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

Class AbstractBipartiteExpansion<T extends Interaction,B extends BinaryInteraction>

java.lang.Object

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

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

All Implemented Interfaces:

ComplexExpansionMethod<T,B>

Direct Known Subclasses:

BipartiteExpansion, InteractionEvidenceBipartiteExpansion, ModelledInteractionBipartiteExpansion

public abstract class AbstractBipartiteExpansion<T extends Interaction,B extends BinaryInteraction>
extends AbstractComplexExpansionMethod<T,B>

Abstract class for BipartiteExpansion. An InteractorFactory can be provided if we want to override the complex created by this expansion method

Since:

19/06/13

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
AbstractBipartiteExpansion()	Constructor for AbstractBipartiteExpansion.

Method Summary

Modifier and Type	Method	Description
protected Collection<B>	collectBinaryInteractionsFromNary(T interaction)	collectBinaryInteractionsFromNary
protected abstract <P extends Participant> B	createBinaryInteraction(T interaction, P c1, P c2)	createBinaryInteraction
protected Complex	createComplexEntity(T interaction)	createComplexEntity
protected abstract <P extends Participant> P	createParticipantForComplexEntity(Complex complexEntity)	createParticipantForComplexEntity
protected String	generateComplexName(Interaction interaction)	generateComplexName
InteractorFactory	getInteractorFactory()	Getter for the field interactorFactory.
void	setInteractorFactory(InteractorFactory interactorFactory)	Setter for the field interactorFactory.

Methods inherited from class psidev.psi.mi.jami.binary.expansion.AbstractComplexExpansionMethod

createBinaryInteractionWrappersFrom, createNewSelfBinaryInteractionsFrom, expand, findInteractionCategory, getBinaryInteractionFactory, getMethod, isInteractionExpandable, setBinaryInteractionFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractBipartiteExpansion

public AbstractBipartiteExpansion()

Constructor for AbstractBipartiteExpansion.

Method Detail

getInteractorFactory

public InteractorFactory getInteractorFactory()

Getter for the field interactorFactory.

Returns:

the interactor factory we want to use to create the complex for bipartite expansion

setInteractorFactory

public void setInteractorFactory(InteractorFactory interactorFactory)

Setter for the field interactorFactory.

Parameters:

interactorFactory - : the interactor factory we want to use to create the complex for bipartite expansion

collectBinaryInteractionsFromNary

protected Collection<B> collectBinaryInteractionsFromNary(T interaction)

collectBinaryInteractionsFromNary

Specified by:

collectBinaryInteractionsFromNary in class AbstractComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

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

createBinaryInteraction

protected abstract <P extends Participant> B createBinaryInteraction(T interaction,
                                                                     P c1,
                                                                     P c2)

createBinaryInteraction

Type Parameters:

P - a P object.

Parameters:

interaction - : the interaction to expand

c1 - : the participant with the created complex

c2 - : the original participant

Returns:

the binary interaction

createParticipantForComplexEntity

protected abstract <P extends Participant> P createParticipantForComplexEntity(Complex complexEntity)

createParticipantForComplexEntity

Type Parameters:

P - a P object.

Parameters:

complexEntity - : the generated complex

Returns:

the participant generated for the generated complex

createComplexEntity

protected Complex createComplexEntity(T interaction)

createComplexEntity

Parameters:

interaction - : the interaction to expand

Returns:

the complex generated from this interaction instance

generateComplexName

protected String generateComplexName(Interaction interaction)

generateComplexName

Parameters:

interaction - : the interaction to expand

Returns:

the generated name for this interaction