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- setAutoFetch(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
tell the parser to fetch missing PDB files from the EBI FTP server automatically.
- setAutoFetch(boolean) - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
Tell the parser to fetch missing PDB files from the FTP server automatically.
- setAutoFetch(boolean) - Method in class org.biojava.bio.structure.server.MMCIFFileInstallation
-
tell the parser to fetch missing mmCif files from the RCSB FTP server automatically.
- setB(Object) - Method in class org.biojava.utils.ListTools.Doublet
-
- setB(Object) - Method in class org.biojava.utils.ListTools.Triplet
-
- setB_iso_max(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setB_iso_mean(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setB_iso_min(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setB_iso_or_equiv(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setB_iso_or_equiv_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setBaseCallAlignment(Alignment) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Provides the list of base calls.
- setBaseColor(Symbol, Color) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Maps a color to a DNA symbol.
- setBeadDepth(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
setBeadDepth sets the depth of a single bead
produced by this renderer.
- setBeadDisplacement(double) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
setBeadDisplacement sets the displacement of
beads from the centre line of the renderer.
- setBeadFill(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
setBeadFill sets the bead fill paint.
- setBeadOutline(Paint) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
setBeadOutline sets the bead outline paint.
- setBeadStroke(Stroke) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
setBeadStroke sets the bead outline stroke.
- setBiol_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setBiologicalUnit(String) - Method in class org.biojava.bio.structure.Compound
-
- setBits(int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Sets the number of significant bits in the trace samples.
- setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- setBlockDepth(double) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- setBlockPainter(BlockPainter) - Method in class org.biojava.bio.gui.DistributionLogo
-
- setBlockWidth(double) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- setBooleanValue(boolean) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
-
Override this method to do something useful with the
boolean we collect.
- setBoundaryFinder(BoundaryFinder) - Method in class org.biojava.bio.program.tagvalue.Aggregator
-
- setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
- setBounds(Rectangle2D.Float) - Method in interface org.biojava.bio.gui.glyph.Glyph
-
- setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.HelixGlyph
-
- setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
-
- setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
-
- setBounds(Rectangle2D.Float) - Method in class org.biojava.bio.gui.glyph.TwoHeadedArrowGlyph
-
- setByteValue(byte) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
-
Override this method to do something useful with the
byte we collect.
- setC(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
-
- setC(double) - Method in class org.biojava.stats.svm.SMOTrainer
-
- setC(Object) - Method in class org.biojava.utils.ListTools.Triplet
-
- setCacheSize(int) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- setCacheSize(int) - Method in interface org.biojava.bio.structure.server.StructureServer
-
set how many structures should be kept in memory - for quicker access
- setCartn_x(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setCartn_x_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setCartn_y(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setCartn_y_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setCartn_z(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setCartn_z_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setCategory(String) - Method in class org.biojava.ontology.Synonym
-
- setCell(String) - Method in class org.biojava.bio.structure.Compound
-
- setCellLine(String) - Method in class org.biojava.bio.structure.Compound
-
- setCellularLocation(String) - Method in class org.biojava.bio.structure.Compound
-
- setCenter1(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setCenter2(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setChain(Chain) - Method in class org.biojava.bio.structure.gui.util.SequenceMouseListener
-
- setChain(Chain) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- setChainId(List<String>) - Method in class org.biojava.bio.structure.Compound
-
Sets the list of chain IDs.
- setChainId(Character) - Method in class org.biojava.bio.structure.DBRef
-
The chain ID of the corresponding chain.
- setChainID1(String) - Method in class org.biojava.bio.structure.SSBond
-
- setChainID2(String) - Method in class org.biojava.bio.structure.SSBond
-
- setChainInfoFile(File) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- setChains(List<Chain>) - Method in class org.biojava.bio.structure.Compound
-
- setChains(List<Chain>) - Method in interface org.biojava.bio.structure.Structure
-
set the chains of a structure, if this is a NMR structure,
this will only set model 0.
- setChains(int, List<Chain>) - Method in interface org.biojava.bio.structure.Structure
-
set the chains for a model
- setChains(List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
-
- setChains(int, List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
-
- setChanger(Object, ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
-
Set the Changer to be used for all values of a particular tag.
- setChangeTable(ChangeTable) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
- setCharacter(char) - Method in class org.biojava.utils.RepeatedCharSequence
-
- setCharValue(char) - Method in class org.biojava.utils.stax.CharElementHandlerBase
-
Override this method to do something useful with the
char we collect.
- setChildrenRaw(Set) - Method in class org.biojava.bio.taxa.WeakTaxon
-
Deprecated.
- setChromatogram(Chromatogram) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Sets the chromatogram to draw.
- setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- setChromImpl(SymbolList[]) - Method in class org.biojavax.ga.impl.SimpleOrganism
-
- setChromosome(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- setChromosomes(SymbolList[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- setChromosomes(SymbolList[]) - Method in interface org.biojavax.ga.Organism
-
Sets the organisms 'chromosome' sequences.
- setCircular(boolean) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setCircular(boolean) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setCircular(boolean) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Defined this sequence being parser as circular.
- setCircular(boolean) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Defined this sequence being parser as circular.
- setCircular(boolean) - Method in interface org.biojavax.bio.seq.RichSequence
-
Circularises the Sequence.
- setCircular(boolean) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Circularises the Sequence.
- setCircularLength(int) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Sets the circular length of this location.
- setCircularLength(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sets the circular length of this location.
- setCircularLength(int) - Method in class org.biojavax.bio.seq.MultiSourceCompoundRichLocation
-
Sets the circular length of this location.
- setCircularLength(int) - Method in interface org.biojavax.bio.seq.RichLocation
-
Sets the circular length of this location.
- setCircularLength(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the circular length of this location.
- setClassification(String) - Method in class org.biojava.bio.structure.PDBHeader
-
- setCluster(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
set the number of the cluster this alignment belongs to.
- setCluster(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setCol(short) - Method in class org.biojava.bio.structure.align.helper.IndexPair
-
- setCollapsing(boolean) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
Specifies if the renderer should collapse to zero depth when no
features are visible (default true).
- setCommands(String) - Method in class org.biojava.utils.process.ExternalProcess
-
Sets the command line including the path or name of the external program
and its command line arguments.
- setComment(String) - Method in class org.biojava.bio.AnnotationType.Impl
-
- setComment(Object, String) - Method in class org.biojava.bio.AnnotationType.Impl
-
- setComment(String) - Method in interface org.biojava.bio.AnnotationType
-
Set the comment for the whole AnnotationType.
- setComment(Object, String) - Method in interface org.biojava.bio.AnnotationType
-
Set the comment for a particular property.
- setComment(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the comment to comment.
- setComment(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Sets the user comment for the AAindex entry.
- setComment(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setComment(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setComment(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
about a comment in the record being read.
- setComment(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
about a comment in the record being read.
- setComment(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
-
Setter for property comment.
- setComment(String) - Method in class org.biojavax.SimpleComment
-
- setCommentType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property commentType.
- setCommonName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
With this method the common name of the given taxon can be changed or created,
if there was none before.
- setCommonName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- setCommonName(String) - Method in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
Set the new common name of this Taxon.
- setComp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- setCompounds(List<Compound>) - Method in interface org.biojava.bio.structure.Structure
-
set the compounts
- setCompounds(List<Compound>) - Method in class org.biojava.bio.structure.StructureImpl
-
- setConnections(List<Map<String, Integer>>) - Method in interface org.biojava.bio.structure.Structure
-
sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
- setConnections(List<Map<String, Integer>>) - Method in class org.biojava.bio.structure.StructureImpl
-
- setConstant(double) - Method in class org.biojava.stats.svm.PolynomialKernel
-
- setConstant(double) - Method in class org.biojava.stats.svm.SigmoidKernel
-
- setConstraint(Object, CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
-
- setConstraint(Object, CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType
-
Specifies the constraint to apply to the specified property.
- setConstraints(Object, PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- setConstraints(Object, PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
-
Set the constraints associated with a property.
- setContacts(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
-
sets the ContentHandler for this object
- setContentHandler(ContentHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
this sets the ContentHandler that receives
SAX events from the internal Blast XML parser which
is the actual ContentHandler.
- setContig(int) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
-
- setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Choose whether to treat empty tags as a continuation of previous tags or as a
new tag with the value of the empty string.
- setContinueOnEmptyTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Decide whether to treat empty tags as continuations of the previous non
-empty tag.
- setCoords(double[]) - Method in interface org.biojava.bio.structure.Atom
-
set the coordinates.
- setCoords(double[]) - Method in class org.biojava.bio.structure.AtomImpl
-
the coordinates.
- setCorrelation_coeff_Fo_to_Fc(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setCorrelation_coeff_Fo_to_Fc_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setCount(AtomicSymbol, double) - Method in interface org.biojava.bio.dist.Count
-
Set the count for the Symbol s.
- setCount(AtomicSymbol, double) - Method in class org.biojava.bio.dist.IndexedCount
-
- setCounts(Count) - Method in interface org.biojava.bio.dist.Count
-
Set the counts in this Counts to be equal to the counts in c.
- setCounts(Count) - Method in class org.biojava.bio.dist.IndexedCount
-
- setCovered(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setCreate_co(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setCreateOnUnderlyingSequence(boolean) - Method in class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- setCrossOverFunction(CrossOverFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
-
Changes the CrossOverFunction used to CrossOver Chromosomes
- setCrossOverFunction(CrossOverFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
-
- setCrossOverProbs(double[]) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- setCrossOverProbs(double[]) - Method in interface org.biojavax.ga.functions.CrossOverFunction
-
Sets the probability of crossing at each base.
- setCrossRef(CrossRef) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
- setCrossref(CrossRef) - Method in interface org.biojavax.DocRef
-
The document reference may refer to an object in another database.
- setCrossref(CrossRef) - Method in class org.biojavax.SimpleDocRef
-
The document reference may refer to an object in another database.
- setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Sets the cross ref resolver to use when retrieving remote symbols.
- setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sets the cross ref resolver to use when retrieving remote symbols.
- setCrossRefResolver(CrossReferenceResolver) - Method in interface org.biojavax.bio.seq.RichLocation
-
Sets the cross ref resolver to use when retrieving remote symbols.
- setCrossRefResolver(CrossReferenceResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the cross ref resolver to use when retrieving remote symbols.
- setCrystals_number(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setCurrentSequenceName(String) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
-
- setCurrentSequenceName(String) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
-
Set the name of the sequence which is about to be received.
- setDatabase(String) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- setDatabase(String) - Method in class org.biojava.bio.structure.DBRef
-
Specifies the database value.
- setDatabaseID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- setDatabaseID(String) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
- setDatabaseID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
-
- setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentFilter
-
- setDatabaseID(String) - Method in interface org.biojava.bio.search.SearchContentHandler
-
setDatabaseID identifies the database searched by
a name, ID or URN.
- setDatabaseID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- setDatabaseName(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property databaseName.
- setDate(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- setDate_original(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- setDb_align_beg(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setDb_align_end(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setDb_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setDb_name(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setDbAccession(String) - Method in class org.biojava.bio.structure.DBRef
-
Sequence database accession code.
- setDbCode(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- setDBConnection(String, String, String, String) - Method in class org.biojava.bio.structure.io.PDBMSDReader
-
open a database conenction to the MSD search database
- setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- setDbId(AGAVEDbId) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- setDbIdCode(String) - Method in class org.biojava.bio.structure.DBRef
-
Sequence database identification code.
- setDBRefs(List<DBRef>) - Method in interface org.biojava.bio.structure.Structure
-
set the list of database references for this structure
- setDBRefs(List<DBRef>) - Method in class org.biojava.bio.structure.StructureImpl
-
- setDbSeqBegin(int) - Method in class org.biojava.bio.structure.DBRef
-
Initial sequence number of the
database seqment.
- setDbSeqEnd(int) - Method in class org.biojava.bio.structure.DBRef
-
The begin of the sequence position in the database
- setDebug(boolean) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
set the debug flag
- setDEBUG(boolean) - Method in class org.biojava.bio.structure.io.SeqRes2AtomAligner
-
- setDefaultChanger(ChangeTable.Changer) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
The changer that will be applied to the values of tags not registered
explicitly to any changer or splitter instance.
- setDefaultConstraint(CollectionConstraint) - Method in class org.biojava.bio.AnnotationType.Impl
-
- setDefaultConstraint(CollectionConstraint) - Method in interface org.biojava.bio.AnnotationType
-
Specifies the default constraint to apply to properties where no
other constraint is specified.
- setDefaultConstraints(PropertyConstraint, Location) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- setDefaultConstraints(PropertyConstraint, Location) - Method in interface org.biojava.bio.AnnotationType
-
Set the constraints that will apply to all properties without an
explicitly defined set of constraints.
- setDefaultCrossReferenceResolver(CrossReferenceResolver) - Static method in class org.biojavax.RichObjectFactory
-
Sets the default crossref resolver to use when resolving remote entries.
- setDefaultNamespaceName(String) - Static method in class org.biojavax.RichObjectFactory
-
Sets the default namespace name to use when loading sequences.
- setDefaultOntologyName(String) - Static method in class org.biojavax.RichObjectFactory
-
Sets the default ontology name to use when loading sequences.
- setDefaultPaint(Paint) - Method in class org.biojava.bio.gui.sequence.PeptideDigestRenderer
-
- setDefaultPositionResolver(PositionResolver) - Static method in class org.biojavax.RichObjectFactory
-
Sets the default position resolver to use when creating new rich feature locations.
- setDefaultRichSequenceHandler(RichSequenceHandler) - Static method in class org.biojavax.RichObjectFactory
-
Sets the default sequence handler to use when performing sequence manipulation.
- setDefaultSplitter(ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
The splitter that will be applied to the values of tags not registered
explicitly to any changer or splitter instance.
- setDefaultTransitions(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
specify fallback TransitionTable for this State
- setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
-
- setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
-
- setDelegate(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
TagValueWrapper interface
- setDelegate(TagValueListener) - Method in interface org.biojava.bio.program.tagvalue.TagValueWrapper
-
set listener to which all calls will be delegated
- setDelegateParser(TagValueParser) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
setDelegateRenderer associates an
OptimizableFilter with a
BeadFeatureRenderer.
- setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in interface org.biojava.bio.gui.sequence.BeadFeatureRenderer
-
setDelegateRenderer associates an
OptimizableFilter with a
BeadFeatureRenderer.
- setDelegateRenderer(OptimizableFilter, BeadFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
setDelegateRenderer for the specified filter.
- setDelete(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Sets the penalty for a delete operation to the specified value.
- setDelete(short) - Method in class org.biojava.bio.alignment.SmithWaterman
-
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a delete operation to the specified value.
- setDensityCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDepDate(Date) - Method in class org.biojava.bio.structure.PDBHeader
-
- setDepth(double) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- setDepth(double) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
- setDepth(SequenceRenderer, double) - Method in class org.biojava.bio.gui.sequence.LineInfo
-
- setDepth(double) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- setDepthScaler(SuffixTreeKernel.DepthScaler) - Method in class org.biojava.stats.svm.tools.SuffixTreeKernel
-
Change the current DepthScaler to
depthScaler.
- setDescription(String) - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
Sets the description to the given value.
- setDescription(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Sets the description for the AAindex entry.
- setDescription(String) - Method in class org.biojava.bio.structure.PDBHeader
-
- setDescription(String) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
-
- setDescription(String) - Method in class org.biojava.ontology.AbstractTerm
-
- setDescription(String) - Method in class org.biojava.ontology.IntegerOntology.IntTerm
-
- setDescription(String) - Method in class org.biojava.ontology.IntegerOntology
-
- setDescription(String) - Method in class org.biojava.ontology.Ontology.Impl
-
- setDescription(String) - Method in interface org.biojava.ontology.Ontology
-
set the description of this ontology
- setDescription(String) - Method in class org.biojava.ontology.OntologyTerm.Impl
-
- setDescription(String) - Method in interface org.biojava.ontology.Term
-
set the description of the term;
- setDescription(String) - Method in class org.biojava.ontology.Triple.Impl
-
- setDescription(String) - Method in interface org.biojavax.bio.BioEntry
-
Sets the description for this bioentry.
- setDescription(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setDescription(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setDescription(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the description of the record being read.
- setDescription(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the description of the record being read.
- setDescription(String) - Method in class org.biojavax.bio.SimpleBioEntry
-
Sets the description for this bioentry.
- setDescription(String) - Method in interface org.biojavax.Namespace
-
This method sets a description for the namespace.
- setDescription(String) - Method in interface org.biojavax.ontology.ComparableOntology
-
Sets a human-readable description of this ontology.
- setDescription(String) - Method in interface org.biojavax.ontology.ComparableTerm
-
Sets the description associated with this term.
- setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Sets a human-readable description of this ontology.
- setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Sets the description associated with this term.
- setDescription(String) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
set the description of the term;
- setDescription(String) - Method in class org.biojavax.SimpleNamespace
-
This method sets a description for the namespace.
- setDescriptors(Set) - Method in interface org.biojavax.ontology.ComparableTriple
-
Clears the current set of descriptors and replaces it with the content of
the set passed.
- setDescriptors(Set) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Clears the current set of descriptors and replaces it with the content of
the set passed.
- setDetails(String) - Method in class org.biojava.bio.structure.Compound
-
- setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- setDetails(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setDiagonalDistance(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDiagonalDistance2(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDimensionRatio(double) - Method in class org.biojava.bio.gui.sequence.EllipticalBeadRenderer
-
setDimensionRatio sets the minimum ratio of
long dimension to short dimension of the bead.
- setDirection(int) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
This method allows you to decide in which direction the arrow has to point.
- setDirection(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setDirection sets the direction in which this
context will render the sequence - HORIZONTAL or VERTICAL.
- setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Set the direction that this SequencePanel renders in.
- setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setDirection(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Set the direction that this SequencePoster renders in.
- setDirection(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
setDirection sets the direction in which this
context will render sequences - HORIZONTAL or VERTICAL.
- setDistanceBetweenFeatures(int) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- setDistanceMatrix(Matrix) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
The distance matrix this alignment is based on
- setDistribution(Symbol, Distribution) - Method in interface org.biojava.bio.dist.OrderNDistribution
-
Set the distribution assocated with a symbol.
- setDistribution(Distribution) - Method in interface org.biojava.bio.dp.EmissionState
-
Set the Distribution associated with this state.
- setDistribution(Distribution) - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- setDistribution(Distribution) - Method in class org.biojava.bio.gui.DistributionLogo
-
Set the dist to render.
- setDivision(String) - Method in interface org.biojavax.bio.BioEntry
-
Sets the division of this bioentry.
- setDivision(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setDivision(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setDivision(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the division of the record being read.
- setDivision(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the division of the record being read.
- setDivision(String) - Method in class org.biojavax.bio.SimpleBioEntry
-
Sets the division of this bioentry.
- setDoAngleCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDocumentLocator(Locator) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
- setDocumentLocator(Locator) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
-
- setDocumentLocator(Locator) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
- setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
-
- setDocumentLocator(Locator) - Method in interface org.biojava.utils.stax.StAXContentHandler
-
- setDocumentLocator(Locator) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
- setDoDensityCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDoDistanceCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDoi(String) - Method in class org.biojava.bio.structure.JournalArticle
-
Set the value of doi
- setDoRMSCheck(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setDoubleProperty(Symbol, String) - Method in class org.biojava.bio.symbol.SimpleSymbolPropertyTable
-
- setDoubleValue(double) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
-
Override this method to do something useful with the
double we collect.
- setDTDHandler(DTDHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- setEcNums(List<String>) - Method in class org.biojava.bio.structure.Compound
-
- setEditorList(List<Author>) - Method in class org.biojava.bio.structure.JournalArticle
-
- setElementId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- setElideComments(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Use this method to toggle reading of comments data.
- setElideComments(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Use this method to toggle reading of comments data.
- setElideFeatures(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Use this method to toggle reading of feature data.
- setElideFeatures(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Use this method to toggle reading of feature data.
- setElideReferences(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Use this method to toggle reading of bibliographic reference data.
- setElideReferences(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Use this method to toggle reading of bibliographic reference data.
- setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
Specifies whether the symbols (SQ) part of the entry should
be ignored.
- setElideSymbols(boolean) - Method in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
Use this method to toggle reading of sequence data.
- setElideSymbols(boolean) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Use this method to toggle reading of sequence data.
- setElideSymbols(boolean) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Use this method to toggle reading of sequence data.
- setEnd(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the end coordinate to end.
- setEnd(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- setEnd(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Set the string indicating that a record has ended.
- setEndOfRecord(String) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Set the explicit end-of-record string.
- setEngineered(String) - Method in class org.biojava.bio.structure.Compound
-
- setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- setEntity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setEntityResolver(EntityResolver) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
This class has an EntityResolver that
resolves the public ID specifying the
NCBI DTDs to resource files within the
BioJava libraries.
- setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- setEntry_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- setEnvironmentProperties(String[]) - Method in class org.biojava.utils.process.ExternalProcess
-
Sets environment variables for the external process.
- setEpsilon(double) - Method in class org.biojava.stats.svm.SMORegressionTrainer
-
- setEpsilon(double) - Method in class org.biojava.stats.svm.SMOTrainer
-
- setEquivalent(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff.GFFParser
-
Set the error handler used by this parser.
- setErrorHandler(GFFErrorHandler) - Method in class org.biojava.bio.program.gff3.GFF3Parser
-
Set the error handler used by this parser.
- setErrorHandler(ErrorHandler) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- setErrorHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
-
Sets the output error handler which is responsible for the standard error
output of the external process.
- setEvalCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setEvents(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property events.
- setExceptionOnNullDelegate(boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
-
determines if an exception is thrown when an event
arrives without the delegate being set.
- setExpressionSystem(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemAtccNumber(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemCell(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemCellLine(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemCellularLocation(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemGene(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemOrgan(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemOrganelle(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemOtherDetails(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemPlasmid(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemStrain(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemTaxId(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemTissue(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemVariant(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemVector(String) - Method in class org.biojava.bio.structure.Compound
-
- setExpressionSystemVectorType(String) - Method in class org.biojava.bio.structure.Compound
-
- setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Setter for property factory.
- setFactory(RichSequenceBuilderFactory) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Setter for property factory.
- setFallback(StateMachine.TransitionTable) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
-
set the specified TransitionTable to be looked
looked up if the Transition cannot be found in
this one.
- setFeature(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FeatureFilter
-
Set the feature to feature.
- setFeature(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the feature type to type.
- setFeature(String, boolean) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
by default, we set the parser to non-validating.
- setFeature(RichFeature) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Sets the feature this location is associated with.
- setFeature(RichFeature) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sets the feature this location is associated with.
- setFeature(RichFeature) - Method in interface org.biojavax.bio.seq.RichLocation
-
Sets the feature this location is associated with.
- setFeature(RichFeature) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the feature this location is associated with.
- setFeatureFilter(FeatureFilter) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Replace the current FeatureFilter with
filter.
- setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
Set the object which receives startFeature/endFeature notifications.
- setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- setFeatureListener(SeqIOListener) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
- setFeatureProperty(Object, Object) - Method in class org.biojava.bio.program.xff.FeatureHandler
-
Set a property.
- setFeatureRealizer(FeatureRealizer) - Method in class org.biojava.bio.seq.impl.SimpleSequenceFactory
-
Set the FeatureRealizer used by new sequences created by this
factory.
- setFeatureRelationshipSet(Set) - Method in interface org.biojavax.bio.seq.RichFeatureRelationshipHolder
-
Clears the relations from this feautre holder and replaces them with a new set.
- setFeatureRelationshipSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Clears the relations from this feautre holder and replaces them with a new set.
- setFeatureRenderer(FeatureRenderer) - Method in class org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer
-
setFeatureRenderer sets the renderer to be used.
- setFeatureSet(Set<Feature>) - Method in interface org.biojavax.bio.seq.RichSequence
-
Sets the features of this sequence.
- setFeatureSet(Set<Feature>) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Sets the features of this sequence.
- setFeatureSource(FeatureSource) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- setFilePath(File) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- setFill(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- setFill(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- setFill(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- setFill(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- setFillColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Set the background color of the label area.
- setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
-
- setFillPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
Allows you to set the paint properties of this glyph.
- setFillPaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- setFilter(FeatureFilter) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
setFilter sets the filter.
- setFilter(GFFRecordFilter) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.NotFilter
-
- setFirstIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Setter for property firstIntActID.
- setFitness(double[]) - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- setFitness(double[]) - Method in interface org.biojavax.ga.Organism
-
This method allows to set the fitness of this organism to the specified
value.
- setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.functions.SelectionFunction.SelectAll
-
- setFitnessFunction(FitnessFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
-
The fitness function that will be used to compute the fitness of each
organism.
- setFitnessFunction(FitnessFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- setFloatValue(float) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
-
Override this method to do something useful with the
float we collect.
