org.forester.phylogeny.data

Class Sequence

java.lang.Object

org.forester.phylogeny.data.Sequence

All Implemented Interfaces:

Comparable<Sequence>, MultipleUris, PhylogenyData

public class Sequence
extends Object
implements PhylogenyData, MultipleUris, Comparable<Sequence>

Constructor Summary

Constructors

Constructor and Description
Sequence()
Sequence(MolecularSequence mol_seq)

Method Summary

Modifier and Type	Method and Description
void	addAnnotation(Annotation annotation)
void	addCrossReference(Accession cross_reference)
void	addSequenceRelation(SequenceRelation sr)
void	addUri(Uri uri)
StringBuffer	asSimpleText()
StringBuffer	asText()
int	compareTo(Sequence o)
PhylogenyData	copy() Not a deep copy.
boolean	equals(Object o)
Accession	getAccession()
Annotation	getAnnotation(int i)
SortedSet<Annotation>	getAnnotations()
SortedSet<Accession>	getCrossReferences()
DomainArchitecture	getDomainArchitecture()
String	getGeneName()
String	getLocation()
String	getMolecularSequence()
String	getName()
List<SequenceRelation>	getSequenceRelations()
String	getSourceId()
String	getSymbol()
String	getType()
Uri	getUri(int index)
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(String gene_name)
void	setLocation(String description)
void	setMolecularSequence(String mol_sequence)
void	setMolecularSequenceAligned(boolean aligned)
void	setName(String name)
void	setSourceId(String source_id)
void	setSymbol(String symbol)
void	setType(String type)
void	setUris(List<Uri> uris)
StringBuffer	toNHX()
void	toPhyloXML(Writer writer, int level, String indentation) Writes a phyloXML representation of this phylogeny data.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Sequence

public Sequence()

Sequence

public Sequence(MolecularSequence mol_seq)

Method Detail

addAnnotation

public void addAnnotation(Annotation annotation)

addCrossReference

public void addCrossReference(Accession cross_reference)

addSequenceRelation

public void addSequenceRelation(SequenceRelation sr)

addUri

public void addUri(Uri uri)

Specified by:

addUri in interface MultipleUris

asSimpleText

public StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()

Specified by:

asText in interface PhylogenyData

compareTo

public int compareTo(Sequence o)

Specified by:

compareTo in interface Comparable<Sequence>

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(Object o)

Overrides:

equals in class Object

getAccession

public Accession getAccession()

getAnnotation

public Annotation getAnnotation(int i)

getAnnotations

public SortedSet<Annotation> getAnnotations()

getCrossReferences

public SortedSet<Accession> getCrossReferences()

getDomainArchitecture

public DomainArchitecture getDomainArchitecture()

getGeneName

public String getGeneName()

getLocation

public String getLocation()

getMolecularSequence

public String getMolecularSequence()

getName

public String getName()

getSequenceRelations

public List<SequenceRelation> getSequenceRelations()

getSourceId

public String getSourceId()

getSymbol

public String getSymbol()

getType

public String getType()

getUri

public Uri getUri(int index)

Specified by:

getUri in interface MultipleUris

getUris

public List<Uri> getUris()

Specified by:

getUris in interface MultipleUris

hashCode

public int hashCode()

Overrides:

hashCode in class Object

hasSequenceRelations

public boolean hasSequenceRelations()

init

public void init()

isEmpty

public boolean isEmpty()

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

isMolecularSequenceAligned

public boolean isMolecularSequenceAligned()

setAccession

public void setAccession(Accession accession)

setDomainArchitecture

public void setDomainArchitecture(DomainArchitecture ds)

setGeneName

public void setGeneName(String gene_name)

setLocation

public void setLocation(String description)

setMolecularSequence

public void setMolecularSequence(String mol_sequence)

setMolecularSequenceAligned

public void setMolecularSequenceAligned(boolean aligned)

setName

public void setName(String name)

setSourceId

public void setSourceId(String source_id)

setSymbol

public void setSymbol(String symbol)
               throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setType

public void setType(String type)
             throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setUris

public void setUris(List<Uri> uris)

Specified by:

setUris in interface MultipleUris

toNHX

public StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(Writer writer,
                       int level,
                       String indentation)
                throws IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object