Package org.forester.phylogeny.data
Class Sequence
- java.lang.Object
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- org.forester.phylogeny.data.Sequence
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- All Implemented Interfaces:
java.lang.Comparable<Sequence>
,MultipleUris
,PhylogenyData
public class Sequence extends java.lang.Object implements PhylogenyData, MultipleUris, java.lang.Comparable<Sequence>
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Constructor Summary
Constructors Constructor Description Sequence()
Sequence(MolecularSequence mol_seq)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Constructor Detail
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Sequence
public Sequence()
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Sequence
public Sequence(MolecularSequence mol_seq)
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Method Detail
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addAnnotation
public void addAnnotation(Annotation annotation)
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addCrossReference
public void addCrossReference(Accession cross_reference)
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addSequenceRelation
public void addSequenceRelation(SequenceRelation sr)
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addUri
public void addUri(Uri uri)
- Specified by:
addUri
in interfaceMultipleUris
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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compareTo
public int compareTo(Sequence o)
- Specified by:
compareTo
in interfacejava.lang.Comparable<Sequence>
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copy
public PhylogenyData copy()
Not a deep copy.- Specified by:
copy
in interfacePhylogenyData
- Returns:
- a ~deep~ copy of this PhylogenyData
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equals
public boolean equals(java.lang.Object o)
- Overrides:
equals
in classjava.lang.Object
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getAccession
public Accession getAccession()
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getAnnotation
public Annotation getAnnotation(int i)
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getAnnotations
public java.util.SortedSet<Annotation> getAnnotations()
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getCrossReferences
public java.util.SortedSet<Accession> getCrossReferences()
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getDomainArchitecture
public DomainArchitecture getDomainArchitecture()
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getGeneName
public java.lang.String getGeneName()
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getLocation
public java.lang.String getLocation()
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getMolecularSequence
public java.lang.String getMolecularSequence()
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getName
public java.lang.String getName()
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getSequenceRelations
public java.util.List<SequenceRelation> getSequenceRelations()
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getSourceId
public java.lang.String getSourceId()
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getSymbol
public java.lang.String getSymbol()
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getType
public java.lang.String getType()
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getUri
public Uri getUri(int index)
- Specified by:
getUri
in interfaceMultipleUris
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getUris
public java.util.List<Uri> getUris()
- Specified by:
getUris
in interfaceMultipleUris
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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hasSequenceRelations
public boolean hasSequenceRelations()
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init
public void init()
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isEmpty
public boolean isEmpty()
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isEqual
public boolean isEqual(PhylogenyData data)
Description copied from interface:PhylogenyData
Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.- Specified by:
isEqual
in interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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isMolecularSequenceAligned
public boolean isMolecularSequenceAligned()
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setAccession
public void setAccession(Accession accession)
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setDomainArchitecture
public void setDomainArchitecture(DomainArchitecture ds)
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setGeneName
public void setGeneName(java.lang.String gene_name)
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setLocation
public void setLocation(java.lang.String description)
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setMolecularSequence
public void setMolecularSequence(java.lang.String mol_sequence)
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setMolecularSequenceAligned
public void setMolecularSequenceAligned(boolean aligned)
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setName
public void setName(java.lang.String name)
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setSourceId
public void setSourceId(java.lang.String source_id)
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setSymbol
public void setSymbol(java.lang.String symbol) throws PhyloXmlDataFormatException
- Throws:
PhyloXmlDataFormatException
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setType
public void setType(java.lang.String type) throws PhyloXmlDataFormatException
- Throws:
PhyloXmlDataFormatException
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setUris
public void setUris(java.util.List<Uri> uris)
- Specified by:
setUris
in interfaceMultipleUris
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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toPhyloXML
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
Description copied from interface:PhylogenyData
Writes a phyloXML representation of this phylogeny data.- Specified by:
toPhyloXML
in interfacePhylogenyData
- Throws:
java.io.IOException
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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