- setFont(Font) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setFormula(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setFormula_weight(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setFormula_weight(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setFragCompat(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setFragment(String) - Method in class org.biojava.bio.structure.Compound
-
- setFragmentLength(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setFragmentMiniDistance(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
- setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setFragmentPairs(FragmentPair[]) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- setFrame(int) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.FrameFilter
-
- setFrame(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the frame to frame.
- setFullName(String) - Method in interface org.biojava.bio.structure.Atom
-
set full name of atom e.g.
- setFullName(String) - Method in class org.biojava.bio.structure.AtomImpl
-
set full name of atom e.g.
- setGapExt(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Sets the penalty for an extension of any gap (insert or delete) to the
specified value.
- setGapExt(short) - Method in class org.biojava.bio.alignment.SmithWaterman
-
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for an extension of any gap (insert or delete) to the specified
value.
- setGapExtCol(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setGapExtCol(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setGapExtension(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setGapExtRow(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setGapExtRow(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setGapOpen(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setGapOpenCol(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setGapOpenCol(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setGapOpenRow(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setGapOpenRow(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setGene(String) - Method in class org.biojava.bio.structure.Compound
-
- setGenerateSequenceHeader(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Specify whether a per-sequence header line, giving the length of the
sequence, should be generated.
- setGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Sets the genetic code of this taxon, which may be null, which will unset it.
- setGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Sets the genetic code of this taxon, which may be null, which will unset it.
- setGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Updates the taxon in the database and sets its genetic code id to the specified value.
- setGlyphForFilter(FeatureFilter, Glyph) - Method in class org.biojava.bio.gui.sequence.GlyphFeatureRenderer
-
Allows setting another
Glyph object to be painted for the given
FeatureFilter.
- setGroup_PDB(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setGroupAttributes(Map) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Replace the group-attribute Map with
ga.
- setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
Sets the element name that the class responds to.
- setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
Sets the element name that the class responds to.
- setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
Sets the element name that the class responds to.
- setHandlerCharacteristics(String, boolean) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
-
Sets the element name that the class responds to.
- setHeader(Compound) - Method in interface org.biojava.bio.structure.Chain
-
Set the Header from the PDB file.
- setHeader(Compound) - Method in class org.biojava.bio.structure.ChainImpl
-
Set the Header from the PDB file.
- setHeader(Map<String, Object>) - Method in interface org.biojava.bio.structure.Structure
-
set the Header data .
- setHeader(Map<String, Object>) - Method in class org.biojava.bio.structure.StructureImpl
-
set the Header data.
- setHeader(FastaHeader) - Method in class org.biojavax.bio.seq.io.FastaFormat
-
- setHeaderVars(String) - Method in class org.biojava.bio.structure.Compound
-
- setHeight(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Sets the height (in pixels).
- setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularBeadRenderer
-
setHeightScaling sets the height scaling
policy.
- setHeightScaling(boolean) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
setHeightScaling sets the height scaling
policy.
- setHetero(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- setHetero(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setHorizontalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Sets the horizontal scale (proportional).
- setId(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- setId(long) - Method in class org.biojava.bio.structure.AtomImpl
-
Set the Hibernate database ID.
- setId(Long) - Method in interface org.biojava.bio.structure.Chain
-
Set the ID used by Hibernate.
- setId(Long) - Method in class org.biojava.bio.structure.ChainImpl
-
Set the ID used by Hibernate.
- setId(Long) - Method in class org.biojava.bio.structure.Compound
-
set the ID used by Hibernate
- setId(Long) - Method in class org.biojava.bio.structure.DBRef
-
Set the ID used by Hibernate.
- setId(long) - Method in class org.biojava.bio.structure.HetatomImpl
-
the Hibernate database ID
- setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
-
- setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- setId(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setId(Long) - Method in interface org.biojava.bio.structure.Structure
-
set the ID used by Hibernate
- setId(Long) - Method in class org.biojava.bio.structure.StructureImpl
-
set the ID used by Hibernate
- setID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Setter for property ID.
- setId(Integer) - Method in class org.biojavax.bio.seq.SimplePosition
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntry
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.ontology.SimpleComparableTriple
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.SimpleComment
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.SimpleCrossRef
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.SimpleDocRef
-
Sets the Hibernate ID.
- setId(Integer) - Method in class org.biojavax.SimpleNamespace
-
Sets the Hibernate ID.
- setIdbnsBegin(char) - Method in class org.biojava.bio.structure.DBRef
-
Insertion code of initial residue of the segment, if PDB is the
reference.
- setIdbnsEnd(char) - Method in class org.biojava.bio.structure.DBRef
-
Insertion code of the ending
residue of the segment, if PDB is
the reference.
- setIdCode(String) - Method in class org.biojava.bio.structure.DBRef
-
Set the idCode for this entry.
- setIdCode(String) - Method in class org.biojava.bio.structure.PDBHeader
-
The PDB code for this protein structure.
- setIdentifier(String) - Method in interface org.biojavax.bio.BioEntry
-
Sets the identifier of this bioentry.
- setIdentifier(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setIdentifier(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setIdentifier(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the identifier of the record being read.
- setIdentifier(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the identifier of the record being read.
- setIdentifier(String) - Method in class org.biojavax.bio.SimpleBioEntry
-
Sets the identifier of this bioentry.
- setIdentifier(String) - Method in interface org.biojavax.ontology.ComparableTerm
-
Sets the (optional) identifier associated with this term.
- setIdentifier(String) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Sets the (optional) identifier associated with this term.
- setIdxlist(List<int[]>) - Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.BasicImapRenderer
-
setImageMap sets the current image map.
- setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.RectangularImapRenderer
-
setImageMap sets the current image map.
- setImageMap(ImageMap) - Method in class org.biojava.bio.gui.sequence.ZiggyImapRenderer
-
setImageMap sets the current image map.
- setIndex(int) - Method in class org.biojava.bio.structure.align.helper.GapArray
-
- setInitialK(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setInitials(String) - Method in class org.biojava.bio.structure.Author
-
- setInput(InputStream) - Method in interface org.biojava.utils.process.OutputHandler
-
Sets the input stream.
- setInput(InputStream) - Method in class org.biojava.utils.process.StreamPipe
-
Sets the input stream
- setInput(InputStream) - Method in class org.biojava.utils.process.WriterOutputHandler
-
Sets the input stream.
- setInputHandler(InputHandler) - Method in class org.biojava.utils.process.ExternalProcess
-
Sets the input handler which is responsible for the standard input
of the external process.
- setInsCode1(String) - Method in class org.biojava.bio.structure.SSBond
-
- setInsCode2(String) - Method in class org.biojava.bio.structure.SSBond
-
- setInsert(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Sets the penalty for an insert operation to the specified value.
- setInsert(short) - Method in class org.biojava.bio.alignment.SmithWaterman
-
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for an insert operation to the specified value.
- setInsertBegin(char) - Method in class org.biojava.bio.structure.DBRef
-
Initial insertion code of the PDB sequence segment.
- setInsertEnd(char) - Method in class org.biojava.bio.structure.DBRef
-
Ending insertion code of the PDB sequence segment.
- setInteractions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property interactions.
- setIntValue(int) - Method in class org.biojava.utils.stax.IntElementHandlerBase
-
Override this method to do something useful with the
int we collect.
- setIsoforms(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property isoforms.
- setIsoIDs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Setter for property isoIDs.
- setIsPublished(Boolean) - Method in class org.biojava.bio.structure.JournalArticle
-
Sets the publication state of a JournalArticle - TO BE PUBLISHED == false
- setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter
-
Selects strict mode.
- setIsStrict(boolean) - Method in class org.biojava.bio.seq.io.filterxml.XMLFilterWriter
-
Selects strict mode.
- setJoiner(String) - Method in class org.biojava.bio.program.tagvalue.Aggregator
-
- setJoinPlo(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setJoinRMSCutoff(double) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setJournalArticle(JournalArticle) - Method in interface org.biojava.bio.structure.Structure
-
set the associated publication as defined by the JRNL records in a PDB
file.
- setJournalArticle(JournalArticle) - Method in class org.biojava.bio.structure.StructureImpl
-
set the associated publication as defined by the JRNL records in a PDB
file.
- setJournalName(String) - Method in class org.biojava.bio.structure.JournalArticle
-
- setJournalReference(String) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Sets a reference to the journal which published the article about the
AAindex entry.
- setKernel(SVMKernel) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- setKernel(SVMKernel) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Set the kernel used for classification.
- setKey(Object) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer.AnnotationLabelMaker
-
- setKineticsNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property kineticsNote.
- setKMs(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property KMs.
- setLabel(Object) - Method in class org.biojava.bio.gui.sequence.AlignmentRenderer
-
- setLabel(String) - Method in class org.biojava.bio.gui.sequence.SimpleLabelRenderer
-
- setLabel(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Setter for property label.
- setLabel_alt_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setLabel_asym_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setLabel_atom_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setLabel_comp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setLabel_entity_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setLabel_seq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setLabelMaker(FeatureLabelRenderer.LabelMaker) - Method in class org.biojava.bio.gui.sequence.FeatureLabelRenderer
-
- setLambda(double) - Method in class org.biojava.stats.svm.DiagonalAddKernel
-
Set the scale factor.
- setLeadingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- setLeftValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Updates the taxon and sets the left value to the specified value.
- setLeftValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Sets the left value.
- setLeftValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Sets the left value.
- setLength(int) - Method in class org.biojava.bio.search.SeqContentPattern
-
Set the pattern length.
- setLength(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- setLength(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
-
- setLength(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setLength(int) - Method in class org.biojava.bio.structure.gui.util.CoordManager
-
- setLength(int) - Method in class org.biojava.utils.RepeatedCharSequence
-
- setLimit(int) - Method in class org.biojava.utils.cache.FixedSizeCache
-
- setLines(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Set the absolute number of lines that the sequence will be rendered on.
- setLineWidth(int) - Method in class org.biojava.bio.program.phred.PhredFormat
-
Set the line width.
- setLineWidth(int) - Method in class org.biojava.bio.seq.io.FastaFormat
-
Deprecated.
Set the line width.
- setLineWidth(int) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Set the line width.
- setLineWidth(int) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Set the line width.
- setListener(TagValueListener) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
set a TagValueListener for this State.
- setListener(Object, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- setListener(PatternListener) - Method in class org.biojava.utils.automata.PatternBlitz
-
- setListener(PatternListener) - Method in interface org.biojava.utils.automata.StateMachineFactory
-
- setListener(Search.Listener) - Method in class org.biojava.utils.regex.Search
-
- setLITDBEntryNumbers(String[]) - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Sets the list of literature database identifiers for the AAindex entry.
- setLoc(Location) - Method in interface org.biojava.bio.alignment.AlignmentElement
-
- setLoc(Location) - Method in class org.biojava.bio.alignment.SimpleAlignmentElement
-
- setLocation(Location) - Method in interface org.biojava.bio.seq.Feature
-
The new location for this feature.
- setLocation(Location) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- setLocation(Location) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
The new location for this feature.
- setLocation(RichLocation) - Method in interface org.biojavax.RankedDocRef
-
Set the location of this reference.
- setLocation(RichLocation) - Method in class org.biojavax.SimpleRankedDocRef
-
Set the location of this reference.
- setLocationValue(Location) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
-
Override this method to do something useful with the
location we collect.
- setLogoFont(Font) - Method in class org.biojava.bio.gui.TextBlock
-
Set the current logo font.
- setLogoFont(Font) - Method in class org.biojava.bio.gui.TextLogoPainter
-
Set the current logo font.
- setLogoPainter(LogoPainter) - Method in class org.biojava.bio.gui.DistributionLogo
-
Set the logo painter.
- setLongValue(long) - Method in class org.biojava.utils.stax.LongElementHandlerBase
-
Override this method to do something useful with the
long we collect.
- setLRUCacheSize(int) - Static method in class org.biojavax.RichObjectFactory
-
Sets the size of the LRU cache.
- setLRUCacheSize(Class, int) - Static method in class org.biojavax.RichObjectFactory
-
Sets the size of the LRU cache.
- setLs_d_res_high(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_d_res_low(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_number_parameters(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_all(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_number_reflns_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_number_restraints(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_percent_reflns_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_percent_reflns_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_all(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_free_error(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_free_error_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_R_factor_R_work(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_redundancy_reflns_obs(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_wR_factor_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setLs_wR_factor_R_work(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setMapAll(boolean) - Method in class org.biojava.bio.molbio.RestrictionMapper
-
setMapAll sets whether all sites should be marked,
including those which have recognition sites within the
sequence, but cut outside it.
- setMapType(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- setMatch(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Sets the penalty for a match operation to the specified value.
- setMatch(short) - Method in class org.biojava.bio.alignment.SmithWaterman
-
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a match operation to the specified value.
- setMatrix(Matrix) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
sets the distance matrix to be displayed
- setMatrix(Matrix) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- setMatrix(int, int, int, int, Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix(int[], int[], Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix(int[], int, int, Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Set a submatrix.
- setMatrix(int, int, int[], Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Set a submatrix.
- setMaxCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern
-
Set the maximum counts required for a symbol.
- setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.AbstractCrossOverFunction
-
- setMaxCrossOvers(int) - Method in class org.biojavax.ga.functions.CrossOverFunction.NoCross
-
- setMaxCrossOvers(int) - Method in interface org.biojavax.ga.functions.CrossOverFunction
-
Sets an upper limit on the number of crosses.
- setMaxIter(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setMaxMissedCleavages(int) - Method in class org.biojava.bio.proteomics.Digest
-
Sets the maximum number of partial digest products to be annotated.
- setMaxPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
- setMaxrefine(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setMaxRunTimeSecs(int) - Method in class org.biojava.utils.ExecRunner
-
Sets the maximum run time in seconds.
- setMergeAnnotation(Annotation) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
- setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Enable or disable treating runs of identical tags as a single tag start
event with multiple values or each as a separate tag start, value, and tag
end.
- setMergeSameTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Decide if multiple examples of a single tag should be merged into a single
start/endTag pair with multiple values, or multiple start/endTag pairs each
with a single value.
- setMethod(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setMethod(String) - Method in class org.biojava.bio.structure.PDBHeader
-
- setMethod_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Exptl
-
- setMinCounts(AtomicSymbol, int) - Method in class org.biojava.bio.search.SeqContentPattern
-
Set the minimum counts required for a symbol.
- setMinPosition(Position) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
- setMismatches(int) - Method in class org.biojava.bio.search.MaxMismatchPattern
-
- setMitochondrialGeneticCodeID(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Updates the given taxon and sets it's so called mitochondrial genetic code id to
the specified value.
- setMitoGeneticCode(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Sets the mitochondrial genetic code of this taxon, which may be null,
which will unset it.
- setMitoGeneticCode(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Sets the mitochondrial genetic code of this taxon, which may be null,
which will unset it.
- setMod_type(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- setModDate(Date) - Method in class org.biojava.bio.structure.PDBHeader
-
- setModel(MarkovModel) - Method in class org.biojava.bio.dp.DP
-
- setModel(int, List<Chain>) - Method in interface org.biojava.bio.structure.Structure
-
a convenience function if one wants to edit and replace the
models in a structure.
- setModel(int, List<Chain>) - Method in class org.biojava.bio.structure.StructureImpl
-
- setModeLazy() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
-
- setModeLazy() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
-
Setting the mode to lazy means that, if the program is recognised,
e.g.
- setModeStrict() - Method in class org.biojava.bio.program.BlastLikeToXMLConverter
-
- setModeStrict() - Method in class org.biojava.bio.program.sax.BlastLikeSAXParser
-
This is the default, parsing will be attempted only if both
the program e.g.
- setMolecularWeight(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property molecularWeight.
- setMolId(String) - Method in class org.biojava.bio.structure.Compound
-
Set the mol id value.
- setMolName(String) - Method in class org.biojava.bio.structure.Compound
-
- setMolWeightError(Integer) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property molWeightError.
- setMolWeightMethod(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property molWeightMethod.
- setMolWeightRangeEnd(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property molWeightRangeEnd.
- setMolWeightRangeStart(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property molWeightRangeStart.
- setMon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- setMon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setMon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setMon_nstd_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setMon_nstd_parent_comp_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setMoreSearches(boolean) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- setMoreSearches(boolean) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentAdapter
-
- setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentFilter
-
- setMoreSearches(boolean) - Method in interface org.biojava.bio.search.SearchContentHandler
-
setMoreSearches sets the state of the
SearchContentHandler's expectation of receiving
more results.
- setMoreSearches(boolean) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- setMultiplier(double) - Method in class org.biojava.stats.svm.PolynomialKernel
-
- setMultiplier(double) - Method in class org.biojava.stats.svm.SigmoidKernel
-
- setMutation(String) - Method in class org.biojava.bio.structure.Compound
-
- setMutationFunction(MutationFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
-
Sets the current MutationFunction
- setMutationFunction(MutationFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
-
- setMutationProbs(double[]) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- setMutationProbs(double[]) - Method in interface org.biojavax.ga.functions.MutationFunction
-
Set the probability of a mutation occuring at a certain position
Position 0 in the array corresponds to the
probability of the first residue of seq mutating.
- setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.AbstractMutationFunction
-
- setMutationSpectrum(OrderNDistribution) - Method in class org.biojavax.ga.functions.MutationFunction.NoMutation
-
- setMutationSpectrum(OrderNDistribution) - Method in interface org.biojavax.ga.functions.MutationFunction
-
Sets the Distribution of Symbols that will be selected
from when a mutation occurs.
- setName(String) - Method in class org.biojava.bio.dp.SimpleEmissionState
-
- setName(String) - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
set the name of this group.
- setName(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- setName(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
Assign a name to this sequence
- setName(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- setName(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- setName(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- setName(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- setName(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener that the current sequence is generally known
by a particular name.
- setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- setName(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- setName(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
The name is printed out as part of the identifier line.
- setName(String) - Method in interface org.biojava.bio.structure.Atom
-
set trimmed version of atom name, e.g.
- setName(String) - Method in class org.biojava.bio.structure.AtomImpl
-
trimmed version of atom name, e.g.
- setName(String) - Method in interface org.biojava.bio.structure.Chain
-
get and set the name of this chain (Chain id in PDB file ).
- setName(String) - Method in class org.biojava.bio.structure.ChainImpl
-
get and set the name of this chain (Chain id in PDB file ).
- setName(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setName(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxEntityNonPoly
-
- setName(String) - Method in interface org.biojava.bio.structure.Structure
-
set biological name of Structure .
- setName(String) - Method in class org.biojava.bio.structure.StructureImpl
-
set biological name of Structure.
- setName(String) - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
Assign a name to the alphabet
- setName(String) - Method in class org.biojava.ontology.IntegerOntology
-
- setName(String) - Method in class org.biojava.ontology.Ontology.Impl
-
- setName(String) - Method in interface org.biojava.ontology.Ontology
-
Set the name for this ontology
- setName(String) - Method in class org.biojava.ontology.Synonym
-
- setName(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setName(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setName(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener that the current sequence is generally known
by a particular name.
- setName(String) - Method in interface org.biojavax.bio.seq.RichFeature
-
Sets the name of this feature.
- setName(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Sets the name of this feature.
- setName(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Changes the name.
- setName(String) - Method in class org.biojavax.ga.impl.AbstractOrganism
-
- setName(String) - Method in class org.biojavax.ga.impl.AbstractPopulation
-
- setName(String) - Method in interface org.biojavax.ga.Organism
-
Sets the organisms name
- setName(String) - Method in interface org.biojavax.ga.Population
-
Sets the name of the population
- setName(String) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
- setNameClass(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Changes the class of this name.
- setNamedIsoforms(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
-
Setter for property namedIsoforms.
- setNames(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Setter for property names.
- setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenbankRichSequenceDB
-
Setter for property namespace.
- setNamespace(Namespace) - Method in class org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB
-
Setter for property namespace.
- setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setNamespace(Namespace) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the namespace of the record being read.
- setNamespace(Namespace) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the namespace of the record being read.
- setNdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setNdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setNegShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Set the Shape to represent the negative points.
- setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.CachingKernel
-
- setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.DiagonalCachingKernel
-
Set the kernel to nest.
- setNestedKernel(SVMKernel) - Method in class org.biojava.stats.svm.NestedKernel
-
Set the SVMKernel to nest to
k.
- setNewTag(Object, Object) - Method in class org.biojava.bio.program.tagvalue.TagMapper
-
setNewTag.
- setNmr(boolean) - Method in interface org.biojava.bio.structure.Structure
-
set NMR flag.
- setNmr(boolean) - Method in class org.biojava.bio.structure.StructureImpl
-
- setNodeRank(String) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Sets the node rank of this taxon.
- setNodeRank(String) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Setter for property nodeRank.
- setNormalizingVector(SparseVector) - Method in class org.biojava.stats.svm.SparseVector.NormalizingKernel
-
Set the normalizing vector.
- setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Setter for property note.
- setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- setNote(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property note.
- setNoteSet(Set) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in class org.biojavax.bio.SimpleBioEntry
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in class org.biojavax.EmptyRichAnnotation
-
Clears the notes from this annotation and replaces them with
those from the given set.
- setNoteSet(Set) - Method in interface org.biojavax.RichAnnotatable
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in interface org.biojavax.RichAnnotation
-
Clears the notes from this annotation and replaces them with
those from the given set.
- setNoteSet(Set) - Method in class org.biojavax.SimpleCrossRef
-
Clears the notes associated with this object and replaces them with
the contents of this set.
- setNoteSet(Set) - Method in class org.biojavax.SimpleRichAnnotation
-
Clears the notes from this annotation and replaces them with
those from the given set.
- setNullModel(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
-
- setNullModel(Distribution) - Method in interface org.biojava.bio.dist.Distribution
-
Set the null model Distribution that this Distribution recognizes.
- setNullModel(Distribution) - Method in class org.biojava.bio.dist.GapDistribution
-
- setNullModel(Distribution) - Method in class org.biojava.bio.dist.PairDistribution
-
- setNullModel(Distribution) - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractDistribution
-
Implement this to set the null model.
- setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
- setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.SimpleDistribution
-
- setNullModelImpl(Distribution) - Method in class org.biojava.bio.dist.UniformDistribution
-
Assign a background distribution.
- setNullModelWeight(double) - Method in interface org.biojava.bio.dist.DistributionTrainerContext
-
Set the number of pseudocounts to add when training the distribution.
- setNullModelWeight(double) - Method in class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
- setNum(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- setNum(String) - Method in class org.biojava.bio.structure.io.mmcif.model.EntityPolySeq
-
- setNumber(float) - Method in class org.biojava.bio.symbol.SuffixTree.SuffixNode
-
Set the number associated with this node.
- setNumberExperiments(int) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Setter for property numberExperiments.
- setNumRes(String) - Method in class org.biojava.bio.structure.Compound
-
- setObsolete(Boolean) - Method in interface org.biojavax.ontology.ComparableTerm
-
Sets the obsolescence flag associated with this term.
- setObsolete(Boolean) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Sets the obsolescence flag associated with this term.
- setOccupancy(double) - Method in interface org.biojava.bio.structure.Atom
-
set occupancy.
- setOccupancy(double) - Method in class org.biojava.bio.structure.AtomImpl
-
- setOccupancy(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setOccupancy_esd(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setOccupancy_max(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOccupancy_min(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOffset(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- setOne_letter_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setOption(ChromatogramGraphic.Option, Object) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Sets a new value for the specified option.
- setOrder(double) - Method in class org.biojava.stats.svm.PolynomialKernel
-
- setOrgan(String) - Method in class org.biojava.bio.structure.Compound
-
- setOrganelle(String) - Method in class org.biojava.bio.structure.Compound
-
- setOrganismCommon(String) - Method in class org.biojava.bio.structure.Compound
-
- setOrganismScientific(String) - Method in class org.biojava.bio.structure.Compound
-
- setOrganismsDiffer(boolean) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Setter for property organismsDiffer.
- setOrganismTaxId(String) - Method in class org.biojava.bio.structure.Compound
-
- setOrientation(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- setOuterPaint(Paint) - Method in class org.biojava.bio.gui.glyph.ArrowGlyph
-
Allows setting the paint properties of the outer line of this glyph to the
given value.
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ArrowedFeatureRenderer
-
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.CrosshairRenderer
-
setOutline sets the the colour used to draw the
lines.
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.PairwiseDiagonalRenderer
-
setOutline sets the the colour used to draw the
lines.
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.TickFeatureRenderer
-
- setOutline(Paint) - Method in class org.biojava.bio.gui.sequence.ZiggyFeatureRenderer
-
- setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.DNAStyle
-
- setOutlinePaint(Symbol, Paint) - Method in class org.biojava.bio.gui.SimpleSymbolStyle
-
- setOutput(OutputStream) - Method in interface org.biojava.utils.process.InputHandler
-
Sets the output stream.
- setOutput(OutputStream) - Method in class org.biojava.utils.process.ReaderInputHandler
-
Sets the output stream.
