public class Sequence extends java.lang.Object implements PhylogenyData, MultipleUris, java.lang.Comparable<Sequence>
Constructor and Description |
---|
Sequence() |
Sequence(MolecularSequence mol_seq) |
Modifier and Type | Method and Description |
---|---|
void |
addAnnotation(Annotation annotation) |
void |
addCrossReference(Accession cross_reference) |
void |
addSequenceRelation(SequenceRelation sr) |
void |
addUri(Uri uri) |
java.lang.StringBuffer |
asSimpleText() |
java.lang.StringBuffer |
asText() |
int |
compareTo(Sequence o) |
PhylogenyData |
copy()
Not a deep copy.
|
boolean |
equals(java.lang.Object o) |
Accession |
getAccession() |
Annotation |
getAnnotation(int i) |
java.util.SortedSet<Annotation> |
getAnnotations() |
java.util.SortedSet<Accession> |
getCrossReferences() |
DomainArchitecture |
getDomainArchitecture() |
java.lang.String |
getGeneName() |
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 |
setGeneName(java.lang.String gene_name) |
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 Sequence()
public Sequence(MolecularSequence mol_seq)
public void addAnnotation(Annotation annotation)
public void addCrossReference(Accession cross_reference)
public void addSequenceRelation(SequenceRelation sr)
public void addUri(Uri uri)
addUri
in interface MultipleUris
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public int compareTo(Sequence o)
compareTo
in interface java.lang.Comparable<Sequence>
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 java.util.SortedSet<Accession> getCrossReferences()
public DomainArchitecture getDomainArchitecture()
public java.lang.String getGeneName()
public java.lang.String getLocation()
public java.lang.String getMolecularSequence()
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 Uri getUri(int index)
getUri
in interface MultipleUris
public java.util.List<Uri> getUris()
getUris
in interface MultipleUris
public int hashCode()
hashCode
in class java.lang.Object
public boolean hasSequenceRelations()
public void init()
public boolean isEmpty()
public boolean isEqual(PhylogenyData data)
PhylogenyData
isEqual
in interface PhylogenyData
public boolean isMolecularSequenceAligned()
public void setAccession(Accession accession)
public void setDomainArchitecture(DomainArchitecture ds)
public void setGeneName(java.lang.String gene_name)
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