public class StockholmStructure
extends java.lang.Object
Header Section |
Reference Section |
Comment Section |
Alignment Section |
section field | preferred location |
---|---|
#=GF <feature> <Generic per-File annotation, free text> | Above the alignment |
#=GC <feature> <Generic per-Column annotation, exactly 1 char per column> | Below the alignment |
#=GS <seqname> <feature> <Generic per-Sequence annotation, free text> | Above the alignment or just below the corresponding sequence |
#=GR <seqname> <feature> <Generic per-Residue annotation, exactly 1 char per residue> | Just below the corresponding sequence |
Modifier and Type | Class and Description |
---|---|
static class |
StockholmStructure.DatabaseReference |
Constructor and Description |
---|
StockholmStructure() |
Modifier and Type | Method and Description |
---|---|
void |
addActiveSite(java.lang.String seqName,
java.lang.String text) |
void |
addASPFamPredicted(java.lang.String seqName,
java.lang.String text) |
void |
addASSwissProt(java.lang.String seqName,
java.lang.String text) |
void |
addGSAccessionNumber(java.lang.String seqName,
java.lang.String text) |
void |
addGSdbReference(java.lang.String seqName,
java.lang.String text) |
void |
addGSDescription(java.lang.String seqName,
java.lang.String text) |
void |
addGSLook(java.lang.String seqName,
java.lang.String text) |
void |
addGSOrganismClassification(java.lang.String seqName,
java.lang.String text) |
void |
addGSOrganismSpecies(java.lang.String seqName,
java.lang.String text) |
void |
addIntron(java.lang.String seqName,
java.lang.String text) |
void |
addLigandBinding(java.lang.String seqName,
java.lang.String text) |
void |
addPosteriorProbability(java.lang.String seqName,
java.lang.String text) |
void |
addSecondaryStructure(java.lang.String seqName,
java.lang.String text) |
void |
addSequence(java.lang.String seqName,
java.lang.String seqText)
Actually this function should be called appendToSequence
|
void |
addSurfaceAccessibility(java.lang.String seqName,
java.lang.String text) |
void |
addTransMembrane(java.lang.String seqName,
java.lang.String text) |
java.util.List<AbstractSequence<? extends AbstractCompound>> |
getBioSequences() |
java.util.List<AbstractSequence<? extends AbstractCompound>> |
getBioSequences(boolean ignoreCase)
Because some database files have incorrectly small letters (e.g.
|
org.biojava3.alignment.io.StockholmConsensusAnnotation |
getConsAnnotation() |
StockholmFileAnnotation |
getFileAnnotation() |
java.util.Map<java.lang.String,java.lang.StringBuffer> |
getSequences() |
java.lang.String |
toString() |
public StockholmFileAnnotation getFileAnnotation()
public org.biojava3.alignment.io.StockholmConsensusAnnotation getConsAnnotation()
public void addSequence(java.lang.String seqName, java.lang.String seqText)
seqName
- seqText
- public java.util.Map<java.lang.String,java.lang.StringBuffer> getSequences()
public void addGSAccessionNumber(java.lang.String seqName, java.lang.String text)
seqName
- text
- public void addGSDescription(java.lang.String seqName, java.lang.String text)
public void addGSdbReference(java.lang.String seqName, java.lang.String text)
seqName
- text
- public void addGSOrganismSpecies(java.lang.String seqName, java.lang.String text)
public void addGSOrganismClassification(java.lang.String seqName, java.lang.String text)
public void addGSLook(java.lang.String seqName, java.lang.String text)
public void addSurfaceAccessibility(java.lang.String seqName, java.lang.String text)
public void addTransMembrane(java.lang.String seqName, java.lang.String text)
public void addPosteriorProbability(java.lang.String seqName, java.lang.String text)
public void addLigandBinding(java.lang.String seqName, java.lang.String text)
public void addActiveSite(java.lang.String seqName, java.lang.String text)
public void addASPFamPredicted(java.lang.String seqName, java.lang.String text)
public void addASSwissProt(java.lang.String seqName, java.lang.String text)
public void addIntron(java.lang.String seqName, java.lang.String text)
public void addSecondaryStructure(java.lang.String seqName, java.lang.String text)
public java.util.List<AbstractSequence<? extends AbstractCompound>> getBioSequences()
public java.util.List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolean ignoreCase)
ignoreCase
- if true
, the function will deal with small letters as if they are capital onespublic java.lang.String toString()
toString
in class java.lang.Object