org.biojava.bio.program.homologene

Class SimpleOrthologue

java.lang.Object

org.biojava.bio.program.homologene.SimpleOrthologue

All Implemented Interfaces:

Orthologue

public class SimpleOrthologue
extends java.lang.Object
implements Orthologue

this entry contains data about the orthologue.

Constructor Summary

Constructors

Constructor and Description
SimpleOrthologue(int taxonID, java.lang.String locusID, java.lang.String homologeneID, java.lang.String accession) this constructor does the Taxon lookup for you too
SimpleOrthologue(Taxon taxon, java.lang.String locusID, java.lang.String homologeneID, java.lang.String accession)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
java.lang.String	getAccession() get the Accession ID associated with this orthologue.
java.lang.String	getHomologeneID() get the Homologene ID.
java.lang.String	getLocusID() get the locus ID associated with this orthologue.
Taxon	getTaxon() return the Taxon associated with this orthologue
int	getTaxonID() a convenience method to return the TaxonID for thsi orhtologue.
java.lang.String	getTitle() return the title used by Genbank for this protein
void	setTitle(java.lang.String title)

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleOrthologue

public SimpleOrthologue(Taxon taxon,
                java.lang.String locusID,
                java.lang.String homologeneID,
                java.lang.String accession)

SimpleOrthologue

public SimpleOrthologue(int taxonID,
                java.lang.String locusID,
                java.lang.String homologeneID,
                java.lang.String accession)
                 throws java.lang.IllegalArgumentException

this constructor does the Taxon lookup for you too

Throws:

java.lang.IllegalArgumentException

Method Detail

getTitle

public java.lang.String getTitle()

Description copied from interface: Orthologue

return the title used by Genbank for this protein

Specified by:

getTitle in interface Orthologue

getTaxon

public Taxon getTaxon()

Description copied from interface: Orthologue

return the Taxon associated with this orthologue

Specified by:

getTaxon in interface Orthologue

getTaxonID

public int getTaxonID()

Description copied from interface: Orthologue

a convenience method to return the TaxonID for thsi orhtologue.

Specified by:

getTaxonID in interface Orthologue

getLocusID

public java.lang.String getLocusID()

Description copied from interface: Orthologue

get the locus ID associated with this orthologue. It can be null.

Specified by:

getLocusID in interface Orthologue

getHomologeneID

public java.lang.String getHomologeneID()

Description copied from interface: Orthologue

get the Homologene ID. This is unique and always defined.

Specified by:

getHomologeneID in interface Orthologue

getAccession

public java.lang.String getAccession()

Description copied from interface: Orthologue

get the Accession ID associated with this orthologue.

Specified by:

getAccession in interface Orthologue

setTitle

public void setTitle(java.lang.String title)

Specified by:

setTitle in interface Orthologue

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object