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

Class ModelledInteractionBipartiteExpansion

java.lang.Object

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

psidev.psi.mi.jami.binary.expansion.AbstractBipartiteExpansion<ModelledInteraction,ModelledBinaryInteraction>

psidev.psi.mi.jami.binary.expansion.ModelledInteractionBipartiteExpansion

All Implemented Interfaces:

ComplexExpansionMethod<ModelledInteraction,ModelledBinaryInteraction>

public class ModelledInteractionBipartiteExpansion
extends AbstractBipartiteExpansion<ModelledInteraction,ModelledBinaryInteraction>

Bipartite expansion for ModelledInteraction

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
ModelledInteractionBipartiteExpansion()

Method Summary

Modifier and Type	Method	Description
protected <P extends Participant> ModelledBinaryInteraction	createBinaryInteraction(ModelledInteraction interaction, P p1, P p2)	createBinaryInteraction
protected Collection<ModelledBinaryInteraction>	createBinaryInteractionWrappersFrom(ModelledInteraction interaction)	createBinaryInteractionWrappersFrom
protected Collection<ModelledBinaryInteraction>	createNewSelfBinaryInteractionsFrom(ModelledInteraction interaction)	createNewSelfBinaryInteractionsFrom
protected ModelledParticipant	createParticipantForComplexEntity(Complex complexEntity)	createParticipantForComplexEntity
protected ComplexType	findInteractionCategory(ModelledInteraction interaction)	findInteractionCategory

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

collectBinaryInteractionsFromNary, 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

ModelledInteractionBipartiteExpansion

public ModelledInteractionBipartiteExpansion()

Method Detail

createNewSelfBinaryInteractionsFrom

protected Collection<ModelledBinaryInteraction> createNewSelfBinaryInteractionsFrom(ModelledInteraction interaction)

createNewSelfBinaryInteractionsFrom

Overrides:

createNewSelfBinaryInteractionsFrom in class AbstractComplexExpansionMethod<ModelledInteraction,ModelledBinaryInteraction>

Parameters:

interaction - : the self interaction to expand

Returns:

the collection of binary interaction generated from this self interaction

createBinaryInteractionWrappersFrom

protected Collection<ModelledBinaryInteraction> createBinaryInteractionWrappersFrom(ModelledInteraction interaction)

createBinaryInteractionWrappersFrom

Overrides:

createBinaryInteractionWrappersFrom in class AbstractComplexExpansionMethod<ModelledInteraction,ModelledBinaryInteraction>

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(ModelledInteraction interaction)

findInteractionCategory

Overrides:

findInteractionCategory in class AbstractComplexExpansionMethod<ModelledInteraction,ModelledBinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

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

createBinaryInteraction

protected <P extends Participant> ModelledBinaryInteraction createBinaryInteraction(ModelledInteraction interaction,
                                                                                    P p1,
                                                                                    P p2)

createBinaryInteraction

Specified by:

createBinaryInteraction in class AbstractBipartiteExpansion<ModelledInteraction,ModelledBinaryInteraction>

Type Parameters:

P - a P object.

Parameters:

interaction - : the interaction to expand

p1 - : the participant with the created complex

p2 - : the original participant

Returns:

the binary interaction

createParticipantForComplexEntity

protected ModelledParticipant createParticipantForComplexEntity(Complex complexEntity)

createParticipantForComplexEntity

Specified by:

createParticipantForComplexEntity in class AbstractBipartiteExpansion<ModelledInteraction,ModelledBinaryInteraction>

Parameters:

complexEntity - : the generated complex

Returns:

the participant generated for the generated complex