org.biojava.bio.program.homologene
Class SimpleHomologeneDB

java.lang.Object
  extended by org.biojava.bio.program.homologene.AbstractOrthoPairCollection
      extended by org.biojava.bio.program.homologene.SimpleOrthoPairCollection
          extended by 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
SimpleHomologeneDB()
           
 
Method Summary
 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