org.intermine.bio.postprocess
Class UpdateOrthologues

java.lang.Object
  org.intermine.postprocess.PostProcessor
      org.intermine.bio.postprocess.UpdateOrthologues

public class UpdateOrthologues
extends PostProcessor

Orthologues from INPARANOID are attched to Proteins not Genes, this class finds all Orthologues and Paralogues on Proteins and creates references to to corresponding Genes, duplicating the [Orth|Para]logues if the Protein references multiple Genes.

Field Summary

protected ObjectStore

os

Fields inherited from class org.intermine.postprocess.PostProcessor

osw

Constructor Summary

UpdateOrthologues(ObjectStoreWriter osw)
Create a new UpdateOrthologes object from an ObjectStoreWriter

Method Summary

void	postProcess() Find orthologues with protein and homologueProtein set and, where possible, set object and subject to corresponding genes.

Methods inherited from class org.intermine.postprocess.PostProcessor

getObjectStoreWriter

Methods inherited from class java.lang.Object

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

Field Detail

os

protected ObjectStore os

Constructor Detail

UpdateOrthologues

public UpdateOrthologues(ObjectStoreWriter osw)

Create a new UpdateOrthologes object from an ObjectStoreWriter

Parameters:

osw - writer on genomic ObjectStore

Method Detail

postProcess

public void postProcess()
                 throws ObjectStoreException

Find orthologues with protein and homologueProtein set and, where possible, set object and subject to corresponding genes.

Specified by:

postProcess in class PostProcessor

Throws:

ObjectStoreException - if anything goes wrong