- setOutput(OutputStream) - Method in class org.biojava.utils.process.StreamPipe
-
Sets the output stream
- setOutputHandler(OutputHandler) - Method in class org.biojava.utils.process.ExternalProcess
-
Sets the output handler which is responsible for the standard output
of the external process.
- setOverall_FOM_free_R_set(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOverall_FOM_work_R_set(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOverall_SU_B(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOverall_SU_ML(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOverall_SU_R_Cruickshank_DPI(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setOverall_SU_R_free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPadding(double) - Method in class org.biojava.bio.gui.sequence.PaddingRenderer
-
Set the padding.
- setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.RectangleGlyph
-
Allows you to set the paint properties of this glyph, i.e., its color.
- setPaint(Paint) - Method in class org.biojava.bio.gui.glyph.TurnGlyph
-
Allows you to set the paint properties of this glyph, i.e., its color.
- setPaintDefaults(Graphics2D) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
set some default rendering hints, like text antialiasing on
- setParams(StrucAligParameters) - Method in class org.biojava.bio.structure.align.StructurePairAligner
-
set the parameters to be used for the algorithm
- setParent(Connection, Taxon, Taxon) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
This updates the taxonomic tree in the database and sets the parent of the given
child taxon to the parent taxon.
- setParent(Group) - Method in interface org.biojava.bio.structure.Atom
-
Sets the back-reference to its parent Group.
- setParent(Group) - Method in class org.biojava.bio.structure.AtomImpl
-
- setParent(Structure) - Method in interface org.biojava.bio.structure.Chain
-
Set the back-reference to its parent Structure.
- setParent(Structure) - Method in class org.biojava.bio.structure.ChainImpl
-
Set the back-reference to its parent Structure.
- setParent(Structure) - Method in class org.biojava.bio.structure.DBRef
-
Set the structure object that this DBRef relates to.
- setParent(Chain) - Method in interface org.biojava.bio.structure.Group
-
Set the back-reference (to its parent Chain).
- setParent(Chain) - Method in class org.biojava.bio.structure.HetatomImpl
-
Set the back-reference (to its parent Chain)
- setParent(FeatureHolder) - Method in interface org.biojavax.bio.seq.RichFeature
-
Sets the parent of this feature.
- setParent(FeatureHolder) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Sets the parent of this feature.
- setParentNCBITaxID(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Sets the parent NCBI taxon ID.
- setParentNCBITaxID(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Sets the parent NCBI taxon ID.
- setParseCAOnly(boolean) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
- setParseCAOnly(boolean) - Method in class org.biojava.bio.structure.io.PDBFileParser
-
the flag if only the C-alpha atoms of the structure should be parsed.
- setParseCAOnly(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
only the CA atoms should be parsed from the PDB file
- setParserListener(Object, TagValueParser, TagValueListener) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- setParseSecStruc(boolean) - Method in class org.biojava.bio.structure.io.PDBFileParser
-
a flag to tell the parser to parse the Author's secondary structure assignment from the file
default is set to false, i.e.
- setParseSecStruc(boolean) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
- setPath(IndexPair[]) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setPath(IndexPair[]) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setPath(String) - Method in class org.biojava.bio.structure.io.MMCIFFileReader
-
- setPath(String) - Method in class org.biojava.bio.structure.io.PDBFileReader
-
directory where to find PDB files
- setPath(String) - Method in interface org.biojava.bio.structure.io.StructureIOFile
-
Set path to file / connection string to db.
- setPathPrefix(File) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
setPathPrefix sets the abstract path to be
appended to sequence database filenames retrieved from the
binary index.
- setPathSize(int) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setPathSize(int) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setPattern(Pattern) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Set the Pattern used to split lines.
- setPattern(SymbolList) - Method in class org.biojava.bio.search.MaxMismatchPattern
-
- setPdb_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdb_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_mon_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_seq_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPdb_strand_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setPdb_strand_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setPDBCode(String) - Method in interface org.biojava.bio.structure.Group
-
Specifies the PDBCode (residue number + insertion code) value.
- setPDBCode(String) - Method in class org.biojava.bio.structure.HetatomImpl
-
set the PDB code.
- setPDBCode(String) - Method in interface org.biojava.bio.structure.server.StructureEvent
-
- setPDBCode(String) - Method in class org.biojava.bio.structure.server.StructureEventImpl
-
- setPDBCode(String) - Method in interface org.biojava.bio.structure.Structure
-
set PDB code of structure .
- setPDBCode(String) - Method in class org.biojava.bio.structure.StructureImpl
-
set PDB code of structure .
- setPDBFlag(boolean) - Method in interface org.biojava.bio.structure.Group
-
flag if group has 3D data .
- setPDBFlag(boolean) - Method in class org.biojava.bio.structure.HetatomImpl
-
flag if group has 3D data.
- setPDBHeader(PDBHeader) - Method in interface org.biojava.bio.structure.Structure
-
the the header information for this PDB file
- setPDBHeader(PDBHeader) - Method in class org.biojava.bio.structure.StructureImpl
-
- setPDBInfoFile(File) - Method in class org.biojava.bio.structure.server.FlatFileInstallation
-
- setPDBInstallation(PDBInstallation) - Method in class org.biojava.bio.structure.server.SimpleStructureServer
-
- setPDBInstallation(PDBInstallation) - Method in interface org.biojava.bio.structure.server.StructureServer
-
- setPDBline(String) - Method in interface org.biojava.bio.structure.Atom
-
store the whole line.
- setPDBline(String) - Method in class org.biojava.bio.structure.AtomImpl
-
store the whole line.
- setPDBName(String) - Method in class org.biojava.bio.structure.AminoAcidImpl
-
set three character name of AminoAcid.
- setPDBName(String) - Method in interface org.biojava.bio.structure.Group
-
Set the PDB 3 letter name for this group.
- setPDBName(String) - Method in class org.biojava.bio.structure.HetatomImpl
-
set three character name of Group .
- setPDBresnum1(String[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- setPDBresnum2(String[]) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- setPDBserial(int) - Method in interface org.biojava.bio.structure.Atom
-
set PDB atom number.
- setPDBserial(int) - Method in class org.biojava.bio.structure.AtomImpl
-
set PDB atom number.
- setPdbx_align_begin(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setPdbx_ambiguous_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_auth_seq_align_beg(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_auth_seq_align_end(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_blank_PDB_chainid_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- setPdbx_data_cutoff_high_absF(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_data_cutoff_high_rms_absF(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_data_cutoff_low_absF(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_db_accession(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setPdbx_db_accession(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_db_align_beg_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_db_align_end_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_description(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setPdbx_descriptor(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- setPdbx_ec(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setPdbx_formal_charge(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setPdbx_formal_charge(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_fragment(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setPdbx_ideal_coordinates_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_ideal_coordinates_missing_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_initial_date(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_isotropic_thermal_model(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_keywords(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- setPdbx_ls_cross_valid_method(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_ls_sigma_F(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_ls_sigma_I(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_method_to_determine_struct(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_model_coordinates_db_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_model_coordinates_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_model_coordinates_missing_flag(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_model_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- setPdbx_model_type_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- setPdbx_modified(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- setPdbx_modified_date(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_mutation(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setPdbx_number_of_molecules(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setPdbx_overall_ESU_R(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_ESU_R_Free(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_overall_phase_error(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_PDB_id_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_PDB_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setPdbx_PDB_model_num(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setPdbx_processing_site(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_R_Free_selection_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_refine_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_release_status(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_replaced_by(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_replaces(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_seq_align_beg_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_seq_align_end_ins_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_seq_one_letter_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- setPdbx_solvent_ion_probe_radii(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_solvent_shrinkage_radii(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_solvent_vdw_probe_radii(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_starting_model(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_stereochem_target_val_spec_case(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_stereochemistry_target_values(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setPdbx_strand_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setPdbx_subcomponent_list(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_synonyms(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPdbx_type(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPercId(int) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- setPermutationSize(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setPhase(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setPHDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property PHDependence.
- setPmid(String) - Method in class org.biojava.bio.structure.JournalArticle
-
Set the value of pmid
- setPolymerType(PolymerType) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setPopulation(Population) - Method in interface org.biojavax.ga.GeneticAlgorithm
-
Sets the Population of Organisms to the
Algorithm.
- setPopulation(Population) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- setPos(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPosition
-
- setPos(int, int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- setPos1(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setPos1(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- setPos2(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setPos2(int) - Method in class org.biojava.bio.structure.gui.util.AlignedPosition
-
- setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sets the resolver to use when working out actual base coordinates from
fuzzy positions.
- setPositionResolver(PositionResolver) - Method in interface org.biojavax.bio.seq.RichLocation
-
Sets the resolver to use when working out actual base coordinates from
fuzzy positions.
- setPositionResolver(PositionResolver) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the resolver to use when working out actual base coordinates from
fuzzy positions.
- setPositions(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- setPosShape(Shape) - Method in class org.biojava.stats.svm.tools.ClassifierExample.PointClassifier
-
Set the Shape to represent the positive points.
- setPreferredSize() - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setPrimaryKey(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
setPrimaryKey sets the primary identifier
namespace.
- setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Index2Model
-
Set the tag to use as a primary key in the index.
- setPrimaryKeyName(String) - Method in class org.biojava.bio.program.tagvalue.Indexer
-
Set the tag to use as a primary key in the index.
- setPrintConnections(boolean) - Method in class org.biojava.bio.structure.io.FileConvert
-
enable/disable printing of connections
connections are sometimes buggy in PDB files
so there are some cases where one might turn this off.
- setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- setPrintStream(PrintStream) - Method in interface org.biojava.bio.seq.io.SeqFileFormer
-
Deprecated.
setPrintStream informs an instance which
PrintStream to use.
- setPrintStream(PrintStream) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
setPrintStream informs an instance which
PrintStream to use.
- setPrintStream(PrintStream) - Method in class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
-
Sets the stream to write to.
- setPrintStream(PrintStream) - Method in interface org.biojavax.bio.seq.io.RichSequenceFormat
-
Sets the stream to write to.
- setPrintWriter(PrintWriter) - Method in class org.biojava.bio.program.blast2html.HTMLRenderer
-
Set the PrintWriter to output the HTML
to.
- setProfileHMM() - Method in class org.biojava.bio.program.hmmer.HmmerProfileParser
-
- setProperties(Map<String, Object>) - Method in interface org.biojava.bio.structure.Group
-
properties of this amino acid.
- setProperties(Map<String, Object>) - Method in class org.biojava.bio.structure.HetatomImpl
-
properties of this amino acid.
- setProperty(Object, Object) - Method in class org.biojava.bio.AbstractAnnotation
-
- setProperty(Object, Object) - Method in interface org.biojava.bio.Annotation
-
Set the value of a property.
- setProperty(Annotation, Object, Object) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- setProperty(Annotation, Object, Object) - Method in interface org.biojava.bio.AnnotationType
-
Set the property in an annotation bundle according to the type we believe
it should be.
- setProperty(Object, Object) - Method in class org.biojava.bio.MergeAnnotation
-
- setProperty(Object, Object) - Method in class org.biojava.bio.OverlayAnnotation
-
- setProperty(String, Object) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
-
- setProperty(String, String, boolean) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- setProperty(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
- setProperty(String, Object) - Method in interface org.biojava.bio.structure.Group
-
set a single property .
- setProperty(String, Object) - Method in class org.biojava.bio.structure.HetatomImpl
-
set a single property .
- setProperty(Object, Object) - Method in class org.biojavax.EmptyRichAnnotation
-
Set the value of a property.
- setProperty(Object, Object) - Method in class org.biojavax.SimpleRichAnnotation
-
Deprecated.
- setProtease(Protease) - Method in class org.biojava.bio.proteomics.Digest
-
- setPublicationDate(int) - Method in class org.biojava.bio.structure.JournalArticle
-
- setPublished(boolean) - Method in class org.biojava.bio.structure.JournalArticle
-
- setPublisher(String) - Method in class org.biojava.bio.structure.JournalArticle
-
- setQuery(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentClient
-
Specifies the query.
- setQueryID(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- setQueryID(String) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- setQueryID(String) - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- setQueryID(String) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- setQueryID(String) - Method in class org.biojava.bio.search.SearchContentAdapter
-
- setQueryID(String) - Method in class org.biojava.bio.search.SearchContentFilter
-
- setQueryID(String) - Method in interface org.biojava.bio.search.SearchContentHandler
-
setQueryID identifies the query sequence by a
name, ID or URN.
- setQueryID(String) - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- setQuerySeq(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
Deprecated.
use setQueryID instead.
- setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
setQuerySeqHolder sets the query sequence holder
to a specific database.
- setQuerySeqHolder(SequenceDB) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
setQuerySeqHolder sets the query sequence holder
to a specific database.
- setRadius(double) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- setRange(RangeLocation) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- setRange(RangeLocation) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- setRank(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Updates a taxon and sets it's rank to the specified String.
- setRank(Integer) - Method in interface org.biojavax.bio.BioEntryRelationship
-
Sets the rank of this relationship.
- setRank(int) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sets the rank for this location.
- setRank(int) - Method in interface org.biojavax.bio.seq.RichFeature
-
Sets the rank of this feature.
- setRank(int) - Method in interface org.biojavax.bio.seq.RichFeatureRelationship
-
Sets the rank of this relationship.
- setRank(int) - Method in interface org.biojavax.bio.seq.RichLocation
-
Sets the rank for this location.
- setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Sets the rank of this feature.
- setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Sets the rank of this relationship.
- setRank(int) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the rank for this location.
- setRank(Integer) - Method in class org.biojavax.bio.SimpleBioEntryRelationship
-
Sets the rank of this relationship.
- setRank(int) - Method in interface org.biojavax.Comment
-
Sets the rank of this comment.
- setRank(int) - Method in interface org.biojavax.Note
-
Sets the rank for this note.
- setRank(int) - Method in interface org.biojavax.RankedCrossRef
-
Set the rank associated with the cross reference.
- setRank(int) - Method in interface org.biojavax.RankedDocRef
-
Set the rank of this reference.
- setRank(int) - Method in class org.biojavax.SimpleComment
-
Sets the rank of this comment.
- setRank(int) - Method in class org.biojavax.SimpleNote
-
Sets the rank for this note.
- setRank(int) - Method in class org.biojavax.SimpleRankedCrossRef
-
Set the rank associated with the cross reference.
- setRank(int) - Method in class org.biojavax.SimpleRankedDocRef
-
Set the rank of this reference.
- setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setRankedCrossRef(RankedCrossRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener about a cross reference.
- setRankedCrossRef(RankedCrossRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener about a cross reference.
- setRankedCrossRefs(Set) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Sets the ranked cross references associated with an object.
- setRankedCrossRefs(Set) - Method in class org.biojavax.bio.SimpleBioEntry
-
- setRankedCrossRefs(Set) - Method in class org.biojavax.ontology.SimpleComparableTerm
-
Sets the ranked cross references associated with an object.
- setRankedCrossRefs(Set) - Method in interface org.biojavax.RankedCrossRefable
-
Sets the ranked cross references associated with an object.
- setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setRankedDocRef(RankedDocRef) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
about a literature reference in the record being read.
- setRankedDocRef(RankedDocRef) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
about a literature reference in the record being read.
- setReader(Reader) - Method in class org.biojava.utils.process.ReaderWriterPipe
-
Sets the reader.
- setRecordType(String) - Method in interface org.biojava.bio.structure.AminoAcid
-
Allows to distinguish between amino acids that are provided
as ATOM records and a SEQRES records.
- setRecordType(String) - Method in class org.biojava.bio.structure.AminoAcidImpl
-
- setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.FilteringRenderer
-
- setRecurse(boolean) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
setRecurse sets the recursion flag on the filter.
- setRecurse(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Set whether features will be filtered recursively to
recurse.
- setRecursive(boolean) - Method in interface org.biojava.bio.seq.io.agave.DelegationManager
-
- setRedoxPotential(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property redoxPotential.
- setReduceInitialFragments(boolean) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setRef(String) - Method in class org.biojava.bio.structure.JournalArticle
-
Set the value of the ref.
- setRef_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setRefChainId(String) - Method in class org.biojava.bio.structure.Compound
-
Returns the ref chain id value.
- setRefn(String) - Method in class org.biojava.bio.structure.JournalArticle
-
Set the value of the refn
- setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- setRel(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEXref
-
- setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setRelationship(BioEntryRelationship) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
about a relationship between the bioentry or sequence in the
record being read and another bioentry.
- setRelationship(BioEntryRelationship) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
about a relationship between the bioentry or sequence in the
record being read and another bioentry.
- setRemark(String) - Method in interface org.biojavax.DocRef
-
Set the remarks for this document reference using this method.
- setRemark(String) - Method in class org.biojavax.SimpleDocRef
-
Set the remarks for this document reference using this method.
- setRenderer(CircularFeatureRenderer) - Method in class org.biojava.bio.gui.sequence.CircularFeaturesRenderer
-
- setRenderer(CircularRenderer) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Set the child renderer responsible for drawing the contents of this track
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.OverlayRendererWrapper
-
- setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseFilteringRenderer
-
setRenderer sets the renderer.
- setRenderer(PairwiseSequenceRenderer) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setRenderer sets the current
PairwiseSequenceRenderer.
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.SequenceRendererWrapper
-
- setRenderer(SequenceRenderer) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
setRenderer sets the current
SequenceRenderer.
- setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.DistributionLogo
-
- setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setRenderingHints sets the
RenderingHints which will be used by the
Graphics2D instances of delegate renderers.
- setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Use this to switch on effects like Anti-aliasing etc
- setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Use this to switch on effects like Anti-aliasing etc
- setRenderingHints(RenderingHints) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
setRenderingHints sets the
RenderingHints which will be used by the
Graphics2D instances of delegate renderers.
- setReplace(short) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Sets the penalty for a replace operation to the specified value.
- setReplace(short) - Method in class org.biojava.bio.alignment.SmithWaterman
-
Overrides the method inherited from the NeedlemanWunsch and sets the
penalty for a replace operation to the specified value.
- setReplaces(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- setResidueType(ResidueType) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setResNames(String) - Method in class org.biojava.bio.structure.Compound
-
- setResnum1(String) - Method in class org.biojava.bio.structure.SSBond
-
- setResnum2(String) - Method in class org.biojava.bio.structure.SSBond
-
- setResolution(float) - Method in class org.biojava.bio.structure.PDBHeader
-
- setRetain(boolean) - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
Set wether known tags are to be retained or dropped.
- setRichObjectBuilder(RichObjectBuilder) - Static method in class org.biojavax.RichObjectFactory
-
Sets the builder to use when instantiating new Rich objects.
- setRightValue(Connection, Taxon, int) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
Updates the taxon in the database and sets the right value to the specified value.
- setRightValue(Integer) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
Sets the right value.
- setRightValue(Integer) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Sets the right value.
- setRms(double) - Method in class org.biojava.bio.structure.align.helper.JointFragments
-
- setRms(double) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
the rms in the structurally equivalent regions
- setRms(double) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setRot(Matrix) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setRow(short) - Method in class org.biojava.bio.structure.align.helper.IndexPair
-
- setSaturation(float) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setScale(double) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setScale sets the scale in pixels per
Symbol.
- setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Set the scale.
- setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setScale(double) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Set the scale.
- setScale(double) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
setScale sets the scale in pixels per
Symbol.
- setScale(float) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setScale(float) - Method in class org.biojava.bio.structure.gui.util.CoordManager
-
- setScale(float) - Method in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- setScaleByInformation(boolean) - Method in class org.biojava.bio.gui.DistributionLogo
-
- setScalevalue(float) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setScientificName(Connection, Taxon, String) - Static method in class org.biojava.bio.seq.db.biosql.TaxonSQL
-
Deprecated.
This changes the scientific name of the given taxon and stores the new name persistent
in the database.
- setScientificName(String) - Method in class org.biojava.bio.taxa.AbstractTaxon
-
Deprecated.
- setScientificName(String) - Method in interface org.biojava.bio.taxa.Taxon
-
Deprecated.
Change the scientific name of this species.
- setScope(int) - Method in class org.biojava.ontology.Synonym
-
- setScore(double) - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- setScore(double) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the score to score.
- setScore(double) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setScore(String) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnot
-
- setScore(float) - Method in interface org.biojava.bio.structure.align.pairwise.Alignable
-
- setScore(float) - Method in class org.biojava.bio.structure.align.pairwise.AlternativeAlignment
-
- setScore(float) - Method in class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
setSearchContentHandler sets the handler which
will recieve the method calls generated by the adapter.
- setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
-
setSearchContentHandler sets the handler which
will recieve the method calls generated by the adapter.
- setSearchContentHandler(SearchContentHandler) - Method in class org.biojava.bio.search.FilteringContentHandler
-
- setSecondarySequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setSecondarySequence sets the secondary
Sequence to be rendered.
- setSecondarySymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setSecondarySymbolTranslation sets the translation
in Symbols which will be applied when
rendering.
- setSecondIntActID(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Interaction
-
Setter for property secondIntActID.
- setSecretion(String) - Method in class org.biojava.bio.structure.Compound
-
- setSecStruc(Map<String, String>) - Method in interface org.biojava.bio.structure.AminoAcid
-
Specifies the secondary structure as a Map.
- setSecStruc(Map<String, String>) - Method in class org.biojava.bio.structure.AminoAcidImpl
-
set the secondary structure data for this amino acid.
- setSeedFragmentLength(int) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setSeedRmsdCutoff(float) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setSelectedAlignmentPos(int) - Method in class org.biojava.bio.structure.gui.JMatrixPanel
-
- setSelectionFunction(SelectionFunction) - Method in interface org.biojavax.ga.GeneticAlgorithm
-
Changes the SelectionFunction used to select candidates for
the next generation
- setSelectionFunction(SelectionFunction) - Method in class org.biojavax.ga.impl.AbstractGeneticAlgorithm
-
- setSelectionPressure(int) - Method in class org.biojavax.ga.functions.TournamentSelection
-
sets the parameter controlling selection pressure
- setSeq_align_beg(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setSeq_align_end(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- setSeq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxNonPolyScheme
-
- setSeq_id(String) - Method in class org.biojava.bio.structure.io.mmcif.model.PdbxPolySeqScheme
-
- setSeqBegin(int) - Method in class org.biojava.bio.structure.DBRef
-
Initial sequence number of the PDB sequence segment.
- setSeqCautions(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property seqCautions.
- setSeqEnd(int) - Method in class org.biojava.bio.structure.DBRef
-
Ending sequence number of the PDB sequence segment.
- setSeqID(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
-
Deprecated.
- setSeqName(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SequenceFilter
-
Set the sequence name to seqName.
- setSeqName(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the sequence name to seqName.
- setSeqResGroups(List<Group>) - Method in interface org.biojava.bio.structure.Chain
-
Set the list of SeqResGroups for this chain.
- setSeqResGroups(List<Group>) - Method in class org.biojava.bio.structure.ChainImpl
-
Set the list of SeqResGroups for this chain.
- setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.CircularRendererPanel
-
- setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setSequence sets the Sequence
to be rendered.
- setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.SequencePanel
-
Set the SymboList to be rendered.
- setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Set the SymboList to be rendered.
- setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- setSequence(Sequence) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- setSequence(Sequence) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- setSequence(SymbolList) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
setSequence sets the Sequence to be
rendered.
- setSequence(Sequence) - Method in class org.biojava.bio.proteomics.Digest
-
- setSequence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- setSequenceCount(int) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
-
- setSequenceCount(int) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
-
Set the number of sequences in the alignment.
- setSequenceDB(SequenceDB) - Method in class org.biojava.bio.gui.FeatureTree
-
Use this method to provide the sequences for the tree to work with.
- setSequenceFormat(LifeScienceIdentifier) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
setSequenceFormat sets the sequence format name
which will be indicated in the index.
- setSequenceFormat(SequenceFormat) - Method in class org.biojava.bio.seq.db.NCBISequenceDB
-
- setSequenceID(String) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setSequenceLength(int) - Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- setSequenceLength(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
- setSequenceOffset(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- setSequenceRef(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Setter for property sequenceRef.
- setSequenceType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Isoform
-
Setter for property sequenceType.
- setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setSeqVersion(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the version of the sequence of the record being read.
- setSeqVersion(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the version of the sequence of the record being read.
- setSeqVersion(Double) - Method in interface org.biojavax.bio.seq.RichSequence
-
Sets the version of the associated symbol list.
- setSeqVersion(Double) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Sets the version of the associated symbol list.
- setSerNum(int) - Method in class org.biojava.bio.structure.SSBond
-
get serial number of this SSBOND in PDB file
- setServer(StructureServer) - Method in class org.biojava.bio.structure.server.DemoStructureServer
-
- setServerurl(String) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentCall
-
set url of aligmnent service.
- setServerurl(String) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureCall
-
set url of structure service.
- setShatter(boolean) - Method in class org.biojava.bio.program.gff.SequencesAsGFF
-
Specify whether features with non-contiguous locations should be broken
up such that a GFF feature line is emitted for each contiguous block.
