org.intermine.bio.postprocess
Class IntergenicRegionUtil

java.lang.Object
  org.intermine.bio.postprocess.IntergenicRegionUtil

public class IntergenicRegionUtil
extends java.lang.Object

Methods for creating feature for intergenic regions.

Constructor Summary

IntergenicRegionUtil(ObjectStoreWriter osw)
Create a new IntergenicRegionUtil object that will operate on the given ObjectStoreWriter.

Method Summary

void	createIntergenicRegionFeatures() Create IntergenicRegion objects
protected java.util.Iterator<?>	createIntergenicRegionFeatures(java.util.Set<org.intermine.model.bio.Location> locationSet, java.util.Map<org.intermine.model.bio.Location,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.

Methods inherited from class java.lang.Object

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

Constructor Detail

IntergenicRegionUtil

public IntergenicRegionUtil(ObjectStoreWriter osw)

Create a new IntergenicRegionUtil object that will operate on the given ObjectStoreWriter.

Parameters:

osw - the ObjectStoreWriter to use when creating/changing objects

Method Detail

createIntergenicRegionFeatures

public void createIntergenicRegionFeatures()
                                    throws ObjectStoreException

Create IntergenicRegion objects

Throws:

ObjectStoreException - if there is an ObjectStore problem

createIntergenicRegionFeatures

protected java.util.Iterator<?> createIntergenicRegionFeatures(java.util.Set<org.intermine.model.bio.Location> locationSet,
                                                               java.util.Map<org.intermine.model.bio.Location,java.util.Set<org.intermine.model.bio.Gene>> locToGeneMap,
                                                               java.lang.Integer chrId)
                                                        throws 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 and the synonym in the synonyms collection.

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:

ObjectStoreException - if there is an ObjectStore problem