net.sf.basedb.util.biomaterial
Class SampleToBioSourceTransformer

java.lang.Object
  net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer

All Implemented Interfaces:

CollectionTransformer<Sample,BioSource>

public class SampleToBioSourceTransformer
extends Object
implements CollectionTransformer<Sample,BioSource>

Collection transformer that given a collection of samples finds their parent biosources. Note that this transformer is only capable of finding the biosources that are immediate parents to the samples. If you want to follow pooled samples up to biosources, you should combine this transformer and a PooledParentsTransformer with the help of a MultiStepCollectionTransformer.

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2009-01-13 09:20:26 +0100 (Tue, 13 Jan 2009) $

Field Summary

private DbControl

dc

Constructor Summary

SampleToBioSourceTransformer(DbControl dc)

Method Summary

protected ItemQuery<BioSource>	createQuery() Create a query for loading biosources.
int	transform(Collection<? extends Sample> samples, Collection<? super BioSource> bioSources) Add all biosources that are parents to any of the samples in the source collection.

Methods inherited from class java.lang.Object

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

Field Detail

dc

private DbControl dc

Constructor Detail

SampleToBioSourceTransformer

public SampleToBioSourceTransformer(DbControl dc)

Method Detail

transform

public int transform(Collection<? extends Sample> samples,
                     Collection<? super BioSource> bioSources)

Add all biosources that are parents to any of the samples in the source collection.

Specified by:

transform in interface CollectionTransformer<Sample,BioSource>

Parameters:

samples - The source collection

bioSources - The destination collection

Returns:

The number of biosources added

createQuery

protected ItemQuery<BioSource> createQuery()

Create a query for loading biosources. The default implemenation will simply load all biosources. The restriction needed to locate the child samples is automatically applied by the transform method. Subclasses may override this method to create an alternate query (for example, with more filters).

Returns:

A query object