- setShowAccession(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
-
- setShowDescription(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
-
- setShowIdentifier(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
-
- setShowName(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
-
- setShowNamespace(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
-
- setShowVersion(boolean) - Method in class org.biojavax.bio.seq.io.FastaHeader
-
Determines if the version number of a sequence should be displayed.
- setSibling(SimilarityPairFeature) - Method in interface org.biojava.bio.seq.homol.SimilarityPairFeature
-
setSibling sets the sibling feature of the
pair.
- setSibling(SimilarityPairFeature) - Method in class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
-
- setSignificantBits(int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
-
Sets the number of significant bits in the data.
- setSitesCount(int) - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
-
- setSitesCount(int) - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
-
Set the number of sites in the alignment
- setSize(double) - Method in class org.biojava.bio.gui.sequence.SequenceRenderContext.Border
-
Sets the size of the border in number of pixels.
- setSleepTime(int) - Method in class org.biojava.utils.process.ExternalProcess
-
- setSolvent_model_details(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setSolvent_model_param_bsol(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setSolvent_model_param_ksol(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Refine
-
- setSource(String) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.SourceFilter
-
Set the source to source.
- setSource(String) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the feature source to source.
- setSource(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setSource(String) - Method in interface org.biojava.bio.seq.Feature
-
Change the source of the Feature.
- setSource(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- setSource(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- setSource(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Change the source of the Feature.
- setSourceTerm(Term) - Method in interface org.biojava.bio.seq.Feature
-
Set the source ontology-term for this feature.
- setSourceTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- setSourceTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Set the source ontology-term for this feature.
- setSpacer(int) - Method in class org.biojava.bio.gui.sequence.SequencePoster
-
Deprecated.
Set the number of pixels to leave blank between each block of sequence
information.
- setSplitOffset(int) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Set the offset to split lines at.
- setSplitter(Object, ChangeTable.Splitter) - Method in class org.biojava.bio.program.tagvalue.ChangeTable
-
Set the Splitter to be used for all values of a particular tag.
- setSrc_method(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setSSBonds(List<SSBond>) - Method in interface org.biojava.bio.structure.Structure
-
set the list of SSBonds for this structure
- setSSBonds(List<SSBond>) - Method in class org.biojava.bio.structure.StructureImpl
-
set the list of SSBonds for this structure
- setStandard(boolean) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setStart(int) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the start coordinate to start.
- setStart(int) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegion
-
- setStart(int) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegion
-
- setStartPage(String) - Method in class org.biojava.bio.structure.JournalArticle
-
- setStatus(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBrev
-
- setStoreLocation(File) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
setStoreLocation sets the directory of the new
index.
- setStoreName(String) - Method in class org.biojava.bio.program.indexdb.BioStoreFactory
-
setStoreName sets the name to be given to the new
index.
- setStrain(String) - Method in class org.biojava.bio.structure.Compound
-
- setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.GFFRecordFilter.StrandFilter
-
- setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Set the strand to strand.
- setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setStrand(StrandedFeature.Strand) - Method in class org.biojava.bio.seq.impl.SimpleStrandedFeature
-
- setStrand(StrandedFeature.Strand) - Method in interface org.biojava.bio.seq.StrandedFeature
-
Set the strand that this feature lies upon.
- setStrand(StrandedFeature.Strand) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Set the strand that this feature lies upon.
- setStrand(RichLocation.Strand) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
- setStreamParser(StreamParser) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
-
assign a StreamParser object to instance.
- setStringSequence(String) - Method in class org.biojavax.bio.seq.SimpleRichSequence
-
- setStringValue(String) - Method in class org.biojava.bio.program.xff.PropDetailHandler
-
- setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
-
- setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
-
- setStringValue(String) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
-
- setStringValue(String) - Method in class org.biojava.utils.stax.StringElementHandlerBase
-
Override this method to do something useful with the
string we collect.
- setStruct(Struct) - Method in class org.biojava.bio.structure.io.mmcif.ChemCompConsumer
-
- setStruct(Struct) - Method in interface org.biojava.bio.structure.io.mmcif.MMcifConsumer
-
- setStruct(Struct) - Method in class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
- setStructure(Structure) - Method in class org.biojava.bio.structure.gui.BiojavaJmol
-
- setStructure1(Structure) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
-
- setStructure1(Structure) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- setStructure2(Structure) - Method in class org.biojava.bio.structure.gui.events.JmolAlignedPositionListener
-
- setStructure2(Structure) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- setStructurePairAligner(StructurePairAligner) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
-
- setStyle(SymbolStyle) - Method in class org.biojava.bio.gui.DistributionLogo
-
Set the symbol style.
- setSubjectDB(String) - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
Deprecated.
use setDatabaseID instead.
- setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
setSubjectDBInstallation sets the subject database
holder to a specific installation.
- setSubjectDBInstallation(SequenceDBInstallation) - Method in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
setSubjectDBInstallation sets the subject database
holder to a specific installation.
- setSubSeqStart(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- setSubstitutionMatrix(SubstitutionMatrix) - Method in class org.biojava.bio.alignment.NeedlemanWunsch
-
Sets the substitution matrix to be used to the specified one.
- setSurname(String) - Method in class org.biojava.bio.structure.Author
-
- setSwissprotId(String) - Method in interface org.biojava.bio.structure.Chain
-
Set the Swissprot id of this chain.
- setSwissprotId(String) - Method in class org.biojava.bio.structure.ChainImpl
-
set the Swissprot id of this chains .
- setSymbolList(SymbolList) - Method in class org.biojava.bio.molbio.Composition
-
Set the SymbolList to calculation the composition of.
- setSymbolLists(SymbolList, SymbolList) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
-
Set the DNA and OFFSETS symbol lists for the basecall alignment.
- setSymbolModification(char, double) - Method in class org.biojava.bio.proteomics.MassCalc
-
Use this to set a post translational modification for the
Symbol represented by this character.
- setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.PairwiseSequencePanel
-
setSymbolTranslation sets the translation in
Symbols which will be applied when rendering.
- setSymbolTranslation(int) - Method in class org.biojava.bio.gui.sequence.TranslatedSequencePanel
-
setSymbolTranslation sets the translation in
Symbols which will be applied when rendering.
- setSynonyms(List<String>) - Method in class org.biojava.bio.structure.Compound
-
- setSynonyms(Set) - Method in class org.biojava.ontology.Term.Impl
-
- setSynthetic(String) - Method in class org.biojava.bio.structure.Compound
-
- setTableNumber(int) - Method in class org.biojava.bio.symbol.SimpleGeneticCodeTable
-
- setTagGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Set the group number that will match the tag.
- setTarget(Object, double) - Method in class org.biojava.stats.svm.AbstractSVMTarget
-
- setTarget(Object, double) - Method in class org.biojava.stats.svm.SimpleSVMTarget
-
- setTarget(Object, double) - Method in interface org.biojava.stats.svm.SVMTarget
-
- setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.BioEntry
-
Sets the taxon for this bioentry.
- setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setTaxon(NCBITaxon) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the Taxon of the record being read.
- setTaxon(NCBITaxon) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the Taxon of the record being read.
- setTaxon(NCBITaxon) - Method in class org.biojavax.bio.SimpleBioEntry
-
Sets the taxon for this bioentry.
- setTaxonHidden(boolean) - Method in interface org.biojavax.bio.taxa.NCBITaxon
-
determines whether this taxonomy level is displayed in etNameHierarchy()
- setTaxonHidden(boolean) - Method in class org.biojavax.bio.taxa.SimpleNCBITaxon
-
- setTechnique(String) - Method in class org.biojava.bio.structure.PDBHeader
-
- setTemperatureDependence(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property temperatureDependence.
- setTempFactor(double) - Method in interface org.biojava.bio.structure.Atom
-
get set temp factor .
- setTempFactor(double) - Method in class org.biojava.bio.structure.AtomImpl
-
- setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Sets the term for this location.
- setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sets the term for this location.
- setTerm(ComparableTerm) - Method in interface org.biojavax.bio.seq.RichLocation
-
Sets the term for this location.
- setTerm(ComparableTerm) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sets the term for this location.
- setTerm(ComparableTerm) - Method in interface org.biojavax.Note
-
Sets the term for this note.
- setTerm(ComparableTerm) - Method in class org.biojavax.SimpleNote
-
Sets the term for this note.
- setTermSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology
-
Clears out all the terms and populates the ontology with the contents
of the set passed.
- setTermSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Clears out all the terms and populates the ontology with the contents
of the set passed.
- setText(String) - Method in class org.biojava.bio.structure.io.mmcif.model.DatabasePDBremark
-
- setText(String) - Method in class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- setText(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property text.
- setTextColor(Color) - Method in class org.biojava.bio.gui.sequence.LabelledSequenceRenderer
-
Set the color of the label text
- setThreadFetches(boolean) - Static method in class org.biojava.bio.program.das.DAS
-
- setThree_letter_code(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setThreshold() - Method in class org.biojava.stats.svm.AbstractSVMClassifierModel
-
- setThreshold(double) - Method in class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- setThreshold(double) - Method in interface org.biojava.stats.svm.SVMClassifierModel
-
- setThreshold(double) - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- setTickDirection(int) - Method in class org.biojava.bio.gui.sequence.OffsetRulerRenderer
-
- setTissue(String) - Method in class org.biojava.bio.structure.Compound
-
- setTitle(String) - Method in interface org.biojava.bio.program.homologene.Orthologue
-
- setTitle(String) - Method in class org.biojava.bio.program.homologene.SimpleOrthologue
-
- setTitle(String) - Method in class org.biojava.bio.structure.Compound
-
- setTitle(String) - Method in class org.biojava.bio.structure.gui.BiojavaJmol
-
- setTitle(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Struct
-
- setTitle(String) - Method in class org.biojava.bio.structure.JournalArticle
-
Set the value of title
- setTitle(String) - Method in class org.biojava.bio.structure.PDBHeader
-
- setTrace(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.AbstractChromatogram
-
Provides the trace samples for a particular nucleotide.
- setTrace(ABITrace) - Method in class org.biojava.bio.gui.sequence.AbiTraceRenderer
-
- setTraceValues(AtomicSymbol, int[], int) - Method in class org.biojava.bio.chromatogram.SimpleChromatogram
-
Sets the trace array for one of the DNA nucleotides.
- setTrackLayout(TrackLayout) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setTrailingPixles(int) - Method in class org.biojava.bio.gui.sequence.BumpedRenderer
-
- setTrans(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
set a Transition for this State
- setTransition(Object, StateMachine.State) - Method in class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
set a Transition for this State setting notifyOnExit to false.
- setTransition(Object, StateMachine.State, boolean) - Method in class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
-
set a Transition within this TransitionTable (3-argument form)
- setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
-
Alter the translation mapping.
- setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleReversibleTranslationTable
-
Alter the translation mapping.
- setTranslation(AtomicSymbol, AtomicSymbol) - Method in class org.biojava.bio.symbol.SimpleTranslationTable
-
Alter the translation mapping.
- setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Enable or disable trimming of tags.
- setTrimTag(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Enable trimming of the tag using String.trim().
- setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.LineSplitParser
-
Enable or disable trimming of values.
- setTrimValue(boolean) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Enable trimming of the value using String.trim().
- setTripleSet(Set) - Method in interface org.biojavax.ontology.ComparableOntology
-
Clears out all the triples and populates the ontology with the contents
of the set passed.
- setTripleSet(Set) - Method in class org.biojavax.ontology.SimpleComparableOntology
-
Clears out all the triples and populates the ontology with the contents
of the set passed.
- setType(Term) - Method in class org.biojava.bio.program.gff3.GFF3Record.Impl
-
- setType(String) - Method in interface org.biojava.bio.seq.Feature
-
Change the type of this feature.
- setType(AnnotationType) - Method in class org.biojava.bio.seq.FeatureFilter.ByAnnotationType
-
- setType(String) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- setType(String) - Method in class org.biojava.bio.structure.io.mmcif.model.ChemComp
-
- setType(String) - Method in class org.biojava.bio.structure.io.mmcif.model.Entity
-
- setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.Event
-
Setter for property type.
- setType(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser.SeqCaution
-
- setType(String) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Change the type of this feature.
- setType_symbol(String) - Method in class org.biojava.bio.structure.io.mmcif.model.AtomSite
-
- setTypeTerm(Term) - Method in interface org.biojava.bio.seq.Feature
-
Set the type ontology-term for this feature.
- setTypeTerm(Term) - Method in class org.biojava.bio.seq.impl.SimpleFeature
-
- setTypeTerm(Term) - Method in class org.biojavax.bio.seq.SimpleRichFeature
-
Set the type ontology-term for this feature.
- setUnits(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocation
-
- setUnitv(Atom) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setURI(String) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- setURI(String) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- setURI(String) - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- setURI(String) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener of a URI identifying the current sequence.
- setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- setURI(String) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- setURI(String) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Null implementation.
- setURI(String) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setURI(String) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setURI(String) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Deprecated.
There is no clear mapping between URI and BioSQL. This
method is no longer used or supported in biojavax. Don't use it. Calling
it may result in exceptions. Use instead setName(String name),
setAccession(String accession), setVersion(int version) etc as
appropriate.
- setURI(String) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener of a URI identifying the current sequence.
- setUri(String) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property uri.
- setURI(URI) - Method in interface org.biojavax.Namespace
-
Sets an optional URI for the namespace.
- setURI(URI) - Method in class org.biojavax.SimpleNamespace
-
Sets an optional URI for the namespace.
- setURN(String) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
Provide the URN for this sequence
- setUsed(int) - Method in class org.biojava.bio.structure.align.pairwise.FragmentPair
-
- setUsedAtomNames(String[]) - Method in class org.biojava.bio.structure.align.StrucAligParameters
-
- setUserObject(Object) - Method in class org.biojava.bio.gui.sequence.ImageMap.HotSpot
-
setUserObject sets the user object.
- setValue(int) - Method in class org.biojava.bio.structure.align.helper.AligMatEl
-
- setValue(int) - Method in class org.biojava.bio.structure.align.helper.GapArray
-
- setValue(double) - Method in interface org.biojava.stats.svm.ItemValue
-
- setValue(double) - Method in class org.biojava.stats.svm.SimpleItemValue
-
- setValue(String) - Method in interface org.biojavax.Note
-
Sets the value for this note, or null for no value.
- setValue(String) - Method in class org.biojavax.SimpleNote
-
Sets the value for this note, or null for no value.
- setValueGroup(int) - Method in class org.biojava.bio.program.tagvalue.RegexParser
-
Set the group number that will match the value.
- setVariant(String) - Method in class org.biojava.bio.structure.Compound
-
- setVectorNTISupport(boolean) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
VectorNTI requires GenBank format to be a little more specific than
required by the GenBank definition.
- setVersion(String) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbId
-
- setVersion(int) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- setVersion(int) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- setVersion(int) - Method in interface org.biojavax.bio.seq.io.RichSeqIOListener
-
Call back method so the event emitter can tell the listener
the version of the record being read.
- setVersion(int) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Call back method so the event emitter can tell the listener
the version of the record being read.
- setVerticalScale(float) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Sets the vertical scale (proportional).
- setVMaxes(List) - Method in class org.biojavax.bio.seq.io.UniProtCommentParser
-
Setter for property VMaxes.
- setVolume(String) - Method in class org.biojava.bio.structure.JournalArticle
-
- setWeight(Symbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
-
Set the weight of a given symbol in this distribution.
- setWeight(Symbol, double) - Method in interface org.biojava.bio.dist.Distribution
-
Set the probability or odds that Symbol s is emitted by this state.
- setWeight(Symbol, double) - Method in class org.biojava.bio.dist.GapDistribution
-
- setWeight(Symbol, double) - Method in class org.biojava.bio.dist.PairDistribution
-
- setWeight(Symbol, double) - Method in class org.biojava.bio.dist.TranslatedDistribution
-
- setWeight(Object, double) - Method in class org.biojavax.ga.util.WeightedSet
-
Sets the weight of an Object.
- setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractDistribution
-
Implement this to actually set the weight.
- setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.AbstractOrderNDistribution
-
Set a weight in one of the conditioned distributions.
- setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.SimpleDistribution
-
- setWeightImpl(AtomicSymbol, double) - Method in class org.biojava.bio.dist.UniformDistribution
-
- setWeightMatrixID(String) - Method in class org.biojava.bio.dp.WeightMatrixAnnotator
-
Set the weight matrix id.
- setWeights(State, Distribution) - Method in interface org.biojava.bio.dp.MarkovModel
-
Set the probability distribution over the transitions from 'source'.
- setWeights(State, Distribution) - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
Use this methods to customize the transition probabilities.
- setWeights(State, Distribution) - Method in class org.biojava.bio.dp.WMAsMM
-
- setWidth(int) - Method in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Sets the width of the whole graphic (in pixels).
- setWidth(double) - Method in class org.biojava.stats.svm.RadialBaseKernel
-
- setWorkingDirectory(File) - Method in class org.biojava.utils.process.ExternalProcess
-
Sets the working directory for the external process.
- setWrap(int) - Method in class org.biojava.bio.gui.sequence.SequencePanelWrapper
-
- setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- setWrap(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- setWrap(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- setWrapIncrement(int) - Method in interface org.biojava.bio.gui.sequence.tracklayout.TrackLayout
-
- setWrapIncrement(int) - Method in class org.biojava.bio.gui.sequence.tracklayout.UserDefinedTrackLayout
-
- setWrappedKernel(SVMKernel) - Method in class org.biojava.stats.svm.SigmoidKernel
-
- setWriteDocType(boolean) - Method in class org.biojava.bio.seq.io.agave.AgaveWriter
-
Set flag that determines if XML DOCTYPE is written
or not.
- setWriter(Writer) - Method in class org.biojava.utils.process.ReaderWriterPipe
-
Sets the writer.
- setX(double) - Method in interface org.biojava.bio.structure.Atom
-
Set the X coordinate.
- setX(double) - Method in class org.biojava.bio.structure.AtomImpl
-
- setY(double) - Method in interface org.biojava.bio.structure.Atom
-
Set the Y coordinate.
- setY(double) - Method in class org.biojava.bio.structure.AtomImpl
-
- setZ(double) - Method in interface org.biojava.bio.structure.Atom
-
Set the Z coordinate.
- setZ(double) - Method in class org.biojava.bio.structure.AtomImpl
-
- shadow(Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Return a contiguous location running from the minimum to the maximum points of
the specified location.
- shadowContainedByLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features with locations where the interval
between the min and max positions are contained by
the specified Location.
- shadowOverlapsLocation(Location) - Static method in class org.biojava.bio.seq.FilterUtils
-
Construct a filter which matches features with locations where the interval
between the min and max positions are contained by or
overlap the specified Location.
- shannonEntropy(Distribution, double) - Static method in class org.biojava.bio.dist.DistributionTools
-
A method to calculate the Shannon Entropy for a Distribution.
- shift(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
moves the whole sequence
- shift(Structure, Atom) - Static method in class org.biojava.bio.structure.Calc
-
shift a structure with a vector.
- shift(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
Shift a vector.
- shift(Group, Atom) - Static method in class org.biojava.bio.structure.Calc
-
Shift a Group with a vector.
- shiftAll(int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- shiftAtAlignmentLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment
-
loc in this case is the Alignment Location
- shiftAtAlignmentLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
loc in this case is the Alignment Location
- shiftAtSequenceLoc(Object, Location, int) - Method in interface org.biojava.bio.alignment.EditableAlignment
-
loc in this case is the SymbolList Location
- shiftAtSequenceLoc(Object, Location, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
loc in this case is the SymbolList Location
- SHORT_MAX_VALUE - Static variable in class org.biojava.bio.program.scf.SCF
-
Represents the maximum unsigned value
of a short for wrapping purposes
- SHOW_ALL - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
Return default styles
- SHOW_DIFF - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
As NORMAL except only return if the two colour classes for
query and subject are the different
- SHOW_SAME - Static variable in class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
Only return if the two colour classes for
query and subject are the same
- showAlternative(int) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
-
- showCompound() - Method in class org.biojava.bio.structure.Compound
-
- showDistanceMatrix(int) - Method in class org.biojava.bio.structure.gui.util.AlternativeAlignmentFrame
-
- showHeader() - Method in class org.biojava.bio.structure.Compound
-
Print some debug statements to System.out
- showSource() - Method in class org.biojava.bio.structure.Compound
-
- SIBLING - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
-
The sibling of this feature has altered.
- sibling - Variable in class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
-
sibling SimilarityPairFeature
field.
- SigmoidKernel - Class in org.biojava.stats.svm
-
This kernel implements a three layer neural net.
- SigmoidKernel() - Constructor for class org.biojava.stats.svm.SigmoidKernel
-
- sign(double) - Static method in class org.biojava.stats.svm.tools.Classify
-
- similarEntries() - Method in class org.biojava.bio.proteomics.aaindex.AAindex
-
Returns a map with the names of similar AAindex entries and its
correlation coefficients.
- SIMILARITY_PAIR_FEATURE_TYPE - Static variable in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
Constant SIMILARITY_PAIR_FEATURE_TYPE the type
String used by SimilarityPairBuilder when creating
SimilarityPairFeatures.
- SimilarityPairBuilder - Class in org.biojava.bio.program.ssbind
-
SimilarityPairBuilder annotates query and subject
Sequence with SimilarityPairFeatures
created from SAX events supplied via a
SeqSimilarityAdapter.
- SimilarityPairBuilder() - Constructor for class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- SimilarityPairFeature - Interface in org.biojava.bio.seq.homol
-
SimilarityPairFeature describes a pairwise
similarity between two nucleotide sequences (as it extends
StrandedFeature).
- SimilarityPairFeature.EmptyPairwiseAlignment - Class in org.biojava.bio.seq.homol
-
EmptyPairwiseAlignment empty pairwise alignment
which has labels to empty symbol lists.
- SimilarityPairFeature.Template - Class in org.biojava.bio.seq.homol
-
Template for construction of
SimilarityPairFeatures.
- SimilarityPairFeature.Template() - Constructor for class org.biojava.bio.seq.homol.SimilarityPairFeature.Template
-
- SIMILARITYTYPE - Static variable in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
- SimilarityType - Interface in org.biojava.bio.program.homologene
-
Each HomologeneEntry represents a single
Homologene record that relates two
presumptive orthologues.
- SimilarityType.PlaceHolder - Class in org.biojava.bio.program.homologene
-
- SIMPLE_ANNOT_FILTER_FACTORY - Static variable in class org.biojava.bio.seq.io.agave.SimpleAnnotFilter
-
- SimpleAlignment - Class in org.biojava.bio.symbol
-
A simple implementation of an Alignment.
- SimpleAlignment(Map) - Constructor for class org.biojava.bio.symbol.SimpleAlignment
-
Generate an alignment from a list of SymbolLists.
- SimpleAlignmentElement - Class in org.biojava.bio.alignment
-
SimpleSimpleAlignment is a simple implementation of
AlignmentElement.
- SimpleAlignmentElement(Object, SymbolList, Location) - Constructor for class org.biojava.bio.alignment.SimpleAlignmentElement
-
- SimpleAlignmentStyler - Class in org.biojava.bio.program.blast2html
-
Simple implementation for specifying markup styles.
- SimpleAlignmentStyler(int) - Constructor for class org.biojava.bio.program.blast2html.SimpleAlignmentStyler
-
Creates a new SimpleAlignmentStyler instance.
- SimpleAlphabet - Class in org.biojava.bio.symbol
-
A simple no-frills implementation of the FiniteAlphabet interface.
- SimpleAlphabet() - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
-
- SimpleAlphabet(Set) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
-
- SimpleAlphabet(String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
-
- SimpleAlphabet(Set, String) - Constructor for class org.biojava.bio.symbol.SimpleAlphabet
-
- SimpleAnnotation - Class in org.biojava.bio
-
A no-frills implementation of Annotation that is just a wrapper
around a LinkedHashMap.
- SimpleAnnotation() - Constructor for class org.biojava.bio.SimpleAnnotation
-
Create a new, empty SimpleAnnotation instance.
- SimpleAnnotation(Annotation) - Constructor for class org.biojava.bio.SimpleAnnotation
-
Create a new SimpleAnnotation by copying the properties from another
one.
- SimpleAnnotation(Map) - Constructor for class org.biojava.bio.SimpleAnnotation
-
Create a new SimpleAnnotation using the values in a Map.
- SimpleAnnotationDB - Class in org.biojava.bio.annodb
-
A no-frills implementation of AnnotationDB.
- SimpleAnnotationDB(String, Set, AnnotationType) - Constructor for class org.biojava.bio.annodb.SimpleAnnotationDB
-
Create a no-frills AnnotationDB instancec.
- SimpleAnnotFilter - Class in org.biojava.bio.seq.io.agave
-
Basic implementation of AGAVEAnnotFilter
- SimpleAssembly - Class in org.biojava.bio.seq
-
A Sequence which is assembled from other sequences contained
in a set of ComponentFeature objects.
