Package psidev.psi.mi.jami.binary.expansion

Class AbstractComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

java.lang.Object

psidev.psi.mi.jami.binary.expansion.AbstractComplexExpansionMethod<T,B>

All Implemented Interfaces:

ComplexExpansionMethod<T,B>

Direct Known Subclasses:

AbstractBipartiteExpansion, AbstractMatrixExpansion, AbstractSpokeExpansion

public abstract class AbstractComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>
extends Object
implements ComplexExpansionMethod<T,B>

Abstract class for ComplexExpansionMethod. It needs a BinaryInteractionFactory to be able to create the proper binary interaction instance.

Since:

05/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.binary.expansion.ComplexExpansionMethod

BIPARTITE, BIPARTITE_EXPANSION, BIPARTITE_EXPANSION_MI, MATRIX, MATRIX_EXPANSION, MATRIX_EXPANSION_MI, SPOKE, SPOKE_EXPANSION, SPOKE_EXPANSION_MI

Constructor Summary

Constructors

Constructor	Description
AbstractComplexExpansionMethod(CvTerm method)	Constructor for AbstractComplexExpansionMethod.

Method Summary

Modifier and Type	Method	Description
protected abstract Collection<B>	collectBinaryInteractionsFromNary(T interaction)	collectBinaryInteractionsFromNary
protected Collection<B>	createBinaryInteractionWrappersFrom(T interaction)	createBinaryInteractionWrappersFrom
protected Collection<B>	createNewSelfBinaryInteractionsFrom(T interaction)	createNewSelfBinaryInteractionsFrom
Collection<B>	expand(T interaction)	expand
protected ComplexType	findInteractionCategory(T interaction)	findInteractionCategory
BinaryInteractionFactory	getBinaryInteractionFactory()	getBinaryInteractionFactory
CvTerm	getMethod()	The CvTerm that describe the method used to expand.
boolean	isInteractionExpandable(T interaction)	By default, a complex expansion can only expand interactions having at least one participant and where the provided interaction is not null.
void	setBinaryInteractionFactory(BinaryInteractionFactory factory)	Sets the binary interaction factory

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractComplexExpansionMethod

public AbstractComplexExpansionMethod(CvTerm method)

Constructor for AbstractComplexExpansionMethod.

Parameters:

method - : the CvTerm that describe the method used to expand

Method Detail

getMethod

public CvTerm getMethod()

The CvTerm that describe the method used to expand. It cannot be null

Specified by:

getMethod in interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Returns:

CvTerm that describe the method used to expand

isInteractionExpandable

public boolean isInteractionExpandable(T interaction)

By default, a complex expansion can only expand interactions having at least one participant and where the provided interaction is not null.

Specified by:

isInteractionExpandable in interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Parameters:

interaction - : the interaction we want to expand

Returns:

true if this complex expansion method can expand such an interaction, false otherwise.

expand

public Collection<B> expand(T interaction)
                     throws ComplexExpansionException

expand

Specified by:

expand in interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

the collection of binary interactions generated from the given interaction.

Throws:

ComplexExpansionException - : when the interaction is not expandable by this method

getBinaryInteractionFactory

public BinaryInteractionFactory getBinaryInteractionFactory()

getBinaryInteractionFactory

Specified by:

getBinaryInteractionFactory in interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Returns:

the factory used by the complex epxansion to create new binaryInteraction instances

setBinaryInteractionFactory

public void setBinaryInteractionFactory(BinaryInteractionFactory factory)

Sets the binary interaction factory

Specified by:

setBinaryInteractionFactory in interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Parameters:

factory - a BinaryInteractionFactory object.

createNewSelfBinaryInteractionsFrom

protected Collection<B> createNewSelfBinaryInteractionsFrom(T interaction)

createNewSelfBinaryInteractionsFrom

Parameters:

interaction - : the self interaction to expand

Returns:

the collection of binary interaction generated from this self interaction

createBinaryInteractionWrappersFrom

protected Collection<B> createBinaryInteractionWrappersFrom(T interaction)

createBinaryInteractionWrappersFrom

Parameters:

interaction - : the interaction with only two participants

Returns:

the collection of binary interaction wrappers generated from this interaction with two partcipants

findInteractionCategory

protected ComplexType findInteractionCategory(T interaction)

findInteractionCategory

Parameters:

interaction - : the interaction to expand

Returns:

the complexType that match this interaction and which will be used to expand

collectBinaryInteractionsFromNary

protected abstract Collection<B> collectBinaryInteractionsFromNary(T interaction)

collectBinaryInteractionsFromNary

Parameters:

interaction - : the interaction to expand

Returns:

the collection of binary interaction generated from this n-ary interaction