org.intermine.bio.util
Class BioQueries

java.lang.Object
  org.intermine.bio.util.BioQueries

public abstract class BioQueries
extends java.lang.Object

Bio utility methods for queries.

Constructor Summary

BioQueries()

Method Summary

static Results

findLocationAndObjects(ObjectStore os, java.lang.Class<?> objectCls, java.lang.Class<?> subjectCls, boolean orderBySubject, boolean hasLength, boolean hasChromosomeLocation, int batchSize) Query ObjectStore for all Location object between given object (eg.

Methods inherited from class java.lang.Object

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

Constructor Detail

BioQueries

public BioQueries()

Method Detail

findLocationAndObjects

public static Results findLocationAndObjects(ObjectStore os,
                                             java.lang.Class<?> objectCls,
                                             java.lang.Class<?> subjectCls,
                                             boolean orderBySubject,
                                             boolean hasLength,
                                             boolean hasChromosomeLocation,
                                             int batchSize)
                                      throws ObjectStoreException

Query ObjectStore for all Location object between given object (eg. Chromosome) and subject (eg. Gene) classes. Return an iterator over the results ordered by subject if orderBySubject is true, otherwise order by object.

Parameters:

os - the ObjectStore to find the Locations in

objectCls - object type of the Location

subjectCls - subject type of the Location

orderBySubject - if true order the results using the subjectCls, otherwise order by objectCls

hasLength - if true, only query locations where the objectCls object has a non-zero length

batchSize - the batch size for the results object

hasChromosomeLocation - if true, only query where the subject has a chromosome location

Returns:

a Results object: object.id, location, subject

Throws:

ObjectStoreException - if problem reading ObjectStore