- SimpleAssembly(int, String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly
-
Construct a new SimpleAssembly using the DNA alphabet.
- SimpleAssembly(String, String) - Constructor for class org.biojava.bio.seq.SimpleAssembly
-
Construct a new SimpleAssembly using the DNA alphabet.
- SimpleAssemblyBuilder - Class in org.biojava.bio.seq.io
-
Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleAssembly.
- SimpleAssemblyBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleAssemblyBuilder
-
- SimpleAtomicSymbol - Class in org.biojava.bio.symbol
-
A basic implementation of AtomicSymbol.
- SimpleAtomicSymbol(Annotation, List) - Constructor for class org.biojava.bio.symbol.SimpleAtomicSymbol
-
- SimpleBioEntry - Class in org.biojavax.bio
-
Reference implementation of a BioEntry object which has no features or sequence.
- SimpleBioEntry(Namespace, String, String, int) - Constructor for class org.biojavax.bio.SimpleBioEntry
-
Creates a new bioentry representing the sequence in the given namespace
with the given name, accession and version.
- SimpleBioEntry() - Constructor for class org.biojavax.bio.SimpleBioEntry
-
- SimpleBioEntryRelationship - Class in org.biojavax.bio
-
Represents a relationship between two bioentries that is described by a term
and given a rank.
- SimpleBioEntryRelationship(BioEntry, BioEntry, ComparableTerm, Integer) - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
-
Creates a new instance of SimpleBioEntryRelationship.
- SimpleBioEntryRelationship() - Constructor for class org.biojavax.bio.SimpleBioEntryRelationship
-
- SimpleChromatogram - Class in org.biojava.bio.chromatogram
-
A basic chromatogram implementation which provides public mutators
for setting the various attributes of the chromatogram.
- SimpleChromatogram() - Constructor for class org.biojava.bio.chromatogram.SimpleChromatogram
-
Creates a new instance of SimpleChromatogram.
- SimpleCodonPref - Class in org.biojava.bio.symbol
-
a simple no-frills implementation of the
CodonPref object that encapsulates
codon preference data.
- SimpleCodonPref(String, Distribution, String) - Constructor for class org.biojava.bio.symbol.SimpleCodonPref
-
- SimpleComment - Class in org.biojavax
-
An implementaion of Comment.
- SimpleComment(String, int) - Constructor for class org.biojavax.SimpleComment
-
Constructs a new, immutable comment, given some text and a rank.
- SimpleComment() - Constructor for class org.biojavax.SimpleComment
-
- SimpleComparableOntology - Class in org.biojavax.ontology
-
Represents an ontology that can be compared to other ontologies.
- SimpleComparableOntology(String) - Constructor for class org.biojavax.ontology.SimpleComparableOntology
-
Creates a new instance of SimpleComparableOntology with the given,
immutable, non-nullable name.
- SimpleComparableOntology() - Constructor for class org.biojavax.ontology.SimpleComparableOntology
-
- SimpleComparableTerm - Class in org.biojavax.ontology
-
A Term object that can be compared and thus sorted.
- SimpleComparableTerm() - Constructor for class org.biojavax.ontology.SimpleComparableTerm
-
- SimpleComparableTriple - Class in org.biojavax.ontology
-
Basic comparable triple, BioSQL style.
- SimpleComparableTriple() - Constructor for class org.biojavax.ontology.SimpleComparableTriple
-
- SimpleCrossOverFunction - Class in org.biojavax.ga.functions
-
Simple Implementation of the CrossOverFunction interface
- SimpleCrossOverFunction() - Constructor for class org.biojavax.ga.functions.SimpleCrossOverFunction
-
- SimpleCrossRef - Class in org.biojavax
-
A basic CrossRef implementation.
- SimpleCrossRef(String, String, int) - Constructor for class org.biojavax.SimpleCrossRef
-
Creates a new instance of SimpleCrossRef with the values to use for
the immutable database name, accession and version.
- SimpleCrossRef(String, String, Integer) - Constructor for class org.biojavax.SimpleCrossRef
-
Creates a new instance of SimpleCrossRef with the values to use for
the immutable database name, accession and version.
- SimpleCrossRef() - Constructor for class org.biojavax.SimpleCrossRef
-
- SimpleDistribution - Class in org.biojava.bio.dist
-
A simple implementation of a distribution, which works with any finite alphabet.
- SimpleDistribution(FiniteAlphabet) - Constructor for class org.biojava.bio.dist.SimpleDistribution
-
make an instance of SimpleDistribution for the specified Alphabet.
- SimpleDistribution(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistribution
-
make an instance of SimpleDistribution with weights identical
to the specified Distribution.
- SimpleDistribution.Trainer - Class in org.biojava.bio.dist
-
A simple implementation of a trainer for this class.
- SimpleDistribution.Trainer() - Constructor for class org.biojava.bio.dist.SimpleDistribution.Trainer
-
Create a new trainer.
- SimpleDistributionTrainer - Class in org.biojava.bio.dist
-
Deprecated.
Distribution impls should be providing custom trainers.
- SimpleDistributionTrainer(Distribution) - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainer
-
Deprecated.
- SimpleDistributionTrainerContext - Class in org.biojava.bio.dist
-
A no-frills implementation of DistributionTrainerContext.
- SimpleDistributionTrainerContext() - Constructor for class org.biojava.bio.dist.SimpleDistributionTrainerContext
-
Create a new context with no initial distributions or trainers.
- SimpleDocRef - Class in org.biojavax
-
A basic DocRef implementation.
- SimpleDocRef(List, String) - Constructor for class org.biojavax.SimpleDocRef
-
Creates a new document reference from the given immutable authors and
location and title.
- SimpleDocRef(String, String) - Constructor for class org.biojavax.SimpleDocRef
-
Creates a new document reference from the given immutable authors and
location and title.
- SimpleDocRef(String, String, String) - Constructor for class org.biojavax.SimpleDocRef
-
Creates a new document reference from the given immutable authors and
location and title.
- SimpleDocRef(List, String, String) - Constructor for class org.biojavax.SimpleDocRef
-
Creates a new document reference from the given immutable authors and
location and title.
- SimpleDocRef() - Constructor for class org.biojavax.SimpleDocRef
-
- SimpleDocRefAuthor - Class in org.biojavax
-
Represents an author of a documentary reference.
- SimpleDocRefAuthor(String, boolean, boolean) - Constructor for class org.biojavax.SimpleDocRefAuthor
-
Constructs a new author instance.
- SimpleDocRefAuthor(String) - Constructor for class org.biojavax.SimpleDocRefAuthor
-
Constructs a new author instance from a string.
- SimpleDotState - Class in org.biojava.bio.dp
-
A Dot state that you can make and use.
- SimpleDotState(char, String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
-
Deprecated.
token is ignored since 1.2. Use the 2-arg constructor instead.
- SimpleDotState(String, Annotation) - Constructor for class org.biojava.bio.dp.SimpleDotState
-
Construct a new state with the specified name and annotation
- SimpleDotState(String) - Constructor for class org.biojava.bio.dp.SimpleDotState
-
- SimpleEmissionState - Class in org.biojava.bio.dp
-
- SimpleEmissionState(String, Annotation, int[], Distribution) - Constructor for class org.biojava.bio.dp.SimpleEmissionState
-
- SimpleFeature - Class in org.biojava.bio.seq.impl
-
A no-frills implementation of a feature.
- SimpleFeature(Sequence, FeatureHolder, Feature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFeature
-
Create a SimpleFeature on the given sequence.
- SimpleFeatureHolder - Class in org.biojava.bio.seq
-
A no-frills implementation of FeatureHolder.
- SimpleFeatureHolder() - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
-
Construct a new SimpleFeatureHolder with a non-informative schema.
- SimpleFeatureHolder(FeatureFilter) - Constructor for class org.biojava.bio.seq.SimpleFeatureHolder
-
Construct a new SimpleFeatureHolder with the specified schema.
- SimpleFeatureRealizer - Class in org.biojava.bio.seq
-
FeatureRealizer which uses a lookup table to map template classes
to implementations.
- SimpleFeatureRealizer() - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
-
- SimpleFeatureRealizer(FeatureRealizer) - Constructor for class org.biojava.bio.seq.SimpleFeatureRealizer
-
- SimpleFramedFeature - Class in org.biojava.bio.seq.impl
-
Title: SimpleFramedFeature.
- SimpleFramedFeature(Sequence, FeatureHolder, FramedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleFramedFeature
-
- SimpleGACrossResult - Class in org.biojavax.ga.functions
-
Simple implementation of the GACross interface.
- SimpleGACrossResult(PointLocation[], SymbolList[]) - Constructor for class org.biojavax.ga.functions.SimpleGACrossResult
-
- SimpleGappedSequence - Class in org.biojava.bio.seq.impl
-
Simple implementation of GappedSequence.
- SimpleGappedSequence(Sequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- SimpleGappedSequence(GappedSequence) - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence
-
- SimpleGappedSequence.GappedContext - Class in org.biojava.bio.seq.impl
-
- SimpleGappedSequence.GappedContext() - Constructor for class org.biojava.bio.seq.impl.SimpleGappedSequence.GappedContext
-
- SimpleGappedSymbolList - Class in org.biojava.bio.symbol
-
This implementation of GappedSymbolList wraps a SymbolList, allowing you to
insert gaps.
- SimpleGappedSymbolList(GappedSymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Create a new SimpleGappedSymbolList that will view source,
inheriting all existing gaps.
- SimpleGappedSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Create a new SimpleGappedSymbolList that will view source.
- SimpleGappedSymbolList.Block - Class in org.biojava.bio.symbol
-
An aligned block.
- SimpleGappedSymbolList.Block(int, int, int, int) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
-
- SimpleGappedSymbolList.Block(SimpleGappedSymbolList.Block) - Constructor for class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
-
- SimpleGeneticAlgorithm - Class in org.biojavax.ga.impl
-
A simple implementation of the GeneticAlgorithm interface it
is not intended that this class be overidden, hence it is final.
- SimpleGeneticAlgorithm() - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
-
- SimpleGeneticAlgorithm(Population, MutationFunction, CrossOverFunction, SelectionFunction) - Constructor for class org.biojavax.ga.impl.SimpleGeneticAlgorithm
-
- SimpleGeneticCodeTable - Class in org.biojava.bio.symbol
-
A genetic code translation table representing a translation table in the
DDBJ/EMBL/GenBank Feature Table (appendix V).
- SimpleGeneticCodeTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleGeneticCodeTable
-
Creates a new instance of SimpleGeneticCodeTable
- SimpleGFFRecord - Class in org.biojava.bio.program.gff
-
A no-frills implementation of a GFFRecord.
- SimpleGFFRecord(GFFRecord) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
-
Create a new SimpleGFFRecord from GFFRecord object
- SimpleGFFRecord(String, String, String, int, int, double, StrandedFeature.Strand, int, String, Map) - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
-
- SimpleGFFRecord() - Constructor for class org.biojava.bio.program.gff.SimpleGFFRecord
-
Create a new SimpleGFFRecord with values set to null or zero
- SimpleHMMTrainer - Class in org.biojava.bio.dp
-
- SimpleHMMTrainer(MarkovModel) - Constructor for class org.biojava.bio.dp.SimpleHMMTrainer
-
- SimpleHomologeneBuilder - Class in org.biojava.bio.program.homologene
-
A simple no-frills implementation of the HomologeneBuilder interface.
- SimpleHomologeneBuilder() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- SimpleHomologeneDB - Class in org.biojava.bio.program.homologene
-
- SimpleHomologeneDB() - Constructor for class org.biojava.bio.program.homologene.SimpleHomologeneDB
-
- SimpleHomology - Class in org.biojava.bio.seq.homol
-
A no-frills implementation of Homology.
- SimpleHomology() - Constructor for class org.biojava.bio.seq.homol.SimpleHomology
-
Creates a new empty SimpleHomology containing no
Alignment and no FeatureHolder.
- SimpleHomologyFeature - Class in org.biojava.bio.seq.impl
-
- SimpleHomologyFeature(Sequence, FeatureHolder, HomologyFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleHomologyFeature
-
- SimpleIndex - Class in org.biojava.bio.seq.db
-
This is a no-frills implementation of the Index interface.
- SimpleIndex(File, long, int, String) - Constructor for class org.biojava.bio.seq.db.SimpleIndex
-
Build the index using the given file, start and id
- SimpleInputHandler - Class in org.biojava.utils.process
-
- SimpleInputHandler(InputStream, String) - Constructor for class org.biojava.utils.process.SimpleInputHandler
-
Initializes the simple input handler.
- SimpleItemValue - Class in org.biojava.stats.svm
-
A no-frills implementation of ItemValue.
- SimpleItemValue(Object, double) - Constructor for class org.biojava.stats.svm.SimpleItemValue
-
- SimpleLabelRenderer - Class in org.biojava.bio.gui.sequence
-
- SimpleLabelRenderer() - Constructor for class org.biojava.bio.gui.sequence.SimpleLabelRenderer
-
- SimpleManyToOneTranslationTable - Class in org.biojava.bio.symbol
-
A no-frills implementation of a translation table that
maps between two alphabets.
- SimpleManyToOneTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleManyToOneTranslationTable
-
Construct a new translation table.
- SimpleMarkovModel - Class in org.biojava.bio.dp
-
- SimpleMarkovModel(int, Alphabet, String) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
-
- SimpleMarkovModel(int, Alphabet) - Constructor for class org.biojava.bio.dp.SimpleMarkovModel
-
Deprecated.
- SimpleMMcifConsumer - Class in org.biojava.bio.structure.io.mmcif
-
A MMcifConsumer implementation that build a in-memory representation of the
content of a mmcif file as a BioJava Structure object.
- SimpleMMcifConsumer() - Constructor for class org.biojava.bio.structure.io.mmcif.SimpleMMcifConsumer
-
- SimpleMMcifParser - Class in org.biojava.bio.structure.io.mmcif
-
A simple mmCif file parser
- SimpleMMcifParser() - Constructor for class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- SimpleModelInState - Class in org.biojava.bio.dp
-
- SimpleModelInState(MarkovModel, String) - Constructor for class org.biojava.bio.dp.SimpleModelInState
-
- SimpleModelTrainer - Class in org.biojava.bio.dp
-
- SimpleModelTrainer() - Constructor for class org.biojava.bio.dp.SimpleModelTrainer
-
- SimpleMutationFunction - Class in org.biojavax.ga.functions
-
Simple no frills Implementation of the MutationFunction interface
- SimpleMutationFunction() - Constructor for class org.biojavax.ga.functions.SimpleMutationFunction
-
- SimpleNamespace - Class in org.biojavax
-
A basic Namespace implemenation.
- SimpleNamespace(String) - Constructor for class org.biojavax.SimpleNamespace
-
Creates a new instance of SimpleNamespace with the given name,
which cannot be null.
- SimpleNamespace() - Constructor for class org.biojavax.SimpleNamespace
-
- SimpleNCBITaxon - Class in org.biojavax.bio.taxa
-
Reference implementation of NCBITaxon.
- SimpleNCBITaxon(int) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
- SimpleNCBITaxon(Integer) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
-
Creates a new instance of SimpleNCBITaxon based on the given taxon ID.
- SimpleNCBITaxon() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxon
-
- SimpleNCBITaxonName - Class in org.biojavax.bio.taxa
-
Represents a name class plus name combination for an NCBITaxon object.
- SimpleNCBITaxonName() - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
- SimpleNCBITaxonName(String, String) - Constructor for class org.biojavax.bio.taxa.SimpleNCBITaxonName
-
Creates a new taxon name based on the given class and name, both of
which cannot be null.
- SimpleNCBITaxonomyLoader - Class in org.biojavax.bio.taxa.io
-
Loads NCBI taxon information from names.dmp and nodes.dmp, which are
two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .
- SimpleNCBITaxonomyLoader() - Constructor for class org.biojavax.bio.taxa.io.SimpleNCBITaxonomyLoader
-
- SimpleNote - Class in org.biojavax
-
Simple implementation of Note.
- SimpleNote(ComparableTerm, String, int) - Constructor for class org.biojavax.SimpleNote
-
Creates a new instance of SimpleNote with a given term, value and rank.
- SimpleNote() - Constructor for class org.biojavax.SimpleNote
-
- SimpleOrganism - Class in org.biojavax.ga.impl
-
A Simple Haploid Organism implementation
- SimpleOrganism() - Constructor for class org.biojavax.ga.impl.SimpleOrganism
-
- SimpleOrganism(String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
-
- SimpleOrganism(Organism, String) - Constructor for class org.biojavax.ga.impl.SimpleOrganism
-
- SimpleOrthologue - Class in org.biojava.bio.program.homologene
-
this entry contains data about the orthologue.
- SimpleOrthologue(Taxon, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
-
- SimpleOrthologue(int, String, String, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologue
-
this constructor does the Taxon lookup for you too
- SimpleOrthologueSet - Class in org.biojava.bio.program.homologene
-
- SimpleOrthologueSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthologueSet
-
- SimpleOrthologueSet.Iterator - Class in org.biojava.bio.program.homologene
-
- SimpleOrthoPair - Class in org.biojava.bio.program.homologene
-
A no-frills implementation of the OrthoPair interface
- SimpleOrthoPair(Orthologue, Orthologue, SimilarityType, double) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair
-
constructor for the computed form
of an orthology relationship.
- SimpleOrthoPair(Orthologue, Orthologue, String) - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPair
-
constructor for the curated form
of an orthology relationship
- SimpleOrthoPairCollection - Class in org.biojava.bio.program.homologene
-
- SimpleOrthoPairCollection() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairCollection
-
- SimpleOrthoPairCollection.Iterator - Class in org.biojava.bio.program.homologene
-
- SimpleOrthoPairSet - Class in org.biojava.bio.program.homologene
-
a no-frills implementation of a Homologene Group
- SimpleOrthoPairSet() - Constructor for class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- SimpleOrthoPairSet.Iterator - Class in org.biojava.bio.program.homologene
-
- SimpleOutputHandler - Class in org.biojava.utils.process
-
- SimpleOutputHandler(OutputStream, String) - Constructor for class org.biojava.utils.process.SimpleOutputHandler
-
Initializes the simple output handler.
- SimplePopulation - Class in org.biojavax.ga.impl
-
Simple concrete implementation of the Population interface
- SimplePopulation(String) - Constructor for class org.biojavax.ga.impl.SimplePopulation
-
- SimplePopulation() - Constructor for class org.biojavax.ga.impl.SimplePopulation
-
- SimplePosition - Class in org.biojavax.bio.seq
-
A simple implementation of the Position interface.
- SimplePosition(int) - Constructor for class org.biojavax.bio.seq.SimplePosition
-
Constructs a point position, with no fuzzy start or
end.
- SimplePosition(int, int) - Constructor for class org.biojavax.bio.seq.SimplePosition
-
Constructs a range position, with no fuzzy start or
end.
- SimplePosition(boolean, boolean, int) - Constructor for class org.biojavax.bio.seq.SimplePosition
-
Constructs a point position, with optionally fuzzy start and
end.
- SimplePosition(boolean, boolean, int, int, String) - Constructor for class org.biojavax.bio.seq.SimplePosition
-
Constructs a range position, with optionally fuzzy start and
end.
- SimplePosition() - Constructor for class org.biojavax.bio.seq.SimplePosition
-
- SimpleRankedCrossRef - Class in org.biojavax
-
Simple implementation of RankedCrossRef.
- SimpleRankedCrossRef(CrossRef, int) - Constructor for class org.biojavax.SimpleRankedCrossRef
-
Constructs a new crossref with a rank.
- SimpleRankedCrossRef() - Constructor for class org.biojavax.SimpleRankedCrossRef
-
- SimpleRankedDocRef - Class in org.biojavax
-
Represents a documentary reference.
- SimpleRankedDocRef(DocRef, Integer, Integer, int) - Constructor for class org.biojavax.SimpleRankedDocRef
-
Constructs a new docref for a given location.
- SimpleRankedDocRef(DocRef, RichLocation, int) - Constructor for class org.biojavax.SimpleRankedDocRef
-
Constructs a new docref for a given location.
- SimpleRankedDocRef() - Constructor for class org.biojavax.SimpleRankedDocRef
-
- SimpleRemoteFeature - Class in org.biojava.bio.seq.impl
-
A no-frills implementation of a remote feature.
- SimpleRemoteFeature(Sequence, FeatureHolder, RemoteFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature
-
- SimpleRemoteFeature.DBResolver - Class in org.biojava.bio.seq.impl
-
- SimpleRemoteFeature.DBResolver(SequenceDB) - Constructor for class org.biojava.bio.seq.impl.SimpleRemoteFeature.DBResolver
-
- SimpleRestrictionSite - Class in org.biojava.bio.seq.impl
-
SimpleRestrictionSite represents the recognition site
of a restriction enzyme.
- SimpleRestrictionSite(Sequence, FeatureHolder, RestrictionSite.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleRestrictionSite
-
Creates a new SimpleRestrictionSite.
- SimpleReversibleTranslationTable - Class in org.biojava.bio.symbol
-
A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.
- SimpleReversibleTranslationTable(FiniteAlphabet, FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SimpleReversibleTranslationTable
-
Construct a new translation table.
- SimpleRichAnnotation - Class in org.biojavax
-
Simple annotation wrapper.
- SimpleRichAnnotation() - Constructor for class org.biojavax.SimpleRichAnnotation
-
Creates a new, empty instance of SimpleRichAnnotation
- SimpleRichFeature - Class in org.biojavax.bio.seq
-
A simple implementation of RichFeature.
- SimpleRichFeature(FeatureHolder, Feature.Template) - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
-
Creates a new instance of SimpleRichFeature based on a template.
- SimpleRichFeature() - Constructor for class org.biojavax.bio.seq.SimpleRichFeature
-
- SimpleRichFeatureRelationship - Class in org.biojavax.bio.seq
-
Represents a relationship between two features that is described by a term.
- SimpleRichFeatureRelationship(RichFeature, RichFeature, ComparableTerm, int) - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
Creates a new instance of SimpleRichFeatureRelationship.
- SimpleRichFeatureRelationship() - Constructor for class org.biojavax.bio.seq.SimpleRichFeatureRelationship
-
- SimpleRichLocation - Class in org.biojavax.bio.seq
-
A simple implementation of RichLocation.
- SimpleRichLocation(Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
Creates a new instance of SimpleRichSequenceLocation that points to a
single position on the positive strand.
- SimpleRichLocation(Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
Creates a new instance of SimpleRichSequenceLocation that points to a
single position.
- SimpleRichLocation(Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
Creates a new instance of SimpleRichSequenceLocation that points to a
single position on another sequence.
- SimpleRichLocation(Position, Position, int) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
Creates a new instance of SimpleRichSequenceLocation that points to a
range position on the positive strand.
- SimpleRichLocation(Position, Position, int, RichLocation.Strand) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
Creates a new instance of SimpleRichSequenceLocation that points to a
range position.
- SimpleRichLocation(Position, Position, int, RichLocation.Strand, CrossRef) - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
Creates a new instance of SimpleRichSequenceLocation that points to a
range position on another sequence.
- SimpleRichLocation() - Constructor for class org.biojavax.bio.seq.SimpleRichLocation
-
- SimpleRichObjectBuilder - Class in org.biojavax
-
Creates objects and returns them, and stores them in an internal
map of singletons for reference.
- SimpleRichObjectBuilder() - Constructor for class org.biojavax.SimpleRichObjectBuilder
-
- SimpleRichSequence - Class in org.biojavax.bio.seq
-
A simple implementation of RichSequence.
- SimpleRichSequence(Namespace, String, String, int, SymbolList, Double) - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
-
Creates a new instance of SimpleRichSequence.
- SimpleRichSequence() - Constructor for class org.biojavax.bio.seq.SimpleRichSequence
-
- SimpleRichSequenceBuilder - Class in org.biojavax.bio.seq.io
-
Constructs BioEntry objects by listening to events.
- SimpleRichSequenceBuilder() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Creates a new instance of SimpleRichSequenceBuilder using a SimpleSymbolListFactory
with a threshold of zero.
- SimpleRichSequenceBuilder(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Creates a new instance of SimpleRichSequenceBuilder with the
desired symbollistfactory and threshold of zero.
- SimpleRichSequenceBuilder(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Creates a new instance of SimpleRichSequenceBuilder with the
desired symbollistfactory and threshold.
- SimpleRichSequenceBuilderFactory - Class in org.biojavax.bio.seq.io
-
Generates RichSequenceBuilder objects.
- SimpleRichSequenceBuilderFactory() - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
-
Creates a new instance of SimpleRichSequenceBuilderFactory
- SimpleRichSequenceBuilderFactory(SymbolListFactory) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
-
Creates a new instance of SimpleRichSequenceBuilderFactory
- SimpleRichSequenceBuilderFactory(SymbolListFactory, int) - Constructor for class org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory
-
Creates a new instance of SimpleRichSequenceBuilderFactory that uses
a specified factory for SymbolLists longer than a specified
length.
