Package net.sf.basedb.util.listable

Class CollectExtracts

java.lang.Object

net.sf.basedb.util.listable.CollectExtracts

public class CollectExtracts
extends Object

Collect extracts seen on derived bioassays and raw bioassays that has been loaded by other transformers. Use the collectFromDerivedBioAssays(boolean) and collectFromRawBioAssays() methods to create transformers that can be inserted into the chain of SourceItemTransformerChain.

Since:

3.5

Author:

Nicklas

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	CollectExtracts.CollectChildren	Transformer implementation that collect the child extracts from the source or collected extracts.
(package private) class	CollectExtracts.CollectFromDerivedBioAssays	Transformer implementation that given a set of derived bioassays load their linked extracts and store that in the parent class.
(package private) class	CollectExtracts.CollectFromExtracts	Transformer implementation that store the given set of extracts in the parent class.
(package private) class	CollectExtracts.CollectFromRawBioAssays	Transformer implementation that given a set of raw bioassays load their linked extracts and store that in the parent class.
(package private) class	CollectExtracts.CollectParents	Transformer implementation that collect the parent extracts from the source or collected extracts.
(package private) class	CollectExtracts.ResetCollected	Transformer implementation that reset the collected extracts before forwarding the call to the parent transformer.

Field Summary

Fields

Modifier and Type	Field	Description
private final Set<Integer>	children
private final Set<Integer>	collected
private boolean	needWrapper
private final Set<Integer>	parents

Constructor Summary

Constructors

Constructor	Description
CollectExtracts()	Create a new derived bioassay to physical bioassay transformer.

Method Summary

Modifier and Type	Method	Description
SourceItemTransformer	collectChildrenOfCollected(boolean includeCollected)	The created transformer collect the ID:s of all child extracts to the already collected extracts and store them in the getCollectedChildren().
SourceItemTransformer	collectChildrenOfSource(boolean includeSource)	The created transformer collect the ID:s of all child extracts to the source extracts and store them in the getCollectedChildren().
SourceItemTransformer	collectFromDerivedBioAssays(boolean loadParents)	The created transformer collect the ID:s of all extracts linked from the source derived bioassays and then return the same set of derived bioassays again.
SourceItemTransformer	collectFromExtracts()	The created transformer collect the ID:s of all extracts in the source collection and return same set of extracts again.
SourceItemTransformer	collectFromRawBioAssays()	The created transformer collect the ID:s of all extracts linked from the source raw bioassays and then return the same set of raw bioassays again.
SourceItemTransformer	collectParentsOfCollected(boolean includeCollected)	The created transformer collect the ID:s of all parent extracts to the already collected extracts and store them in the getCollectedParents().
SourceItemTransformer	collectParentsOfSource(boolean includeSource)	The created transformer collect the ID:s of all parent extracts to the source extracts and store them in the getCollectedParents().
Set<Integer>	getCollected()	Get all extracts that has been collected.
Set<Integer>	getCollectedChildren()	Get child extracts that was collected by the collectChildrenOfCollected(boolean) and/or collectChildrenOfSource(boolean) collectors.
Set<Integer>	getCollectedParents()	Get parent extracts that was collected by the collectParentsOfSource(boolean) or collectParentsOfCollected(boolean) collector.
(package private) void	resetCollected()	Clear all collected extracts in order to prepare for a new collection.
private SourceItemTransformer	wrapForReset(SourceItemTransformer transformer)	Wraps the parent transformer with a ResetCollected transformer the first time this method is called.

Methods inherited from class java.lang.Object

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

Field Details

collected

private final Set<Integer> collected

parents

private final Set<Integer> parents

children

private final Set<Integer> children

needWrapper

private boolean needWrapper

Constructor Details

CollectExtracts

public CollectExtracts()

Create a new derived bioassay to physical bioassay transformer.

Method Details

resetCollected

void resetCollected()

Clear all collected extracts in order to prepare for a new collection.

Since:

3.17

wrapForReset

private SourceItemTransformer wrapForReset(SourceItemTransformer transformer)

Wraps the parent transformer with a ResetCollected transformer the first time this method is called. If called more than once, the parent is return unwrapped.

Since:

3.17

collectFromDerivedBioAssays

public SourceItemTransformer collectFromDerivedBioAssays(boolean loadParents)

The created transformer collect the ID:s of all extracts linked from the source derived bioassays and then return the same set of derived bioassays again. If loadParents is set, extract ID:s will also be collected from all parent derived bioassays (as loaded by DerivedBioAssayToParentDerivedBioAssayTransformer).

collectFromRawBioAssays

public SourceItemTransformer collectFromRawBioAssays()

The created transformer collect the ID:s of all extracts linked from the source raw bioassays and then return the same set of raw bioassays again.

collectFromExtracts

public SourceItemTransformer collectFromExtracts()

The created transformer collect the ID:s of all extracts in the source collection and return same set of extracts again.

collectParentsOfCollected

public SourceItemTransformer collectParentsOfCollected(boolean includeCollected)

The created transformer collect the ID:s of all parent extracts to the already collected extracts and store them in the getCollectedParents(). If the 'includeCollected' flag is set, the collected extracts are included among the parents.

collectParentsOfSource

public SourceItemTransformer collectParentsOfSource(boolean includeSource)

The created transformer collect the ID:s of all parent extracts to the source extracts and store them in the getCollectedParents(). If the 'includeSource' flag is set, the source extracts are included among the parents.

collectChildrenOfCollected

public SourceItemTransformer collectChildrenOfCollected(boolean includeCollected)

The created transformer collect the ID:s of all child extracts to the already collected extracts and store them in the getCollectedChildren(). If the 'includeCollected' flag is set, the collected extracts are included among the children.

collectChildrenOfSource

public SourceItemTransformer collectChildrenOfSource(boolean includeSource)

The created transformer collect the ID:s of all child extracts to the source extracts and store them in the getCollectedChildren(). If the 'includeSource' flag is set, the source extracts are included among the parents.

getCollected

public Set<Integer> getCollected()

Get all extracts that has been collected.

getCollectedParents

public Set<Integer> getCollectedParents()

Get parent extracts that was collected by the collectParentsOfSource(boolean) or collectParentsOfCollected(boolean) collector.

getCollectedChildren

public Set<Integer> getCollectedChildren()

Get child extracts that was collected by the collectChildrenOfCollected(boolean) and/or collectChildrenOfSource(boolean) collectors.