org.intermine.bio.postprocess

Class CreateIntergenicRegionFeaturesProcess

java.lang.Object

org.intermine.postprocess.PostProcessor

org.intermine.bio.postprocess.CreateIntergenicRegionFeaturesProcess

public class CreateIntergenicRegionFeaturesProcess
extends org.intermine.postprocess.PostProcessor

Methods for creating feature for intergenic regions.

Field Summary

Fields inherited from class org.intermine.postprocess.PostProcessor

osw

Constructor Summary

Constructors

Constructor and Description
CreateIntergenicRegionFeaturesProcess(org.intermine.objectstore.ObjectStoreWriter osw) Create a new instance

Method Summary

Modifier and Type	Method and Description
protected java.util.Iterator<org.intermine.model.bio.SequenceFeature>	createFeatures(java.util.Set<org.intermine.model.bio.Location> locationSet, java.util.Map<java.lang.Integer,java.util.Set<org.intermine.model.bio.Gene>> locToGeneMap, java.lang.Integer chrId) Return an iterator over a Set of IntergenicRegion objects that don't overlap the Locations in the locationSet argument.
void	postProcess() Main post-processing routine.

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

Constructor Detail

CreateIntergenicRegionFeaturesProcess

public CreateIntergenicRegionFeaturesProcess(org.intermine.objectstore.ObjectStoreWriter osw)

Create a new instance

Parameters:

osw - object store writer

Method Detail

postProcess

public void postProcess()
                 throws org.intermine.objectstore.ObjectStoreException

Main post-processing routine. Create IntergenicRegion objects

Specified by:

postProcess in class org.intermine.postprocess.PostProcessor

Throws:

org.intermine.objectstore.ObjectStoreException - if the objectstore throws an exception

createFeatures

protected java.util.Iterator<org.intermine.model.bio.SequenceFeature> createFeatures(java.util.Set<org.intermine.model.bio.Location> locationSet,
                                                                                     java.util.Map<java.lang.Integer,java.util.Set<org.intermine.model.bio.Gene>> locToGeneMap,
                                                                                     java.lang.Integer chrId)
                                                                              throws org.intermine.objectstore.ObjectStoreException

Return an iterator over a Set of IntergenicRegion objects that don't overlap the Locations in the locationSet argument. The caller must call ObjectStoreWriter.store() on the IntergenicRegion, its chromosomeLocation. Doesn't create synonyms anymore.

Parameters:

locationSet - a set of Locations for the Genes on a particular chromosome

locToGeneMap - a Map from Location.start to Gene and Location.end to Gene, used by this method to find the next and previous Genes for setting the IntergenicRegion.upstreamGene and downstreamGene fields

chrId - the ID of the Chromosome that the Locations refer to

Returns:

an Iterator over IntergenicRegion objects

Throws:

org.intermine.objectstore.ObjectStoreException - if there is an ObjectStore problem