- SimpleSeqSimilaritySearchHit - Class in org.biojava.bio.search
-
SimpleSeqSimilaritySearchHit objects represent a
similarity search hit of a query sequence to a sequence referenced
in a SequenceDB object.
- SimpleSeqSimilaritySearchHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, String, Annotation, List) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchHit
-
Creates a new SimpleSeqSimilaritySearchHit object.
- SimpleSeqSimilaritySearchResult - Class in org.biojava.bio.search
-
SimpleSeqSimilaritySearchResult objects represent a
result of a search of a SymbolList against the
sequences within a SequenceDB object.
- SimpleSeqSimilaritySearchResult(Sequence, SequenceDB, Map, List, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchResult
-
Creates a new SimpleSeqSimilaritySearchResult.
- SimpleSeqSimilaritySearchSubHit - Class in org.biojava.bio.search
-
SimpleSeqSimilaritySearchSubHit objects represent
sub-hits which make up a hit.
- SimpleSeqSimilaritySearchSubHit(double, double, double, int, int, StrandedFeature.Strand, int, int, StrandedFeature.Strand, Alignment, Annotation) - Constructor for class org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit
-
Creates a new SimpleSeqSimilaritySearchSubHit
object.
- SimpleSequence - Class in org.biojava.bio.seq.impl
-
A basic implementation of the Sequence interface.
- SimpleSequence(SymbolList, String, String, Annotation) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence
-
Create a SimpleSequence with the symbols and alphabet of sym, and the
sequence properties listed.
- SimpleSequence(SymbolList, String, String, Annotation, FeatureRealizer) - Constructor for class org.biojava.bio.seq.impl.SimpleSequence
-
Create a SimpleSequence using a specified FeatureRealizer.
- SimpleSequenceBuilder - Class in org.biojava.bio.seq.io
-
Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleSequence.
- SimpleSequenceBuilder() - Constructor for class org.biojava.bio.seq.io.SimpleSequenceBuilder
-
- SimpleSequenceDBInstallation - Class in org.biojava.bio.seq.db
-
This class is an implementation of interface SequenceDBInstallation
that manages a set of SequenceDB objects.
- SimpleSequenceDBInstallation() - Constructor for class org.biojava.bio.seq.db.SimpleSequenceDBInstallation
-
create an initially empty SimpleSequenceDBInstallation
- SimpleSequenceFactory - Class in org.biojava.bio.seq.impl
-
A no-frills implementation of SequenceFactory that produces SimpleSequence
objects.
- SimpleSequenceFactory() - Constructor for class org.biojava.bio.seq.impl.SimpleSequenceFactory
-
- SimpleSimilarityPairFeature - Class in org.biojava.bio.seq.impl
-
SimpleSimilarityPairFeature represents a similarity
between a query sequence and a subject sequence as produced by a
search program.
- SimpleSimilarityPairFeature(Sequence, FeatureHolder, SimilarityPairFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleSimilarityPairFeature
-
Creates a new SimpleSimilarityPairFeature.
- SimpleStatePath - Class in org.biojava.bio.dp
-
A no-frills implementation of StatePath.
- SimpleStatePath(double, SymbolList, SymbolList, SymbolList) - Constructor for class org.biojava.bio.dp.SimpleStatePath
-
- SimpleStrandedFeature - Class in org.biojava.bio.seq.impl
-
A no-frills implementation of StrandedFeature.
- SimpleStrandedFeature(Sequence, FeatureHolder, StrandedFeature.Template) - Constructor for class org.biojava.bio.seq.impl.SimpleStrandedFeature
-
- SimpleStructureServer - Class in org.biojava.bio.structure.server
-
- SimpleStructureServer() - Constructor for class org.biojava.bio.structure.server.SimpleStructureServer
-
- SimpleSVMClassifierModel - Class in org.biojava.stats.svm
-
A no-frills implementation of an SVM classifier model.
- SimpleSVMClassifierModel(SVMKernel) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- SimpleSVMClassifierModel(SVMKernel, Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- SimpleSVMClassifierModel(SVMKernel, SVMTarget) - Constructor for class org.biojava.stats.svm.SimpleSVMClassifierModel
-
- SimpleSVMTarget - Class in org.biojava.stats.svm
-
No-frills implementation of SVMTarget.
- SimpleSVMTarget() - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
-
- SimpleSVMTarget(Collection) - Constructor for class org.biojava.stats.svm.SimpleSVMTarget
-
- SimpleSymbolList - Class in org.biojava.bio.symbol
-
Basic implementation of SymbolList.
- SimpleSymbolList(Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
-
Construct an empty SimpleSymbolList.
- SimpleSymbolList(Alphabet, List) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
-
Construct a SymbolList containing the symbols in the specified list.
- SimpleSymbolList(SymbolTokenization, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
-
Construct a SymbolList from a string.
- SimpleSymbolList(SymbolList) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
-
Construct a copy of an existing SymbolList.
- SimpleSymbolList(Symbol[], int, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleSymbolList
-
Construct a SimpleSymbolList given the Symbol array that backs it.
- SimpleSymbolListFactory - Class in org.biojava.bio.symbol
-
This class makes SimpleSymbolLists.
- SimpleSymbolListFactory() - Constructor for class org.biojava.bio.symbol.SimpleSymbolListFactory
-
- SimpleSymbolPropertyTable - Class in org.biojava.bio.symbol
-
Class that implements the SymbolPropertyTable interface
- SimpleSymbolPropertyTable(Alphabet, String) - Constructor for class org.biojava.bio.symbol.SimpleSymbolPropertyTable
-
- SimpleSymbolPropertyTableDB - Class in org.biojava.bio.proteomics.aaindex
-
A simple implementation of a symbol property table database.
- SimpleSymbolPropertyTableDB() - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
-
Initializes the database.
- SimpleSymbolPropertyTableDB(SymbolPropertyTableIterator) - Constructor for class org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDB
-
Initializes the database by copying all symbol property tables from
a given iterator into the database.
- SimpleSymbolStyle - Class in org.biojava.bio.gui
-
A no-frills implementation of SymbolStyle.
- SimpleSymbolStyle(FiniteAlphabet) - Constructor for class org.biojava.bio.gui.SimpleSymbolStyle
-
- SimpleTagValueWrapper - Class in org.biojava.bio.program.tagvalue
-
Helper class to wrap one TagValueListener inside another one.
- SimpleTagValueWrapper(TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
-
Build a SimpleTagValueWrapper that will forward everything to a delegate.
- SimpleTagValueWrapper() - Constructor for class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
-
- SimpleTaxon - Class in org.biojava.bio.taxa
-
- SimpleTaxon() - Constructor for class org.biojava.bio.taxa.SimpleTaxon
-
Deprecated.
- SimpleTaxon(String, String) - Constructor for class org.biojava.bio.taxa.SimpleTaxon
-
Deprecated.
Create a new instance with no parent, no children and given
scientific and common names.
- SimpleTaxonFactory - Class in org.biojava.bio.taxa
-
- SimpleTaxonFactory(String) - Constructor for class org.biojava.bio.taxa.SimpleTaxonFactory
-
Deprecated.
- SimpleThreadPool - Class in org.biojava.utils
-
SimpleThreadPool is a basic implementation of
ThreadPool for use where we don't wish to introduce a
dependency on a 3rd-party pool.
- SimpleThreadPool() - Constructor for class org.biojava.utils.SimpleThreadPool
-
Creates a new SimpleThreadPool containing 4
non-daemon threads and starts them.
- SimpleThreadPool(int, boolean) - Constructor for class org.biojava.utils.SimpleThreadPool
-
Creates a new SimpleThreadPool containing the
specified number of threads and starts them.
- SimpleThreadPool(int, boolean, int) - Constructor for class org.biojava.utils.SimpleThreadPool
-
Creates a new SimpleThreadPool containing the
specified number of threads and starts them.
- SimpleTrackLayout - Class in org.biojava.bio.gui.sequence.tracklayout
-
A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues
- SimpleTrackLayout() - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- SimpleTrackLayout(Sequence, int) - Constructor for class org.biojava.bio.gui.sequence.tracklayout.SimpleTrackLayout
-
- SimpleTranslationTable - Class in org.biojava.bio.symbol
-
A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.
- SimpleTranslationTable(FiniteAlphabet, Alphabet) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
-
Create a new translation table that will translate symbols from source to
target.
- SimpleTranslationTable(FiniteAlphabet, Alphabet, Map) - Constructor for class org.biojava.bio.symbol.SimpleTranslationTable
-
Create a new translation table that will translate symbols from source to
target.
- SimpleWeightMatrix - Class in org.biojava.bio.dp
-
- SimpleWeightMatrix(Alphabet, int, DistributionFactory) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
-
- SimpleWeightMatrix(Distribution[]) - Constructor for class org.biojava.bio.dp.SimpleWeightMatrix
-
- SimpleXMLEmitter - Class in org.biojava.bio.program.xml
-
A simple XML DocumentHandler that processes SAX2 events
to create a sensibly formatted XML as it parsed
without populating objects with data.
- SimpleXMLEmitter() - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
-
- SimpleXMLEmitter(boolean) - Constructor for class org.biojava.bio.program.xml.SimpleXMLEmitter
-
- SingleDP - Class in org.biojava.bio.dp.onehead
-
An implementation of DP that aligns a single sequence against a single model.
- SingleDP(MarkovModel) - Constructor for class org.biojava.bio.dp.onehead.SingleDP
-
- SingleDPMatrix - Class in org.biojava.bio.dp.onehead
-
The dynamic programming matrix for a single sequence.
- SingleDPMatrix(DP, SymbolList) - Constructor for class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.AbstractTrainer
-
- singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchSampler
-
- singleSequenceIteration(ModelTrainer, SymbolList, ScoreType) - Method in class org.biojava.bio.dp.BaumWelchSampler
-
- singleSequenceIteration(ModelTrainer, SymbolList) - Method in class org.biojava.bio.dp.BaumWelchTrainer
-
- SingletonAlphabet - Class in org.biojava.bio.symbol
-
An alphabet that contains a single atomic symbol.
- SingletonAlphabet(AtomicSymbol) - Constructor for class org.biojava.bio.symbol.SingletonAlphabet
-
- SingletonList - Class in org.biojava.utils
-
- SingletonList(Object) - Constructor for class org.biojava.utils.SingletonList
-
- SingularValueDecomposition - Class in org.biojava.bio.structure.jama
-
Singular Value Decomposition.
- SingularValueDecomposition(Matrix) - Constructor for class org.biojava.bio.structure.jama.SingularValueDecomposition
-
Construct the singular value decomposition.
- site - Variable in class org.biojava.bio.molbio.RestrictionEnzyme
-
- SITE_FEATURE_SOURCE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
-
SITE_FEATURE_SOURCE the source String
used by RestrictionMapper when creating
restriction site Features.
- SITE_FEATURE_TYPE - Static variable in class org.biojava.bio.molbio.RestrictionMapper
-
SITE_FEATURE_TYPE the type String
used by RestrictionMapper when creating
restriction site Features.
- SixFrameRenderer - Class in org.biojava.bio.gui.sequence
-
Class that handles drawing in six frames for other
classes.
- SixFrameRenderer() - Constructor for class org.biojava.bio.gui.sequence.SixFrameRenderer
-
- SixFrameZiggyRenderer - Class in org.biojava.bio.gui.sequence
-
A feature renderer that computes the data necessary to render
multi-exon transcripts without CDS data.
- SixFrameZiggyRenderer(SixFrameRenderer) - Constructor for class org.biojava.bio.gui.sequence.SixFrameZiggyRenderer
-
- size() - Method in interface org.biojava.bio.annodb.AnnotationDB
-
The number of Annotation instances in the DB.
- size() - Method in class org.biojava.bio.annodb.IndexedAnnotationDB
-
- size() - Method in class org.biojava.bio.annodb.LazyFilteredAnnotationDB
-
- size() - Method in class org.biojava.bio.annodb.LazySearchedAnnotationDB
-
- size() - Method in class org.biojava.bio.annodb.MergingAnnotationDB
-
- size() - Method in class org.biojava.bio.annodb.SimpleAnnotationDB
-
- SIZE - Static variable in class org.biojava.bio.gui.sequence.BasicFeatureRenderer
-
- size() - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Return how many lines are in this set.
- size() - Method in interface org.biojava.bio.program.homologene.OrthoPairSet
-
returns an iterator to the contents of the set.
- size() - Method in class org.biojava.bio.program.homologene.SimpleOrthoPairSet
-
- size() - Method in interface org.biojava.bio.structure.Group
-
getnumber of atoms.
- SIZE - Static variable in class org.biojava.bio.structure.gui.util.SequenceScalePanel
-
- size() - Method in class org.biojava.bio.structure.HetatomImpl
-
getnumber of atoms.
- size() - Method in interface org.biojava.bio.structure.Structure
-
return number of Chains in this Structure.
- size(int) - Method in interface org.biojava.bio.structure.Structure
-
return number of chains of model.
- size() - Method in class org.biojava.bio.structure.StructureImpl
-
return number of chains , if NMR return number of chains of first model .
- size(int) - Method in class org.biojava.bio.structure.StructureImpl
-
return number of chains of model.
- size() - Method in interface org.biojava.bio.symbol.FiniteAlphabet
-
The number of symbols in the alphabet.
- size() - Method in class org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
-
- size() - Method in class org.biojava.bio.symbol.SimpleAlphabet
-
- size() - Method in class org.biojava.bio.symbol.SingletonAlphabet
-
- size() - Method in class org.biojava.bio.symbol.SoftMaskedAlphabet
-
- size() - Method in class org.biojava.stats.svm.SparseVector
-
The number of used dimensions.
- size() - Method in class org.biojava.stats.svm.SVMRegressionModel
-
- size() - Method in class org.biojava.utils.BeanAsMap
-
- size() - Method in class org.biojava.utils.FileAsList
-
- size() - Method in class org.biojava.utils.ListTools.Doublet
-
- size() - Method in class org.biojava.utils.ListTools.SeriesList
-
- size() - Method in class org.biojava.utils.ListTools.Triplet
-
- size() - Method in class org.biojava.utils.MergingSet
-
- size() - Method in class org.biojava.utils.SingletonList
-
- size() - Method in class org.biojava.utils.SmallMap
-
- size() - Method in class org.biojava.utils.SmallSet
-
- size - Variable in class org.biojavax.bio.seq.CompoundRichLocation
-
- size() - Method in class org.biojavax.ga.impl.SimplePopulation
-
- size() - Method in interface org.biojavax.ga.Population
-
Gets the Size of the population
- size() - Method in class org.biojavax.ga.util.WeightedSet
-
- SIZE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- SIZE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- SIZE_THRESHOLD - Static variable in class org.biojava.bio.program.das.DASSequence
-
- skalarProduct(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
skalar product.
- skip(long) - Method in class org.biojava.utils.io.CachingInputStream
-
- skip(long) - Method in class org.biojava.utils.io.CountedBufferedReader
-
- skip(long) - Method in class org.biojava.utils.io.UncompressInputStream
-
- SKIP_RECORD - Static variable in interface org.biojava.bio.program.gff.GFFErrorHandler
-
- skippedEntity(String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
- skippedEntity(String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
-
- skippedEntity(String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
- skippedEntity(String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
-
- skippedEntity(String) - Method in interface org.biojava.utils.stax.StAXContentHandler
-
- skippedEntity(String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
- SLEEP_TIME - Static variable in class org.biojava.utils.process.ExternalProcess
-
Number of milliseconds the execute method should pauses after the
external process has finished the execution.
- SmallAnnotation - Class in org.biojava.bio
-
Annotation that is optimized for memory usage.
- SmallAnnotation() - Constructor for class org.biojava.bio.SmallAnnotation
-
Return a new SmallAnnotation optimised for small sets of properties.
- SmallAnnotation(Annotation) - Constructor for class org.biojava.bio.SmallAnnotation
-
Return a new SmallAnnotation that copies all values from another annoation.
- SmallAnnotation(Map) - Constructor for class org.biojava.bio.SmallAnnotation
-
Return a new SmallAnnotation that copies all values from a Map.
- SmallCursor - Class in org.biojava.bio.dp.onehead
-
Constant-memory implementation of single-head DP cursor.
- SmallCursor(State[], SymbolList, Iterator) - Constructor for class org.biojava.bio.dp.onehead.SmallCursor
-
- SmallMap - Class in org.biojava.utils
-
Lightweight implementation of Map which uses little memory to store a
small number of mappings, at the expense of scalability.
- SmallMap() - Constructor for class org.biojava.utils.SmallMap
-
- SmallMap(int) - Constructor for class org.biojava.utils.SmallMap
-
- SmallMap(Map) - Constructor for class org.biojava.utils.SmallMap
-
- SmallSet - Class in org.biojava.utils
-
Lightweight implementation of Set which uses little memory to store a small
number of items, at the expense of scalability.
- SmallSet() - Constructor for class org.biojava.utils.SmallSet
-
- SmallSet(int) - Constructor for class org.biojava.utils.SmallSet
-
- SmallSet(Collection) - Constructor for class org.biojava.utils.SmallSet
-
- smartAdapter - Static variable in class org.biojava.bio.structure.gui.BiojavaJmol
-
- SmartSequenceBuilder - Class in org.biojava.bio.seq.io
-
Basic SequenceBuilder implementation which accumulates all
notified information and chooses a sequence implementation
suited to the size of the sequence.
- sMatrix - Variable in class org.biojava.bio.dp.twohead.AbstractMatrixPairDPCursor
-
- SmithWaterman - Class in org.biojava.bio.alignment
-
Smith and Waterman developed an efficient dynamic programming algorithm to
perform local sequence alignments, which returns the most conserved region of
two sequences (longest common substring with modifications).
- SmithWaterman(short, short, short, short, short, SubstitutionMatrix) - Constructor for class org.biojava.bio.alignment.SmithWaterman
-
Constructs the new SmithWaterman alignment object.
- SMORegressionTrainer - Class in org.biojava.stats.svm
-
Train a regression support vector machine using the Sequential Minimal
Optimization algorithm.
- SMORegressionTrainer() - Constructor for class org.biojava.stats.svm.SMORegressionTrainer
-
- SMOTrainer - Class in org.biojava.stats.svm
-
Train a support vector machine using the Sequential Minimal
Optimization algorithm.
- SMOTrainer() - Constructor for class org.biojava.stats.svm.SMOTrainer
-
- SoftMaskedAlphabet - Class in org.biojava.bio.symbol
-
Soft masking is usually displayed by making the masked regions somehow
different from the non masked regions.
- SoftMaskedAlphabet.CaseSensitiveTokenization - Class in org.biojava.bio.symbol
-
This SymbolTokenizer works with a delegate to softmask
symbol tokenization as appropriate.
- SoftMaskedAlphabet.MaskingDetector - Interface in org.biojava.bio.symbol
-
Implementations will define how soft masking looks.
- SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector - Class in org.biojava.bio.symbol
-
- SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector() - Constructor for class org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
-
- SoftReferenceCache - Class in org.biojava.utils.cache
-
Cache which is cleared according to memory pressure.
- SoftReferenceCache() - Constructor for class org.biojava.utils.cache.SoftReferenceCache
-
- SolexaFastqReader - Class in org.biojava.bio.program.fastq
-
- SolexaFastqReader() - Constructor for class org.biojava.bio.program.fastq.SolexaFastqReader
-
- SolexaFastqWriter - Class in org.biojava.bio.program.fastq
-
- SolexaFastqWriter() - Constructor for class org.biojava.bio.program.fastq.SolexaFastqWriter
-
- solve(Matrix) - Method in class org.biojava.bio.structure.jama.CholeskyDecomposition
-
Solve A*X = B
- solve(Matrix) - Method in class org.biojava.bio.structure.jama.LUDecomposition
-
Solve A*X = B
- solve(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Solve A*X = B
- solve(Matrix) - Method in class org.biojava.bio.structure.jama.QRDecomposition
-
Least squares solution of A*X = B
- solve(double, double, double, ComputeObject) - Static method in class org.biojava.utils.math.BinarySearch
-
method that will attempt solving the equation.
- solveTranspose(Matrix) - Method in class org.biojava.bio.structure.jama.Matrix
-
Solve X*A = B, which is also A'*X' = B'
- sort(String[], Hashtable) - Method in interface org.biojava.bibliography.BibRefQuery
-
It sorts the current collection and returns another collection which is
a sorted copy of the current collection.
- sort() - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Sorts the member locations of a compound location.
- sort() - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Sorts the member locations of a compound location.
- sort() - Method in interface org.biojavax.bio.seq.RichLocation
-
Sorts the member locations of a compound location.
- sort() - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Sorts the member locations of a compound location.
- SORT_CRITERION - Static variable in class org.biojava.bibliography.BiblioCriterion
-
A sort criterion.
- sortPeptidesIntoLanes() - Method in class org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer
-
- SOURCE - Static variable in interface org.biojava.bio.seq.Feature
-
The source of this feature has altered
- source - Variable in class org.biojava.bio.seq.Feature.Template
-
- SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- SOURCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- SOURCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- sourceEnd - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
-
- sourceStart - Variable in class org.biojava.bio.symbol.SimpleGappedSymbolList.Block
-
- SOURCETERM - Static variable in interface org.biojava.bio.seq.Feature
-
The ontological source of this feature has altered
- sourceTerm - Variable in class org.biojava.bio.seq.Feature.Template
-
- SOURCETERM - Static variable in interface org.biojavax.bio.seq.RichFeature
-
- sourceToView(int) - Method in interface org.biojava.bio.symbol.GappedSymbolList
-
Coordinate conversion from source to view.
- sourceToView(SimpleGappedSymbolList.Block, int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
Coordinate conversion from source to view.
- sourceToView(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- SparseVector - Class in org.biojava.stats.svm
-
An implementation of a sparse vector.
- SparseVector() - Constructor for class org.biojava.stats.svm.SparseVector
-
- SparseVector(int) - Constructor for class org.biojava.stats.svm.SparseVector
-
- SparseVector.NormalizingKernel - Class in org.biojava.stats.svm
-
A version of the standard dot-product kernel that scales each column
independently.
- SparseVector.NormalizingKernel(SparseVector) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
-
Generate a normalizing kernel with the normalizing vector s.
- SparseVector.NormalizingKernel(List) - Constructor for class org.biojava.stats.svm.SparseVector.NormalizingKernel
-
Generate a normalizing kernel defined by the SparseVectors in vectors.
- spatialLocation - Variable in class org.biojava.bibliography.BiblioScope
-
It defines a spatial location of the cited resource.
- SPECIES_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
-
- split(Object) - Method in interface org.biojava.bio.program.tagvalue.ChangeTable.Splitter
-
Produce a list of values from an old value.
- split(Object) - Method in class org.biojava.bio.program.tagvalue.RegexSplitter
-
- splitString(String) - Method in class org.biojava.bio.seq.io.WordTokenization
-
- SQLUnigeneFactory - Class in org.biojava.bio.program.unigene
-
An implementatoin of UnigeneFactory that manages it's data in an SQL
database.
- SQLUnigeneFactory() - Constructor for class org.biojava.bio.program.unigene.SQLUnigeneFactory
-
- SSBond - Class in org.biojava.bio.structure
-
A simple bean to store disulfid bridge information, the SSBOND records in the PDB files.
- SSBond() - Constructor for class org.biojava.bio.structure.SSBond
-
- ssContext - Variable in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
-
- StackedFeatureRenderer - Class in org.biojava.bio.gui.sequence
-
Allows you to stack multiple feature renderers up (for example a label renderer and
a beaded renderer) and have them treated as a single renderer for layout.
- StackedFeatureRenderer() - Constructor for class org.biojava.bio.gui.sequence.StackedFeatureRenderer
-
- StackedLogoPainter - Class in org.biojava.bio.gui
-
A logo painter that paints in stacked areas.
- StackedLogoPainter() - Constructor for class org.biojava.bio.gui.StackedLogoPainter
-
- stackLevel - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- stackLevel - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
- StandardAminoAcid - Class in org.biojava.bio.structure
-
A class that provides a set of standard amino acids.
- StandardAminoAcid() - Constructor for class org.biojava.bio.structure.StandardAminoAcid
-
- standardMutationDistribution(FiniteAlphabet) - Static method in class org.biojavax.ga.util.GATools
-
Makes a mutation Distribution where the probability
of a Symbol being mutated to itself is zero and the
probability of it being changed to any other Symbol in
the Alphabet a is 1.0 / (a.size() - 1.0)
- start() - Method in interface org.biojava.bio.search.BioMatcher
-
Get the first symbol index that matches the pattern.
