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

Constructors

Constructor

Description

SimpleHomologeneBuilder()
Method Summary

Modifier and Type

Method

Description

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 Details
- SimpleHomologeneBuilder
  
  public SimpleHomologeneBuilder()
Method Details
- 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

Class SimpleHomologeneBuilder

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SimpleHomologeneBuilder

Method Details

startDB

startGroup

startOrthoPair

startOrthologue

addOrthologueProperty

endOrthologue

addOrthoPairProperty

endOrthoPair

addTitle

endGroup

endDB

getDB