org.biojava.bio.program.homologene

Class SimpleHomologeneDB

java.lang.Object

org.biojava.bio.program.homologene.AbstractOrthoPairCollection

org.biojava.bio.program.homologene.SimpleOrthoPairCollection

org.biojava.bio.program.homologene.SimpleHomologeneDB

All Implemented Interfaces:

HomologeneDB, OrthoPairCollection

public class SimpleHomologeneDB
extends SimpleOrthoPairCollection
implements HomologeneDB

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection

SimpleOrthoPairCollection.Iterator

Field Summary

Fields inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection

groups

Constructor Summary

Constructors

Constructor and Description
SimpleHomologeneDB()

Method Summary

Methods

Modifier and Type	Method and 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, SimilarityType type, double percentIdentity) Create a computed orthology entry.
OrthoPair	createOrthoPair(Orthologue first, Orthologue second, String ref) Create a curated orthology entry.
OrthoPairSet	createOrthoPairSet() Create a Homologene Group.
Orthologue	getOrthologue(String homologeneID) Returns an orthologue of specified ID.
OrthoPairCollection	getOrthoPairSets() Get the HomologeneGroups in this database.

Methods inherited from class org.biojava.bio.program.homologene.SimpleOrthoPairCollection

add, contains, isEmpty, iterator

Methods inherited from class org.biojava.bio.program.homologene.AbstractOrthoPairCollection

filter

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.program.homologene.HomologeneDB

filter

Constructor Detail

SimpleHomologeneDB

public SimpleHomologeneDB()

Method Detail

createOrthologue

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

Description copied from interface: HomologeneDB

Create an orthologue.

Specified by:

createOrthologue in interface HomologeneDB

Throws:

ChangeVetoException

createOrthologue

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

Description copied from interface: HomologeneDB

Create an orthologue.

Specified by:

createOrthologue in interface HomologeneDB

Throws:

IllegalArgumentException

ChangeVetoException

getOrthologue

public Orthologue getOrthologue(String homologeneID)

Description copied from interface: HomologeneDB

Returns an orthologue of specified ID.

Specified by:

getOrthologue in interface HomologeneDB

createOrthoPair

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

Description copied from interface: HomologeneDB

Create a computed orthology entry.

Specified by:

createOrthoPair in interface HomologeneDB

createOrthoPair

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

Description copied from interface: HomologeneDB

Create a curated orthology entry.

Specified by:

createOrthoPair in interface HomologeneDB

createOrthoPairSet

public OrthoPairSet createOrthoPairSet()

Description copied from interface: HomologeneDB

Create a Homologene Group.

Specified by:

createOrthoPairSet in interface HomologeneDB

getOrthoPairSets

public OrthoPairCollection getOrthoPairSets()

Description copied from interface: HomologeneDB

Get the HomologeneGroups in this database.

Specified by:

getOrthoPairSets in interface HomologeneDB