java.lang.Object

org.biojava.bio.program.homologene.SimpleOrthologue

All Implemented Interfaces:: Orthologue

public class SimpleOrthologue extends Object implements Orthologue

this entry contains data about the orthologue.

Constructor Summary

Constructors

Constructor

Description

SimpleOrthologue(int taxonID, String locusID, String homologeneID, String accession)

this constructor does the Taxon lookup for you too

SimpleOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
Method Summary

Modifier and Type

Method

Description

boolean

equals(Object o)

String

getAccession()

get the Accession ID associated with this orthologue.

String

getHomologeneID()

get the Homologene ID.

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.

String

getTitle()

return the title used by Genbank for this protein

void

setTitle(String title)

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SimpleOrthologue
  
  public SimpleOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)
- SimpleOrthologue
  
  public SimpleOrthologue(int taxonID, String locusID, String homologeneID, String accession) throws IllegalArgumentException
  
  this constructor does the Taxon lookup for you too
  
  Throws:
  
  IllegalArgumentException
Method Details
- getTitle
  
  public 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 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 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 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(String title)
  
  Specified by:
  
  setTitle in interface Orthologue
- equals
  
  public boolean equals(Object o)
  
  Overrides:
  
  equals in class Object

Class SimpleOrthologue

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SimpleOrthologue

SimpleOrthologue

Method Details

getTitle

getTaxon

getTaxonID

getLocusID

getHomologeneID

getAccession

setTitle

equals