- start() - Method in class org.biojava.bio.search.MaxMismatchMatcher
-
- start - Variable in class org.biojava.utils.automata.FiniteAutomaton
-
- start() - Method in class org.biojava.utils.regex.Matcher
-
Returns the start index of the previous match.
- start(int) - Method in class org.biojava.utils.regex.Matcher
-
Returns the start index of the subsequence captured by the given group during the previous match operation.
- start(String[]) - Method in interface org.biojava.utils.xml.AppEntry
-
- START_RECORD_TAG - Static variable in class org.biojava.bio.program.tagvalue.StateMachine
-
- START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- START_SEQUENCE_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.EMBLFormat
-
- START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.GenbankFormat
-
- START_SEQUENCE_TAG - Static variable in class org.biojavax.bio.seq.io.UniProtFormat
-
- startCycle() - Method in interface org.biojava.bio.dp.HMMTrainer
-
called to put the trainer into an initial state for a new
round of training.
- startCycle() - Method in class org.biojava.bio.dp.SimpleHMMTrainer
-
- startDB() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
indicates start of data for a HomologeneDB
- startDB() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- startDocument() - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
-
- startDocument() - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
-
- startDocument(String) - Method in interface org.biojava.bio.program.gff.GFFDocumentHandler
-
Indicates that a new GFF document has been started.
- startDocument(String) - Method in class org.biojava.bio.program.gff.GFFFilterer
-
- startDocument(String) - Method in class org.biojava.bio.program.gff.GFFWriter
-
- startDocument(String) - Method in interface org.biojava.bio.program.gff3.GFF3DocumentHandler
-
Indicates that a new GFF document has been started.
- startDocument() - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- startDocument() - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
- startDocument() - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
-
- startedActivity(Object) - Static method in class org.biojava.bio.program.das.DAS
-
- startedActivity(Object) - Method in interface org.biojava.utils.ActivityListener
-
Notification that an activity has started.
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.dist.XMLDistributionReader
-
Required by SAXParser to be public.
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.blast2html.Blast2HTMLHandler
-
This is called when an element is entered.
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.das.dasalignment.DASAlignmentXMLResponseParser
-
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.das.dasstructure.DASStructureXMLResponseParser
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.sax.blastxml.BlastXMLParser
-
we override the superclass startElement method so we can determine the
the start tag type and use it to set up delegation for the superclass.
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityStAXHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.FeatureHandler
-
StAX callback for element starts.
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.LocationHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.PropDetailHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.StrandedFeatureHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.program.xff.XFFFeatureSetHandler
-
- startElement(String) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
-
- startElement(String, Attributes) - Method in class org.biojava.bio.program.xml.BaseXMLWriter
-
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.program.xml.SimpleXMLEmitter
-
- startElement(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
Handles basic entry processing for all feature handlers.
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
Override this to do any processing required but call this
prior to returning.
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEAspectPropHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEDescriptionPropHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMENamePropHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEResiduesPropHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMETypePropHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.SequenceContentHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
Handles basic entry processing for all feature handlers.
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
-
Override this to do any processing required but call this
prior to returning.
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
-
Handles basic entry processing for all feature handlers.
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.BooleanElementHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.ByteElementHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.CharElementHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.DoubleElementHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.FloatElementHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.IntElementHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.LongElementHandlerBase
-
- startElement(String, String, String, Attributes) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in interface org.biojava.utils.stax.StAXContentHandler
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
- startElement(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.utils.stax.StringElementHandlerBase
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSeqHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEBioSequenceHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECdsHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEChromosomeHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEClassificationHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVECompResultHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEComputationHandler
-
currently we do not handler >computation< as subtag of sciobj yet
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEContigHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEDbIdPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEElementIdPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrderHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEFragmentOrientationHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEGeneHandler
-
- startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.agave.AGAVEHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEIdAliasPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapLocationPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMapPositionPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMatchRegionPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEMrnaHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEPredictedProteinHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQualifierPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEQueryRegionPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVERelatedAnnotPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultGroupHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEResultPropertyPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESciPropertyPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqFeatureHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqLocationPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVESeqMapHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVETranscriptHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEViewPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.AGAVEXrefPropPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
Element-specific handler.
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
Element-specific handler.
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEAnnotationHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSetHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEFeatureSpanHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEGenePropHandler
-
- startElementHandler(String, String, String, Attributes, DelegationManager) - Method in class org.biojava.bio.seq.io.game.GAMEHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMEMapPosPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.GAMESeqPropHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
Element-specific handler.
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game.StAXPropertyHandler
-
Element-specific handler.
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEAnnotationHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSetHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEFeatureSpanHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEGeneHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMEHandler
-
Description of the Method
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.GAMESeqRelHandler
-
- startElementHandler(String, String, String, Attributes) - Method in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
-
Element-specific handler.
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- startFeature(String) - Method in class org.biojava.bio.seq.io.FeatureTableParser
-
Deprecated.
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.ProteinRefSeqFileFormer
-
Deprecated.
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- startFeature(Feature.Template) - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Notify the listener that a new feature object is starting.
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- startFeature(Feature.Template) - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Null implementation.
- startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- startFeature(Feature.Template) - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Notify the listener that a new feature object is starting.
- startFile() - Method in class org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
-
- startFile() - Method in interface org.biojavax.bio.phylo.io.phylip.PHYLIPFileListener
-
About to start a new file.
- startGroup() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
indicates start of data for a OrthoPairSet
- startGroup() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- startHeader() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- startHeader() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- startHeader() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- startHeader() - Method in class org.biojava.bio.search.FilteringContentHandler
-
- startHeader() - Method in class org.biojava.bio.search.SearchContentAdapter
-
- startHeader() - Method in class org.biojava.bio.search.SearchContentFilter
-
- startHeader() - Method in interface org.biojava.bio.search.SearchContentHandler
-
The startHeader method indicates the start of a
formatted header.
- startHeader() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- startHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- startHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- startHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- startHit() - Method in class org.biojava.bio.search.FilteringContentHandler
-
- startHit() - Method in class org.biojava.bio.search.SearchContentAdapter
-
- startHit() - Method in class org.biojava.bio.search.SearchContentFilter
-
- startHit() - Method in interface org.biojava.bio.search.SearchContentHandler
-
The startHit method indicates the start of a
formatted hit.
- startHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- startInstance(int, int) - Method in interface org.biojava.utils.automata.StateMachineFactory
-
Return a StateMachineInstance if the Symbol represented
by the symbol index is valid as the initial symbol of
the pattern.
- startLoc - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- startLoc - Variable in class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
- startOrthologue() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
indicates start of data for an orthologue
- startOrthologue() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- startOrthoPair() - Method in interface org.biojava.bio.program.homologene.HomologeneBuilder
-
indicates start of data for an OrthoPair
- startOrthoPair() - Method in class org.biojava.bio.program.homologene.SimpleHomologeneBuilder
-
- startPrefixMapping(String, String) - Method in class org.biojava.bio.program.ssbind.SeqSimilarityAdapter
-
- startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.SAX2StAXAdaptor
-
- startPrefixMapping(String, String) - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
-
- startPrefixMapping(String, String) - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
- startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.SAX2StAXAdaptor
-
- startPrefixMapping(String, String) - Method in interface org.biojava.utils.stax.StAXContentHandler
-
- startPrefixMapping(String, String) - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.Echo
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.Indexer2
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
-
- startRecord() - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
- startRecord() - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
-
A new record is about to start.
- startSearch() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- startSearch(String) - Method in class org.biojava.bio.program.ssaha.HitMerger
-
- startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Echo
-
- startSearch(String) - Method in interface org.biojava.bio.program.ssaha.SearchListener
-
Indicates that a sequence is about to be searched against a DataStore.
- startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Tee
-
- startSearch(String) - Method in class org.biojava.bio.program.ssaha.SearchListener.Wrapper
-
- startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- startSearch() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- startSearch() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- startSearch() - Method in class org.biojava.bio.search.FilteringContentHandler
-
- startSearch() - Method in class org.biojava.bio.search.SearchContentAdapter
-
- startSearch() - Method in class org.biojava.bio.search.SearchContentFilter
-
- startSearch() - Method in interface org.biojava.bio.search.SearchContentHandler
-
The startSearch method indicates the start of
useful search information.
- startSearch() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- startSequence() - Method in class org.biojava.bio.seq.io.EmblFileFormer
-
Deprecated.
- startSequence() - Method in class org.biojava.bio.seq.io.GenbankFileFormer
-
Deprecated.
- startSequence() - Method in class org.biojava.bio.seq.io.SeqIOAdapter
-
- startSequence() - Method in class org.biojava.bio.seq.io.SeqIOFilter
-
- startSequence() - Method in interface org.biojava.bio.seq.io.SeqIOListener
-
Start the processing of a sequence.
- startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderBase
-
- startSequence() - Method in class org.biojava.bio.seq.io.SequenceBuilderFilter
-
- startSequence() - Method in class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Start the processing of a sequence.
- startSequence() - Method in class org.biojavax.bio.seq.io.DebuggingRichSeqIOListener
-
- startSequence() - Method in class org.biojavax.bio.seq.io.RichSeqIOAdapter
-
- startSequence() - Method in class org.biojavax.bio.seq.io.SimpleRichSequenceBuilder
-
Start the processing of a sequence.
- startSubHit() - Method in class org.biojava.bio.program.sax.FastaSearchSAXParser
-
- startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
-
- startSubHit() - Method in class org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
-
- startSubHit() - Method in class org.biojava.bio.program.ssbind.SimilarityPairBuilder
-
- startSubHit() - Method in class org.biojava.bio.search.FilteringContentHandler
-
- startSubHit() - Method in class org.biojava.bio.search.SearchContentAdapter
-
- startSubHit() - Method in class org.biojava.bio.search.SearchContentFilter
-
- startSubHit() - Method in interface org.biojava.bio.search.SearchContentHandler
-
The startSubHit method indicates the start of a
formatted subhit.
- startSubHit() - Method in class org.biojava.bio.search.SearchContentHandlerDebugger
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AbstractWrapper
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Aggregator
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.AnnotationBuilder
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Echo
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.Indexer2
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.MultiTagger
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.RegexFieldFinder
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.SimpleTagValueWrapper
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.StateMachine
-
TagValueListener interface
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDelegator
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagDropper
-
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.TagRenamer
-
- startTag(Object) - Method in interface org.biojava.bio.program.tagvalue.TagValueListener
-
Start a new tag.
- startTag(Object) - Method in class org.biojava.bio.program.tagvalue.ValueChanger
-
- startThreads() - Method in class org.biojava.utils.SimpleThreadPool
-
- startThreads() - Method in interface org.biojava.utils.ThreadPool
-
startThreads starts all the threads running and
opens the pool to requests.
- startTree() - Method in interface org.biojava.bio.seq.io.agave.StAXContentHandler
-
- startTree() - Method in class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
- startTree() - Method in interface org.biojava.utils.stax.StAXContentHandler
-
- startTree() - Method in class org.biojava.utils.stax.StAXContentHandlerBase
-
- startZiggy(StrandedFeature.Strand) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
Used to initialise the spliced transcript renderer for
a CDS feature where the ends of the feature define the
frame of the feature.
- startZiggy(StrandedFeature.Strand, int) - Method in class org.biojava.bio.gui.sequence.SixFrameRenderer
-
This method is called to initialise the renderer for a
spliced transcript.
- state - Variable in class org.biojava.bio.dp.BackPointer
-
The state with which this backpointer is associated.
- State - Interface in org.biojava.bio.dp
-
A state in a markov process.
- stateAlphabet() - Method in interface org.biojava.bio.dp.MarkovModel
-
FiniteAlphabet of the states.
- stateAlphabet() - Method in class org.biojava.bio.dp.SimpleMarkovModel
-
- stateAlphabet() - Method in class org.biojava.bio.dp.WMAsMM
-
- stateChanged(ChangeEvent) - Method in class org.biojava.bio.structure.gui.ScaleableMatrixPanel
-
- stateChanged(ChangeEvent) - Method in class org.biojava.bio.structure.gui.SequenceDisplay
-
- stateList(MarkovModel) - Method in class org.biojava.bio.dp.DP
-
- StateMachine - Class in org.biojava.bio.program.tagvalue
-
This class implements a state machine for parsing events from
the Parser class.
- StateMachine() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine
-
- StateMachine.BasicState - Class in org.biojava.bio.program.tagvalue
-
Implementation of a State in a state machine
- StateMachine.BasicState(String) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
This is the default constructor
- StateMachine.BasicState(String, TagValueListener) - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.BasicState
-
when this constructor is used, a fixed listener
is used with this state.
- StateMachine.ExitNotification - Interface in org.biojava.bio.program.tagvalue
-
Interface implemented by State listeners that
want notification when a transition leaves the State.
- StateMachine.SimpleStateListener - Class in org.biojava.bio.program.tagvalue
-
a basic listener for a State.
- StateMachine.SimpleStateListener() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.SimpleStateListener
-
- StateMachine.State - Interface in org.biojava.bio.program.tagvalue
-
Interface for a State within this StateMachine
- StateMachine.Transition - Class in org.biojava.bio.program.tagvalue
-
class to represent a State Transition
- StateMachine.TransitionTable - Class in org.biojava.bio.program.tagvalue
-
Table of Transition destination States
and their corresponding Tags.
- StateMachine.TransitionTable() - Constructor for class org.biojava.bio.program.tagvalue.StateMachine.TransitionTable
-
- StateMachineFactory - Interface in org.biojava.utils.automata
-
Class that produces StateMachineInstance objects.
- StateMachineInstance - Interface in org.biojava.utils.automata
-
- StatePath - Interface in org.biojava.bio.dp
-
Extends the Alignment interface so that it is explicitly used to represent
a state path through an HMM, and the associated emitted sequence and
likelihoods.
- states() - Method in interface org.biojava.bio.dp.DPMatrix
-
- states - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- states() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- STATES - Static variable in interface org.biojava.bio.dp.StatePath
-
Alignment label for the state path.
- states() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
-
- StaticMemberPlaceHolder - Class in org.biojava.utils
-
- StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
-
- StaticMemberPlaceHolder() - Constructor for class org.biojava.utils.StaticMemberPlaceHolder
-
- STATUS_ATTR - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat
-
- StAXContentHandler - Interface in org.biojava.bio.seq.io.agave
-
Interface for StAX content handlers.
- StAXContentHandler - Interface in org.biojava.utils.stax
-
Interface for StAX content handlers.
- StAXContentHandlerBase - Class in org.biojava.bio.seq.io.agave
-
Simple implementation of the StAXContentHandler
interface, with empty implementations for all the methods.
- StAXContentHandlerBase() - Constructor for class org.biojava.bio.seq.io.agave.StAXContentHandlerBase
-
- StAXContentHandlerBase - Class in org.biojava.utils.stax
-
Simple implementation of the StAXContentHandler
interface, with empty implementations for all the methods.
- StAXContentHandlerBase() - Constructor for class org.biojava.utils.stax.StAXContentHandlerBase
-
- staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- staxenv - Variable in class org.biojava.bio.seq.io.agave.StAXPropertyHandler
-
- staxenv - Variable in class org.biojava.bio.seq.io.game.StAXPropertyHandler
-
- staxenv - Variable in class org.biojava.bio.seq.io.game12.StAXFeatureHandler
-
Nesting class that provides callback interfaces to nested class
- StAXFeatureHandler - Class in org.biojava.bio.seq.io.agave
-
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
- StAXFeatureHandler - Class in org.biojava.bio.seq.io.game
-
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
- StAXFeatureHandler() - Constructor for class org.biojava.bio.seq.io.game.StAXFeatureHandler
-
- StAXFeatureHandler - Class in org.biojava.bio.seq.io.game12
-
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
- StAXHandlerBinding - Class in org.biojava.bio.program.ssbind
-
StAXHandlerBindings associates an
ElementRecognizer with a factory which creates
StAXContentHandlers for elements which it the
ElementRecognizer accepts.
- StAXHandlerFactory - Interface in org.biojava.bio.program.ssbind
-
StAXHandlerFactory is an interface for factories
producing StAXContentHandlers which are used by the
SeqSimilarityStAXAdapter.
- StAXHandlerFactory - Interface in org.biojava.bio.seq.io.agave
-
Factory for StAX content handlers.
- StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game
-
Factory for StAX content handlers.
- StAXHandlerFactory - Interface in org.biojava.bio.seq.io.game12
-
Factory for StAX content handlers.
- StAXPropertyHandler - Class in org.biojava.bio.seq.io.agave
-
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
- StAXPropertyHandler - Class in org.biojava.bio.seq.io.game
-
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
- stop(GeneticAlgorithm) - Method in class org.biojavax.ga.GAStoppingCriteria.MaximumGeneration
-
Stops the Algorithm if the iterations are >= maxGenerations
- stop(GeneticAlgorithm) - Method in interface org.biojavax.ga.GAStoppingCriteria
-
Determines if an Algorithm should stop spawning new generations
- StoppingCriteria - Interface in org.biojava.bio.dp
-
A callback that is invoked during the training of an HMM.
- StopRenderer - Class in org.biojava.bio.gui.sequence
-
Compute sites of stop codons.
- StopRenderer(SixFrameRenderer, int, StrandedFeature.Strand) - Constructor for class org.biojava.bio.gui.sequence.StopRenderer
-
- stopThreads() - Method in class org.biojava.utils.SimpleThreadPool
-
Waits for all working threads to return and then stops them.
- stopThreads() - Method in interface org.biojava.utils.ThreadPool
-
stopThreads causes all running threads to stop
when their current task is complete.
- store(Index) - Method in class org.biojava.bio.seq.db.BioIndex
-
- store(Index) - Method in class org.biojava.bio.seq.db.EmblCDROMIndexStore
-
store adds an Index to the store.
- store(Index) - Method in interface org.biojava.bio.seq.db.IndexStore
-
Add the Index to the store.
- store(Index) - Method in class org.biojava.bio.seq.db.TabIndexStore
-
- STORE_NAME - Static variable in class org.biojava.bio.program.indexdb.BioStoreFactory
-
STORE_NAME is the key used to identify the
arbitrary name of the store in the OBDA config.dat files.
- str - Variable in class org.biojava.ontology.obo.OboFileParser.SOPair
-
- STRAIN_KEY - Static variable in class org.biojavax.bio.seq.RichSequence.Terms
-
- STRAND - Static variable in interface org.biojava.bio.seq.StrandedFeature
-
The strand of this feature is being altered.
- strand - Variable in class org.biojava.bio.seq.StrandedFeature.Template
-
- STRAND - Static variable in class org.biojava.bio.structure.io.PDBFileParser
-
Strand secondary structure assignment.
- STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.EmblLikeFormat
-
Deprecated.
- STRAND_NUMBER_TAG - Static variable in class org.biojava.bio.seq.io.GenbankFormat
-
Deprecated.
- STRANDED_TAG - Static variable in class org.biojavax.bio.seq.io.INSDseqFormat
-
- StrandedFeature - Interface in org.biojava.bio.seq
-
Adds the concept of 'strand' to features.
- StrandedFeature.Strand - Class in org.biojava.bio.seq
-
Class to represent the 'strandedness' of a feature.
- StrandedFeature.Template - Class in org.biojava.bio.seq
-
Template class for parameterizing the creation of a new
StrandedFeature.
- StrandedFeature.Template() - Constructor for class org.biojava.bio.seq.StrandedFeature.Template
-
- STRANDEDFEATURE_HANDLER_FACTORY - Static variable in class org.biojava.bio.program.xff.StrandedFeatureHandler
-
- StrandedFeatureHandler - Class in org.biojava.bio.program.xff
-
StAX handler for XFF strandedFeature type.
- StrandedFeatureHandler(XFFFeatureSetHandler) - Constructor for class org.biojava.bio.program.xff.StrandedFeatureHandler
-
- StrandParser - Class in org.biojava.bio.seq
-
Process strings and return strand objects.
- StrandParser() - Constructor for class org.biojava.bio.seq.StrandParser
-
- StrCompAlignment - Class in org.biojava.bio.structure.align.pairwise
-
- StrCompAlignment(int, int) - Constructor for class org.biojava.bio.structure.align.pairwise.StrCompAlignment
-
- streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.FileStreamer
-
- streamNext(SeqIOListener) - Method in class org.biojava.bio.program.ssaha.SequenceStreamer.SequenceDBStreamer
-
- streamNext(SeqIOListener) - Method in interface org.biojava.bio.program.ssaha.SequenceStreamer
-
- StreamParser - Interface in org.biojava.bio.seq.io
-
Parse a stream of characters into BioJava symbols.
- StreamPipe - Class in org.biojava.utils.process
-
A multi threaded class
which pipes the contents of an input stream to an output stream.
- StreamPipe(InputStream, OutputStream, String) - Constructor for class org.biojava.utils.process.StreamPipe
-
Initializes the stream pipe.
- StreamReader - Class in org.biojava.bio.seq.io
-
Parses a stream into sequences.
- StreamReader(InputStream, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
-
- StreamReader(BufferedReader, SequenceFormat, SymbolTokenization, SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.StreamReader
-
- streamRecords(GFFDocumentHandler) - Method in class org.biojava.bio.program.gff.GFFEntrySet
-
Write all records in this set out to a handler.
- StreamWriter - Class in org.biojava.bio.seq.io
-
Writes all of the sequences from a SequenceIterator to a stream with a
particular format.
- StreamWriter(OutputStream, SequenceFormat) - Constructor for class org.biojava.bio.seq.io.StreamWriter
-
Generate a new StreamWriter to the stream os and using format.
- STRING_LIMIT - Static variable in class org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
-
- STRING_TO_INT - Static variable in class org.biojava.bio.program.tagvalue.ChangeTable
-
- StringElementHandlerBase - Class in org.biojava.utils.stax
-
StAX handler for any element which just contains a string.
- StringElementHandlerBase() - Constructor for class org.biojava.utils.stax.StringElementHandlerBase
-
- stringifyAttributes(Map) - Static method in class org.biojava.bio.program.gff.SimpleGFFRecord
-
Create a String representation of
attMap.
- stringnifyDescription() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
Converts the description of the matrix to a String.
- stringnifyMatrix() - Method in class org.biojava.bio.alignment.SubstitutionMatrix
-
Creates a String representation of this matrix.
- stringToClob(Connection, ResultSet, int, String) - Method in class org.biojava.bio.seq.db.biosql.OracleDBHelper
-
Deprecated.
- StringTools - Class in org.biojavax.utils
-
Utility class for formatting strings into regular-sized blocks.
- STROKE - Static variable in class org.biojava.bio.gui.sequence.AbstractBeadRenderer
-
Constant STROKE indicating a change to the outline
stroke of the features.
- StrucAligParameters - Class in org.biojava.bio.structure.align
-
A class that contains all the parameters of the structure alignment algorithm.
- StrucAligParameters() - Constructor for class org.biojava.bio.structure.align.StrucAligParameters
-
- Struct - Class in org.biojava.bio.structure.io.mmcif.model
-
a bean to contain the data of the _struct lines
- Struct() - Constructor for class org.biojava.bio.structure.io.mmcif.model.Struct
-
- StructAsym - Class in org.biojava.bio.structure.io.mmcif.model
-
Contains the data for _struct_asym
- StructAsym() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructAsym
-
- StructKeywords - Class in org.biojava.bio.structure.io.mmcif.model
-
- StructKeywords() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructKeywords
-
- StructRef - Class in org.biojava.bio.structure.io.mmcif.model
-
A class to containt the _struct_ref field data
- StructRef() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructRef
-
- StructRefSeq - Class in org.biojava.bio.structure.io.mmcif.model
-
- StructRefSeq() - Constructor for class org.biojava.bio.structure.io.mmcif.model.StructRefSeq
-
- Structure - Interface in org.biojava.bio.structure
-
Interface for a structure object.
- StructureEvent - Interface in org.biojava.bio.structure.server
-
- StructureEventImpl - Class in org.biojava.bio.structure.server
-
- StructureEventImpl(Structure) - Constructor for class org.biojava.bio.structure.server.StructureEventImpl
-
- StructureException - Exception in org.biojava.bio.structure
-
An exception during the parsing of a PDB file.
- StructureException(String) - Constructor for exception org.biojava.bio.structure.StructureException
-
Constructs a StructureException object.
- StructureException(String, Throwable) - Constructor for exception org.biojava.bio.structure.StructureException
-
Constructs a StructureException object.
- StructureException(Throwable, String) - Constructor for exception org.biojava.bio.structure.StructureException
-
Deprecated.
use new StructureException(message, ex) instead
- StructureException(Throwable) - Constructor for exception org.biojava.bio.structure.StructureException
-
Constructs a StructureException object.
- StructureFetcherRunnable - Class in org.biojava.bio.structure.server
-
a Runnable class that talks to a PDBInstallation and requests a new protein
structure.
- StructureFetcherRunnable(PDBInstallation) - Constructor for class org.biojava.bio.structure.server.StructureFetcherRunnable
-
- StructureImpl - Class in org.biojava.bio.structure
-
Implementation of a PDB Structure.
