org.biojava.bio.program.homologene
Class SimpleHomologeneBuilder

java.lang.Object
  org.biojava.bio.program.homologene.SimpleHomologeneBuilder

All Implemented Interfaces:

HomologeneBuilder

public class SimpleHomologeneBuilder
extends Object
implements HomologeneBuilder

A simple no-frills implementation of the HomologeneBuilder interface. Used to instantiate a in-memory copy of the Homologene data.

Author:

David Huen

Field Summary

Fields inherited from interface org.biojava.bio.program.homologene.HomologeneBuilder

ACCESSION, CURATED, HOMOID, LOCUSID, MULTIPLE, PERCENTIDENTITY, REFERENCE, SIMILARITYTYPE, TAXONID, TWIN

Constructor Summary

SimpleHomologeneBuilder()

Method Summary

void	addOrthologueProperty(String key, String value) add a property to the current Orthologue
void	addOrthoPairProperty(String key, String value) add a property to the current OrthoPair
void	addTitle(int taxonID, String homologeneID, String title) add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files.
void	endDB() end of data for DB
void	endGroup() end of data for group
void	endOrthologue() end of data for this Orthologue
void	endOrthoPair() end of data for this OrthoPair
HomologeneDB	getDB() retrieve the DB that has just been built
void	startDB() indicates start of data for a HomologeneDB
void	startGroup() indicates start of data for a OrthoPairSet
void	startOrthologue() indicates start of data for an orthologue
void	startOrthoPair() indicates start of data for an OrthoPair

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleHomologeneBuilder

public SimpleHomologeneBuilder()

Method Detail

startDB

public void startDB()

Description copied from interface: HomologeneBuilder

indicates start of data for a HomologeneDB

Specified by:

startDB in interface HomologeneBuilder

startGroup

public void startGroup()

Description copied from interface: HomologeneBuilder

indicates start of data for a OrthoPairSet

Specified by:

startGroup in interface HomologeneBuilder

startOrthoPair

public void startOrthoPair()

Description copied from interface: HomologeneBuilder

indicates start of data for an OrthoPair

Specified by:

startOrthoPair in interface HomologeneBuilder

startOrthologue

public void startOrthologue()

Description copied from interface: HomologeneBuilder

indicates start of data for an orthologue

Specified by:

startOrthologue in interface HomologeneBuilder

addOrthologueProperty

public void addOrthologueProperty(String key,
                                  String value)

Description copied from interface: HomologeneBuilder

add a property to the current Orthologue

Specified by:

addOrthologueProperty in interface HomologeneBuilder

endOrthologue

public void endOrthologue()

Description copied from interface: HomologeneBuilder

end of data for this Orthologue

Specified by:

endOrthologue in interface HomologeneBuilder

addOrthoPairProperty

public void addOrthoPairProperty(String key,
                                 String value)

Description copied from interface: HomologeneBuilder

add a property to the current OrthoPair

Specified by:

addOrthoPairProperty in interface HomologeneBuilder

endOrthoPair

public void endOrthoPair()

Description copied from interface: HomologeneBuilder

end of data for this OrthoPair

Specified by:

endOrthoPair in interface HomologeneBuilder

addTitle

public void addTitle(int taxonID,
                     String homologeneID,
                     String title)

Description copied from interface: HomologeneBuilder

add title information to an Orthologue (this is not in enclosed in the Orthologue element because it comes completely separate in the Homologene data files. Go figger.)

Specified by:

addTitle in interface HomologeneBuilder

endGroup

public void endGroup()

Description copied from interface: HomologeneBuilder

end of data for group

Specified by:

endGroup in interface HomologeneBuilder

endDB

public void endDB()

Description copied from interface: HomologeneBuilder

end of data for DB

Specified by:

endDB in interface HomologeneBuilder

getDB

public HomologeneDB getDB()

Description copied from interface: HomologeneBuilder

retrieve the DB that has just been built

Specified by:

getDB in interface HomologeneBuilder