public class Sequence extends java.lang.Object implements PhylogenyData
Constructor and Description |
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Sequence() |
Modifier and Type | Method and Description |
---|---|
void |
addAnnotation(Annotation annotation) |
java.lang.StringBuffer |
asSimpleText() |
java.lang.StringBuffer |
asText() |
PhylogenyData |
copy()
Not a deep copy.
|
boolean |
equals(java.lang.Object o) |
Accession |
getAccession() |
PhylogenyData |
getAnnotation(int index) |
java.util.List<PhylogenyData> |
getAnnotations() |
DomainArchitecture |
getDomainArchitecture() |
java.lang.String |
getLocation() |
java.lang.String |
getMolecularSequence() |
java.lang.String |
getName() |
java.lang.String |
getSymbol() |
java.lang.String |
getType() |
Uri |
getUri() |
int |
hashCode() |
void |
init() |
boolean |
isEmpty() |
boolean |
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.
|
void |
setAccession(Accession accession) |
void |
setDomainArchitecture(DomainArchitecture ds) |
void |
setLocation(java.lang.String description) |
void |
setMolecularSequence(java.lang.String mol_sequence) |
void |
setName(java.lang.String name) |
void |
setSymbol(java.lang.String symbol) |
void |
setType(java.lang.String type) |
void |
setUri(Uri uri) |
java.lang.StringBuffer |
toNHX() |
void |
toPhyloXML(java.io.Writer writer,
int level,
java.lang.String indentation)
Writes a phyloXML representation of this phylogeny data.
|
java.lang.String |
toString() |
public void addAnnotation(Annotation annotation)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public PhylogenyData copy()
copy
in interface PhylogenyData
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public Accession getAccession()
public PhylogenyData getAnnotation(int index)
public java.util.List<PhylogenyData> getAnnotations()
public DomainArchitecture getDomainArchitecture()
public java.lang.String getLocation()
public java.lang.String getMolecularSequence()
public java.lang.String getName()
public java.lang.String getSymbol()
public java.lang.String getType()
public Uri getUri()
public int hashCode()
hashCode
in class java.lang.Object
public void init()
public boolean isEmpty()
public boolean isEqual(PhylogenyData data)
PhylogenyData
isEqual
in interface PhylogenyData
public void setAccession(Accession accession)
public void setDomainArchitecture(DomainArchitecture ds)
public void setLocation(java.lang.String description)
public void setMolecularSequence(java.lang.String mol_sequence)
public void setName(java.lang.String name)
public void setSymbol(java.lang.String symbol)
public void setType(java.lang.String type)
public void setUri(Uri uri)
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
java.io.IOException
public java.lang.String toString()
toString
in class java.lang.Object