- StructureImpl() - Constructor for class org.biojava.bio.structure.StructureImpl
-
Constructs a StructureImpl object.
- StructureImpl(Group) - Constructor for class org.biojava.bio.structure.StructureImpl
-
construct a Structure object that only contains a single group
- StructureImpl(Chain) - Constructor for class org.biojava.bio.structure.StructureImpl
-
construct a Structure object that contains a particular chain
- StructureIO - Interface in org.biojava.bio.structure.io
-
Defines the interface how to access Structure (- PDB file) input,output readers, writers.
- StructureIOFile - Interface in org.biojava.bio.structure.io
-
interface StructureIOFile extends the StructureIO interface
and adds a few File specific methods.
- StructureListener - Interface in org.biojava.bio.structure.server
-
- StructurePairAligner - Class in org.biojava.bio.structure.align
-
Perform a pairwise protein structure superimposition.
- StructurePairAligner() - Constructor for class org.biojava.bio.structure.align.StructurePairAligner
-
- StructurePairSelector - Interface in org.biojava.bio.structure.gui.util
-
To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
- StructureServer - Interface in org.biojava.bio.structure.server
-
a server that pre-loads PDB files in memory, for quicker processing by StructureListeners
- StructureTools - Class in org.biojava.bio.proteomics
-
Simple access to protein seccondary structure assignments.
- StructureTools() - Constructor for class org.biojava.bio.proteomics.StructureTools
-
- StructureTools - Class in org.biojava.bio.structure
-
A class that provides some tool methods.
- StructureTools() - Constructor for class org.biojava.bio.structure.StructureTools
-
- subAlignment(Set, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment
-
Retrieves a subalignment specified by the location.
- subAlignment(Set, int, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
-
Retreives a subAlignment
- subAlignment(Set, Location) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- subAlignment(Set, Location) - Method in class org.biojava.bio.dp.SimpleStatePath
-
- subAlignment(Set, Location) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- subAlignment(Set, Location) - Method in interface org.biojava.bio.symbol.Alignment
-
Make a view onto this alignment.
- subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- subAlignment(Set, Location) - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- SubCircularRendererContext - Class in org.biojava.bio.gui.sequence
-
A renderer context that allows some or all properties of another context to
be over-ridden.
- SubCircularRendererContext(CircularRendererContext, SymbolList, FeatureHolder, double) - Constructor for class org.biojava.bio.gui.sequence.SubCircularRendererContext
-
Create a new sub context.
- subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.AllValuesIn
-
- subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.And
-
- subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Contains
-
- subConstraintOf(CollectionConstraint) - Method in class org.biojava.bio.CollectionConstraint.Or
-
- subConstraintOf(CollectionConstraint) - Method in interface org.biojava.bio.CollectionConstraint
-
subConstraintOf returns true if the constraint
is a sub-constraint.
- subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.And
-
- subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByAnnotationType
-
- subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ByClass
-
- subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Enumeration
-
- subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.ExactValue
-
- subConstraintOf(PropertyConstraint) - Method in class org.biojava.bio.PropertyConstraint.Or
-
- subConstraintOf(PropertyConstraint) - Method in interface org.biojava.bio.PropertyConstraint
-
subConstraintOf returns true if the constraint
is a sub-constraint.
- subFeatures - Variable in class org.biojava.bio.seq.io.agave.StAXFeatureHandler
-
- SubIntegerTokenization - Class in org.biojava.bio.seq.io
-
- SubIntegerTokenization(IntegerAlphabet.SubIntegerAlphabet) - Constructor for class org.biojava.bio.seq.io.SubIntegerTokenization
-
- subject - Variable in class org.biojava.bibliography.BibRef
-
It defines the topic of the content of the cited resource.
- SUBJECT_HEADINGS - Static variable in interface org.biojava.bibliography.BibRefSupport
-
A vocabulary name.
- SUBJECT_LABEL - Static variable in interface org.biojava.bio.seq.homol.SimilarityPairFeature
-
Constant SUBJECT_LABEL is the alignment label used
for all subject sequences.
- subjectDBs - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
- subjectHeadings - Variable in class org.biojava.bibliography.BiblioSubject
-
The subject headings usually come from standard lists
such as Sears List of Subject Headings,
or Library of Congress Subject Headings (LCSH).
- subjectHeadingsSource - Variable in class org.biojava.bibliography.BiblioSubject
-
- subjectViewCache - Variable in class org.biojava.bio.program.ssbind.ViewSequenceFactory
-
- subList(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
-
- subList(int, int) - Method in class org.biojava.bio.program.das.DASSequence
-
- subList(int, int) - Method in class org.biojava.bio.seq.CircularView
-
Over rides ViewSequence.
- subList(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- subList(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- subList(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
-
- subList(int, int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
-
- subList(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- subList(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- subList(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- subList(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- subList(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- subList(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
-
- subList(int, int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
-
- subList(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- subList(int, int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
create a subList of the original, this will be a view until
either the original symbolList or the sublist is edited
- subList(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
-
Return a new SymbolList for the symbols start to end inclusive.
- subList(SymbolList, int, int) - Static method in class org.biojava.bio.symbol.SymbolListViews
-
View a portion of a SymbolList.
- subList(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
-
Return a new SymbolList for the symbols start to end inclusive.
- subList(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
-
Return a new SymbolList for the symbols start to end inclusive.
- subList(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Return a new SymbolList for the symbols start to end inclusive.
- subList(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
-
Return a new SymbolList for the symbols start to end inclusive.
- subList(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Return a new SymbolList for the symbols start to end inclusive.
- subMatrix - Variable in class org.biojava.bio.alignment.NeedlemanWunsch
-
A matrix with the size length(alphabet) times length(alphabet)
- SubPairwiseRenderContext - Class in org.biojava.bio.gui.sequence
-
SubPairwiseRenderContext is a rendering context
which wraps a delegate context and effectively hides some of the
delegate's properties with its own.
- SubPairwiseRenderContext(PairwiseRenderContext, SymbolList, SymbolList, FeatureHolder, FeatureHolder, RangeLocation, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubPairwiseRenderContext
-
Creates a new SubPairwiseRenderContext.
- SUBPATH_LENGTH - Static variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic.Option
-
To improve performance, the drawing objects for the chromatogram
traces are precomputed.
- subpathsValid - Variable in class org.biojava.bio.chromatogram.graphic.ChromatogramGraphic
-
Flag for subpaths.
- SubSequence - Class in org.biojava.bio.seq.impl
-
View a sub-section of a given sequence object, including all the
features intersecting that region.
- SubSequence(Sequence, int, int, String) - Constructor for class org.biojava.bio.seq.impl.SubSequence
-
Construct a new SubSequence of the specified sequence.
- SubSequence(Sequence, int, int) - Constructor for class org.biojava.bio.seq.impl.SubSequence
-
Construct a new SubSequence of the specified sequence.
- subSequence(int, int) - Method in class org.biojava.bio.seq.io.SymbolListCharSequence
-
- subSequence(Sequence, int, int) - Static method in class org.biojava.bio.seq.SequenceTools
-
Extract a sub-sequence from a sequence.
- subSequence(Sequence, int, int, String) - Static method in class org.biojava.bio.seq.SequenceTools
-
Extract a sub-sequence from a sequence.
- subSequence(Sequence, int, int, String, StrandedFeature.Strand) - Static method in class org.biojava.bio.seq.SequenceTools
-
Extract a sub-sequence from a sequence.
- subSequence(int, int) - Method in class org.biojava.utils.RepeatedCharSequence
-
- subSequence(RichSequence, int, int, Namespace, String, String, String, int, Double) - Static method in class org.biojavax.bio.seq.RichSequence.Tools
-
Creates a new sequence from a subregion of another sequence.
- SubSequence.SubProjectedFeatureContext - Class in org.biojava.bio.seq.impl
-
TargetContext that implements the mapping between the parent sequence and this
sub-sequence.
- SubSequenceDB - Class in org.biojava.bio.seq.db
-
- SubSequenceDB(SequenceDB, Set) - Constructor for class org.biojava.bio.seq.db.SubSequenceDB
-
- SubSequenceRenderContext - Class in org.biojava.bio.gui.sequence
-
Allows a new renderer to "wrap" another one, replacing one or more values.
- SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- SubSequenceRenderContext(SequenceRenderContext, SymbolList, FeatureHolder, RangeLocation, int) - Constructor for class org.biojava.bio.gui.sequence.SubSequenceRenderContext
-
- SUBSET - Static variable in class org.biojava.ontology.obo.OboFileHandler
-
- SubstitutionMatrix - Class in org.biojava.bio.alignment
-
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
- SubstitutionMatrix(FiniteAlphabet, File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
-
This constructs a SubstitutionMatrix object that contains
two Map data structures having BioJava symbols as keys and
the value being the index of the matrix containing the substitution score.
- SubstitutionMatrix(FiniteAlphabet, String, String) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
-
With this constructor it is possible to construct a SubstitutionMatrix
object from a substitution matrix file.
- SubstitutionMatrix(FiniteAlphabet, short, short) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
-
Constructs a SubstitutionMatrix with every Match and every Replace having
the same expenses given by the parameters.
- SubstitutionMatrix(File) - Constructor for class org.biojava.bio.alignment.SubstitutionMatrix
-
This constructor can be used to guess the alphabet of this substitution
matrix.
- subStr(int, int) - Method in class org.biojava.bio.dp.SimpleStatePath
-
- subStr(int, int) - Method in class org.biojava.bio.program.das.DASSequence
-
- subStr(int, int) - Method in class org.biojava.bio.seq.CircularView
-
Over rides ViewSequence.
- subStr(int, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- subStr(int, int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- subStr(int, int) - Method in class org.biojava.bio.seq.impl.DummySequence
-
- subStr(int, int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- subStr(int, int) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- subStr(int, int) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- subStr(int, int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- subStr(int, int) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- subStr(int, int) - Method in class org.biojava.bio.symbol.AbstractSymbolList
-
- subStr(int, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- subStr(int, int) - Method in interface org.biojava.bio.symbol.SymbolList
-
Return a region of this symbol list as a String.
- subStr(RichSequence, int, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
-
Return a region of this sequence as a String.
- subStr(RichSequence, int, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
-
Return a region of this sequence as a String.
- subStr(int, int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Return a region of this symbol list as a String.
- subStr(RichSequence, int, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
-
Return a region of this sequence as a String.
- subStr(int, int) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Return a region of this symbol list as a String.
- substract(Atom, Atom) - Static method in class org.biojava.bio.structure.Calc
-
substract two atoms ( a - b).
- subStringExists(String) - Method in class org.biojava.bio.symbol.UkkonenSuffixTree
-
- subtract(Location, Location) - Static method in class org.biojava.bio.symbol.LocationTools
-
Subtract one location from another.
- subTypeOf(AnnotationType) - Method in class org.biojava.bio.AnnotationType.Abstract
-
- subTypeOf(AnnotationType) - Method in interface org.biojava.bio.AnnotationType
-
See if an AnnotationType is a specialisation of this type.
- SuffixTree - Class in org.biojava.bio.symbol
-
Suffix tree implementation.
- SuffixTree(FiniteAlphabet) - Constructor for class org.biojava.bio.symbol.SuffixTree
-
Construct a new SuffixTree to contain motifs over the
specified alphabet.
- SuffixTree.SuffixNode - Class in org.biojava.bio.symbol
-
A node in the suffix tree.
- SuffixTree.SuffixNode() - Constructor for class org.biojava.bio.symbol.SuffixTree.SuffixNode
-
- SuffixTreeKernel - Class in org.biojava.stats.svm.tools
-
Computes the dot-product of two suffix-trees as the sum of the products
of the counts of all nodes they have in common.
- SuffixTreeKernel() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel
-
- SuffixTreeKernel.DepthScaler - Interface in org.biojava.stats.svm.tools
-
Encapsulates the scale factor to apply at a given depth.
- SuffixTreeKernel.MultipleScalar - Class in org.biojava.stats.svm.tools
-
Scale using a multiple of two DepthScalers.
- SuffixTreeKernel.MultipleScalar(SuffixTreeKernel.DepthScaler, SuffixTreeKernel.DepthScaler) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.MultipleScalar
-
- SuffixTreeKernel.NullModelScaler - Class in org.biojava.stats.svm.tools
-
Scales by 4^depth - equivalent to dividing by a probablistic flatt prior
null model
- SuffixTreeKernel.NullModelScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.NullModelScaler
-
- SuffixTreeKernel.SelectionScalar - Class in org.biojava.stats.svm.tools
-
Scale using a BitSet to allow/disallow depths.
- SuffixTreeKernel.SelectionScalar(BitSet) - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.SelectionScalar
-
Make a new SelectionScalar that masks in different
depths.
- SuffixTreeKernel.UniformScaler - Class in org.biojava.stats.svm.tools
-
Scale all depths by 1.0
- SuffixTreeKernel.UniformScaler() - Constructor for class org.biojava.stats.svm.tools.SuffixTreeKernel.UniformScaler
-
- SUPPORT - Static variable in class org.biojava.bio.program.abi.ABITools
-
Alignment label for the support row.
- surname - Variable in class org.biojava.bibliography.BiblioPerson
-
The person's sirname (family name).
- svd() - Method in class org.biojava.bio.structure.jama.Matrix
-
Singular Value Decomposition
- SVDSuperimposer - Class in org.biojava.bio.structure
-
A class that calculates the superimposition between two sets of atoms
inspired by the biopython SVDSuperimposer class...
- SVDSuperimposer(Atom[], Atom[]) - Constructor for class org.biojava.bio.structure.SVDSuperimposer
-
Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
- SVM_Light - Class in org.biojava.stats.svm.tools
-
- SVM_Light() - Constructor for class org.biojava.stats.svm.tools.SVM_Light
-
- SVM_Light.LabelledVector - Class in org.biojava.stats.svm.tools
-
- SVM_Light.LabelledVector(SparseVector, double) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
-
- SVM_Light.LabelledVector(SparseVector, double, String) - Constructor for class org.biojava.stats.svm.tools.SVM_Light.LabelledVector
-
- SVMClassifierModel - Interface in org.biojava.stats.svm
-
An SVM classifier model.
- SVMKernel - Interface in org.biojava.stats.svm
-
Kernel for support vector machines and related methods.
- SVMRegressionModel - Class in org.biojava.stats.svm
-
- SVMRegressionModel() - Constructor for class org.biojava.stats.svm.SVMRegressionModel
-
- SVMRegressionModel(int) - Constructor for class org.biojava.stats.svm.SVMRegressionModel
-
- SVMTarget - Interface in org.biojava.stats.svm
-
An SVM classifier model.
- SwapMutationFunction - Class in org.biojavax.ga.functions
-
This class does a sort of mutation by exchanging two positions on the
chromosome.
- SwapMutationFunction(double[]) - Constructor for class org.biojavax.ga.functions.SwapMutationFunction
-
Sets the mutation probabilities to the designated values.
- Swissprot - Class in org.biojava.bio.program.formats
-
- Swissprot() - Constructor for class org.biojava.bio.program.formats.Swissprot
-
- SWISSPROT - Static variable in class org.biojava.bio.seq.io.SeqIOConstants
-
SWISSPROT indicates that the sequence format is
SWISSPROT.
- SWISSPROT_TYPE - Static variable in class org.biojava.bio.program.tagvalue.Formats
-
- SwissprotFileFormer - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- SwissprotFileFormer() - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Creates a new SwissprotFileFormer using
System.out stream.
- SwissprotFileFormer(PrintStream) - Constructor for class org.biojava.bio.seq.io.SwissprotFileFormer
-
Deprecated.
Creates a new SwissprotFileFormer using the
specified stream.
- SwissprotProcessor - Class in org.biojava.bio.seq.io
-
Deprecated.
Use org.biojavax.bio.seq.io framework instead
- SwissprotProcessor(SequenceBuilder, String) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.
Constructor that sets the source of the feature to theSource.
- SwissprotProcessor(SequenceBuilder) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor
-
Deprecated.
- SwissprotProcessor.Factory - Class in org.biojava.bio.seq.io
-
Deprecated.
Factory which wraps SequenceBuilders in a SwissprotProcessor
- SwissprotProcessor.Factory(SequenceBuilderFactory) - Constructor for class org.biojava.bio.seq.io.SwissprotProcessor.Factory
-
Deprecated.
- SwissprotSequenceDB - Class in org.biojava.bio.seq.db
-
This class contains functions accessing sequences in swiss-prot.
- SwissprotSequenceDB() - Constructor for class org.biojava.bio.seq.db.SwissprotSequenceDB
-
- Symbol - Interface in org.biojava.bio.symbol
-
A single symbol.
- symbolAt(Object, int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.alignment.AbstractULAlignment
-
this will return the ambiguity symbol associated with all symbols in that column
- symbolAt(Object, int) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
This gets the symbol for an individual sequence at position in the overall alignment
If the sequence is not aligned at that location it returns null
- symbolAt(int) - Method in class org.biojava.bio.dp.SimpleStatePath
-
- symbolAt(Object, int) - Method in class org.biojava.bio.dp.SimpleStatePath
-
- symbolAt(int) - Method in class org.biojava.bio.program.das.DASSequence
-
- symbolAt(int) - Method in class org.biojava.bio.seq.CircularView
-
Over rides ViewSequence.
- symbolAt(Object, int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.seq.impl.AssembledSymbolList
-
- symbolAt(int) - Method in class org.biojava.bio.seq.impl.DummySequence
-
- symbolAt(int) - Method in class org.biojava.bio.seq.impl.NewAssembledSymbolList
-
- symbolAt(int) - Method in class org.biojava.bio.seq.impl.SimpleSequence
-
- symbolAt(int) - Method in class org.biojava.bio.seq.impl.SubSequence
-
- symbolAt(int) - Method in class org.biojava.bio.seq.impl.ViewSequence
-
- symbolAt(int) - Method in class org.biojava.bio.seq.NewSimpleAssembly
-
- symbolAt(int) - Method in class org.biojava.bio.seq.SimpleAssembly
-
- symbolAt(Object, int) - Method in interface org.biojava.bio.symbol.Alignment
-
Retrieve a symbol by label and column.
- symbolAt(int) - Method in class org.biojava.bio.symbol.ChunkedSymbolList
-
- symbolAt(int) - Method in class org.biojava.bio.symbol.DummySymbolList
-
- symbolAt(int) - Method in class org.biojava.bio.symbol.PackedSymbolList
-
- symbolAt(Object, int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- symbolAt(Object, int) - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleGappedSymbolList
-
- symbolAt(int) - Method in class org.biojava.bio.symbol.SimpleSymbolList
-
Find a symbol at a specified offset in the SymbolList.
- symbolAt(int) - Method in interface org.biojava.bio.symbol.SymbolList
-
Return the symbol at index, counting from 1.
- symbolAt(RichSequence, int) - Method in class org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler
-
Return the symbol at index, counting from 1.
- symbolAt(RichSequence, int) - Method in class org.biojavax.bio.seq.DummyRichSequenceHandler
-
Return the symbol at index, counting from 1.
- symbolAt(int) - Method in class org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
-
Return the symbol at index, counting from 1.
- symbolAt(RichSequence, int) - Method in interface org.biojavax.bio.seq.RichSequenceHandler
-
Return the symbol at index, counting from 1.
- symbolAt(int) - Method in class org.biojavax.bio.seq.ThinRichSequence
-
Return the symbol at index, counting from 1.
- symbolForIndex(int) - Method in interface org.biojava.bio.symbol.AlphabetIndex
-
Retrieve the symbol for an index.
- symbolForLifeScienceID(LifeScienceIdentifier) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Retreives the Symbol for the LSID
- symbolForName(String) - Static method in class org.biojava.bio.symbol.AlphabetManager
-
Deprecated.
use symbolForLifeScienceID() instead
- SymbolList - Interface in org.biojava.bio.symbol
-
A sequence of symbols that belong to an alphabet.
- SymbolListCharSequence - Class in org.biojava.bio.seq.io
-
SymbolListCharSequence is a CharSequence
implementation which wraps a SymbolList.
- SymbolListCharSequence(SymbolList) - Constructor for class org.biojava.bio.seq.io.SymbolListCharSequence
-
Creates a new SymbolListCharSequence wrapping a
SymbolList.
- SymbolListFactory - Interface in org.biojava.bio.symbol
-
This interface exists to hide implementational details
of SymbolLists when making chunked symbol lists.
- symbolListForLabel(Object) - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- symbolListForLabel(Object) - Method in class org.biojava.bio.alignment.FlexibleAlignment
-
- symbolListForLabel(Object) - Method in class org.biojava.bio.dp.SimpleStatePath
-
- symbolListForLabel(Object) - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- symbolListForLabel(Object) - Method in interface org.biojava.bio.symbol.Alignment
-
Retrieve a single row of the alignment by label.
- symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- symbolListForLabel(Object) - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment
-
- symbolListIterator() - Method in class org.biojava.bio.alignment.AbstractULAlignment
-
- symbolListIterator() - Method in class org.biojava.bio.dp.SimpleStatePath
-
- symbolListIterator() - Method in class org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment
-
- symbolListIterator() - Method in interface org.biojava.bio.symbol.Alignment
-
Creates an Iterator over the SymbolLists in the alignment.
- symbolListIterator() - Method in class org.biojava.bio.symbol.RelabeledAlignment
-
- symbolListIterator() - Method in class org.biojava.bio.symbol.SimpleAlignment
-
- SymbolListViews - Class in org.biojava.bio.symbol
-
Tools class for constructing views of SymbolList objects.
- SymbolPropertyTable - Interface in org.biojava.bio.symbol
-
class for maintaining properties associated with a symbol
- SymbolPropertyTableDB - Interface in org.biojava.bio.proteomics.aaindex
-
- SymbolPropertyTableIterator - Interface in org.biojava.bio.proteomics.aaindex
-
- SymbolReader - Interface in org.biojava.bio.seq.io
-
Encapsulate a stream of Symbols being parsed from some input
stream.
- symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractLocationDecorator
-
- symbols(SymbolList) - Method in class org.biojava.bio.symbol.AbstractRangeLocation
-
- SYMBOLS - Static variable in interface org.biojava.bio.symbol.Alphabet
-
This ChangeType indicates that some symbols have been added or removed from
the alphabet.
- symbols(SymbolList) - Method in class org.biojava.bio.symbol.CircularLocation
-
- symbols(SymbolList) - Method in class org.biojava.bio.symbol.FuzzyPointLocation
-
- symbols(SymbolList) - Method in interface org.biojava.bio.symbol.Location
-
Return the symbols in a sequence that fall within this range.
- symbols(SymbolList) - Method in class org.biojavax.bio.seq.CompoundRichLocation
-
Return the symbols in a sequence that fall within this range.
- symbols(SymbolList) - Method in class org.biojavax.bio.seq.EmptyRichLocation
-
Return the symbols in a sequence that fall within this range.
- symbols(SymbolList) - Method in class org.biojavax.bio.seq.SimpleRichLocation
-
Return the symbols in a sequence that fall within this range.
- SymbolSequenceRenderer - Class in org.biojava.bio.gui.sequence
-
SymbolSequenceRenderer renders symbols of a
SymbolList.
- SymbolSequenceRenderer() - Constructor for class org.biojava.bio.gui.sequence.SymbolSequenceRenderer
-
- SymbolStyle - Interface in org.biojava.bio.gui
-
The interface for things that say how to paint a symbol.
- SymbolTokenization - Interface in org.biojava.bio.seq.io
-
Encapsulate a mapping between BioJava Symbol objects and
some string representation.
- SymbolTokenization.TokenType - Class in org.biojava.bio.seq.io
-
- symList() - Method in interface org.biojava.bio.dp.DPMatrix
-
- symList() - Method in interface org.biojava.bio.dp.onehead.DPCursor
-
The symbol list being looped over.
- symList - Variable in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- symList() - Method in class org.biojava.bio.dp.onehead.SingleDPMatrix
-
- symList() - Method in class org.biojava.bio.dp.onehead.SmallCursor
-
- symList() - Method in class org.biojava.bio.dp.twohead.PairDPMatrix
-
- SYMLISTVERSION - Static variable in interface org.biojavax.bio.seq.RichSequence
-
- SYMMETRIC - Static variable in class org.biojava.ontology.OntoTools
-
- SYNONYM - Static variable in class org.biojava.ontology.obo.OboFileHandler
-
- Synonym - Class in org.biojava.ontology
-
- Synonym() - Constructor for class org.biojava.ontology.Synonym
-
- SYNONYM - Static variable in interface org.biojavax.bio.taxa.NCBITaxon
-
Use this to define common names for things.
- SYNONYM_NAME_KEY - Static variable in class org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
-
- SystemRegistry - Class in org.biojava.directory
-
A registry that loads up the standard biodirectory files.
- SystemRegistry() - Constructor for class org.biojava.directory.SystemRegistry
-