public class Sequence extends java.lang.Object implements PhylogenyData, MultipleUris
Constructor and Description |
---|
Sequence() |
Modifier and Type | Method and Description |
---|---|
void |
addAnnotation(Annotation annotation) |
void |
addSequenceRelation(SequenceRelation sr) |
void |
addUri(Uri uri) |
java.lang.StringBuffer |
asSimpleText() |
java.lang.StringBuffer |
asText() |
PhylogenyData |
copy()
Not a deep copy.
|
boolean |
equals(java.lang.Object o) |
Accession |
getAccession() |
Annotation |
getAnnotation(int i) |
java.util.SortedSet<Annotation> |
getAnnotations() |
DomainArchitecture |
getDomainArchitecture() |
java.lang.String |
getLocation() |
java.lang.String |
getMolecularSequence() |
java.lang.String |
getName() |
java.util.List<SequenceRelation> |
getSequenceRelations() |
java.lang.String |
getSourceId() |
java.lang.String |
getSymbol() |
java.lang.String |
getType() |
Uri |
getUri(int index) |
java.util.List<Uri> |
getUris() |
int |
hashCode() |
boolean |
hasSequenceRelations() |
void |
init() |
boolean |
isEmpty() |
boolean |
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.
|
boolean |
isMolecularSequenceAligned() |
void |
setAccession(Accession accession) |
void |
setDomainArchitecture(DomainArchitecture ds) |
void |
setLocation(java.lang.String description) |
void |
setMolecularSequence(java.lang.String mol_sequence) |
void |
setMolecularSequenceAligned(boolean aligned) |
void |
setName(java.lang.String name) |
void |
setSourceId(java.lang.String source_id) |
void |
setSymbol(java.lang.String symbol) |
void |
setType(java.lang.String type) |
void |
setUris(java.util.List<Uri> uris) |
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 boolean isEmpty()
public void addAnnotation(Annotation annotation)
public void addUri(Uri uri)
addUri
in interface MultipleUris
public void addSequenceRelation(SequenceRelation sr)
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 Annotation getAnnotation(int i)
public java.util.SortedSet<Annotation> getAnnotations()
public DomainArchitecture getDomainArchitecture()
public java.lang.String getLocation()
public java.lang.String getMolecularSequence()
public boolean isMolecularSequenceAligned()
public java.lang.String getName()
public java.util.List<SequenceRelation> getSequenceRelations()
public java.lang.String getSourceId()
public java.lang.String getSymbol()
public java.lang.String getType()
public java.util.List<Uri> getUris()
getUris
in interface MultipleUris
public Uri getUri(int index)
getUri
in interface MultipleUris
public int hashCode()
hashCode
in class java.lang.Object
public boolean hasSequenceRelations()
public void init()
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 setMolecularSequenceAligned(boolean aligned)
public void setName(java.lang.String name)
public void setSourceId(java.lang.String source_id)
public void setSymbol(java.lang.String symbol) throws PhyloXmlDataFormatException
PhyloXmlDataFormatException
public void setType(java.lang.String type) throws PhyloXmlDataFormatException
PhyloXmlDataFormatException
public void setUris(java.util.List<Uri> uris)
setUris
in interface MultipleUris
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