org.forester.phylogeny.data

Class Sequence

java.lang.Object

org.forester.phylogeny.data.Sequence

All Implemented Interfaces:

MultipleUris, PhylogenyData

public class Sequence
extends java.lang.Object
implements PhylogenyData, MultipleUris

Constructor Summary

Constructors

Constructor and Description
Sequence()

Method Summary

Methods

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()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Sequence

public Sequence()

Method Detail

isEmpty

public boolean isEmpty()

addAnnotation

public void addAnnotation(Annotation annotation)

addUri

public void addUri(Uri uri)

Specified by:

addUri in interface MultipleUris

addSequenceRelation

public void addSequenceRelation(SequenceRelation sr)

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

copy

public PhylogenyData copy()

Not a deep copy.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getAccession

public Accession getAccession()

getAnnotation

public Annotation getAnnotation(int i)

getAnnotations

public java.util.SortedSet<Annotation> getAnnotations()

getDomainArchitecture

public DomainArchitecture getDomainArchitecture()

getLocation

public java.lang.String getLocation()

getMolecularSequence

public java.lang.String getMolecularSequence()

isMolecularSequenceAligned

public boolean isMolecularSequenceAligned()

getName

public java.lang.String getName()

getSequenceRelations

public java.util.List<SequenceRelation> getSequenceRelations()

getSourceId

public java.lang.String getSourceId()

getSymbol

public java.lang.String getSymbol()

getType

public java.lang.String getType()

getUris

public java.util.List<Uri> getUris()

Specified by:

getUris in interface MultipleUris

getUri

public Uri getUri(int index)

Specified by:

getUri in interface MultipleUris

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

hasSequenceRelations

public boolean hasSequenceRelations()

init

public void init()

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 interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

setAccession

public void setAccession(Accession accession)

setDomainArchitecture

public void setDomainArchitecture(DomainArchitecture ds)

setLocation

public void setLocation(java.lang.String description)

setMolecularSequence

public void setMolecularSequence(java.lang.String mol_sequence)

setMolecularSequenceAligned

public void setMolecularSequenceAligned(boolean aligned)

setName

public void setName(java.lang.String name)

setSourceId

public void setSourceId(java.lang.String source_id)

setSymbol

public void setSymbol(java.lang.String symbol)
               throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setType

public void setType(java.lang.String type)
             throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setUris

public void setUris(java.util.List<Uri> uris)

Specified by:

setUris in interface MultipleUris

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

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 interface PhylogenyData

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object