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

Class InteractionEvidenceBipartiteExpansion

java.lang.Object

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

psidev.psi.mi.jami.binary.expansion.AbstractBipartiteExpansion<InteractionEvidence,BinaryInteractionEvidence>

psidev.psi.mi.jami.binary.expansion.InteractionEvidenceBipartiteExpansion

All Implemented Interfaces:

ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>

public class InteractionEvidenceBipartiteExpansion
extends AbstractBipartiteExpansion<InteractionEvidence,BinaryInteractionEvidence>

BipartiteExpansion for InteractionEvidence

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
InteractionEvidenceBipartiteExpansion()

Method Summary

Modifier and Type	Method	Description
protected Collection<BinaryInteractionEvidence>	collectBinaryInteractionsFromNary(InteractionEvidence interaction)	collectBinaryInteractionsFromNary
protected <P extends Participant> BinaryInteractionEvidence	createBinaryInteraction(InteractionEvidence interaction, P c1, P c2)	createBinaryInteraction
protected Collection<BinaryInteractionEvidence>	createBinaryInteractionWrappersFrom(InteractionEvidence interaction)	createBinaryInteractionWrappersFrom
protected Collection<BinaryInteractionEvidence>	createNewSelfBinaryInteractionsFrom(InteractionEvidence interaction)	createNewSelfBinaryInteractionsFrom
protected ParticipantEvidence	createParticipantForComplexEntity(Complex complexEntity)	createParticipantForComplexEntity
protected ComplexType	findInteractionCategory(InteractionEvidence interaction)	findInteractionCategory

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

createComplexEntity, generateComplexName, getInteractorFactory, setInteractorFactory

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

expand, getBinaryInteractionFactory, getMethod, isInteractionExpandable, setBinaryInteractionFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractionEvidenceBipartiteExpansion

public InteractionEvidenceBipartiteExpansion()

Method Detail

createNewSelfBinaryInteractionsFrom

protected Collection<BinaryInteractionEvidence> createNewSelfBinaryInteractionsFrom(InteractionEvidence interaction)

createNewSelfBinaryInteractionsFrom

Overrides:

createNewSelfBinaryInteractionsFrom in class AbstractComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>

Parameters:

interaction - : the self interaction to expand

Returns:

the collection of binary interaction generated from this self interaction

createBinaryInteractionWrappersFrom

protected Collection<BinaryInteractionEvidence> createBinaryInteractionWrappersFrom(InteractionEvidence interaction)

createBinaryInteractionWrappersFrom

Overrides:

createBinaryInteractionWrappersFrom in class AbstractComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>

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(InteractionEvidence interaction)

findInteractionCategory

Overrides:

findInteractionCategory in class AbstractComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>

Parameters:

interaction - : the interaction to expand

Returns:

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

collectBinaryInteractionsFromNary

protected Collection<BinaryInteractionEvidence> collectBinaryInteractionsFromNary(InteractionEvidence interaction)

collectBinaryInteractionsFromNary

Overrides:

collectBinaryInteractionsFromNary in class AbstractBipartiteExpansion<InteractionEvidence,BinaryInteractionEvidence>

Parameters:

interaction - : the interaction to expand

Returns:

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

createBinaryInteraction

protected <P extends Participant> BinaryInteractionEvidence createBinaryInteraction(InteractionEvidence interaction,
                                                                                    P c1,
                                                                                    P c2)

createBinaryInteraction

Specified by:

createBinaryInteraction in class AbstractBipartiteExpansion<InteractionEvidence,BinaryInteractionEvidence>

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 ParticipantEvidence createParticipantForComplexEntity(Complex complexEntity)

createParticipantForComplexEntity

Specified by:

createParticipantForComplexEntity in class AbstractBipartiteExpansion<InteractionEvidence,BinaryInteractionEvidence>

Parameters:

complexEntity - : the generated complex

Returns:

the participant generated for the generated complex