Package org.biojava.bio.program.homologene

Interface HomologeneDB

All Known Implementing Classes:

SimpleHomologeneDB

public interface HomologeneDB

Homologene is a NCBI dataset that curates sets of orthologues from the reference model organisms.

This class is a Collection of methods for handling data from the Homologene dataset.

Author:

David Huen, Matthew Pocock

Method Summary

Modifier and Type	Method	Description
Orthologue	createOrthologue(int taxonID, String locusID, String homologeneID, String accession)	Create an orthologue.
Orthologue	createOrthologue(Taxon taxon, String locusID, String homologeneID, String accession)	Create an orthologue.
OrthoPair	createOrthoPair(Orthologue first, Orthologue second, String ref)	Create a curated orthology entry.
OrthoPair	createOrthoPair(Orthologue first, Orthologue second, SimilarityType type, double percentIdentity)	Create a computed orthology entry.
OrthoPairSet	createOrthoPairSet()	Create a Homologene Group.
OrthoPairCollection	filter(OrthoPairSetFilter filters)	Filter the database for a specified group.
Orthologue	getOrthologue(String homologeneID)	Returns an orthologue of specified ID.
OrthoPairCollection	getOrthoPairSets()	Get the HomologeneGroups in this database.

Method Detail

createOrthologue

Orthologue createOrthologue(Taxon taxon,
                            String locusID,
                            String homologeneID,
                            String accession)
                     throws ChangeVetoException

Create an orthologue.

Throws:

ChangeVetoException

createOrthologue

Orthologue createOrthologue(int taxonID,
                            String locusID,
                            String homologeneID,
                            String accession)
                     throws ChangeVetoException

Create an orthologue.

Throws:

ChangeVetoException

getOrthologue

Orthologue getOrthologue(String homologeneID)

Returns an orthologue of specified ID.

createOrthoPair

OrthoPair createOrthoPair(Orthologue first,
                          Orthologue second,
                          SimilarityType type,
                          double percentIdentity)

Create a computed orthology entry.

createOrthoPair

OrthoPair createOrthoPair(Orthologue first,
                          Orthologue second,
                          String ref)

Create a curated orthology entry.

createOrthoPairSet

OrthoPairSet createOrthoPairSet()

Create a Homologene Group.

getOrthoPairSets

OrthoPairCollection getOrthoPairSets()

Get the HomologeneGroups in this database.

filter

OrthoPairCollection filter(OrthoPairSetFilter filters)

Filter the database for a specified group.