org.biojava.bio.program.homologene
Class SimpleHomologeneBuilder

java.lang.Object
  extended by org.biojava.bio.program.homologene.SimpleHomologeneBuilder
All Implemented Interfaces:
HomologeneBuilder

public class SimpleHomologeneBuilder
extends java.lang.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(java.lang.String key, java.lang.String value)
          add a property to the current Orthologue
 void addOrthoPairProperty(java.lang.String key, java.lang.String value)
          add a property to the current OrthoPair
 void addTitle(int taxonID, java.lang.String homologeneID, java.lang.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(java.lang.String key,
                                  java.lang.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(java.lang.String key,
                                 java.lang.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,
                     java.lang.String homologeneID,
                     java.lang.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