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

Class ModelledInteractionSpokeExpansion

java.lang.Object

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

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

psidev.psi.mi.jami.binary.expansion.ModelledInteractionSpokeExpansion

All Implemented Interfaces:

ComplexExpansionMethod<ModelledInteraction,ModelledBinaryInteraction>

public class ModelledInteractionSpokeExpansion
extends AbstractSpokeExpansion<ModelledInteraction,ModelledBinaryInteraction>

Spoke 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
ModelledInteractionSpokeExpansion()

Method Summary

Modifier and Type	Method	Description
protected ModelledParticipant	collectBestBaitForSpokeExpansion(ModelledInteraction interaction)	collectBestBaitForSpokeExpansion
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 ComplexType	findInteractionCategory(ModelledInteraction interaction)	findInteractionCategory

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

collectBinaryInteractionsFromNary

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

ModelledInteractionSpokeExpansion

public ModelledInteractionSpokeExpansion()

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 AbstractSpokeExpansion<ModelledInteraction,ModelledBinaryInteraction>

Type Parameters:

P - a P object.

Parameters:

interaction - : the interaction to expand

p1 - : the bait

p2 - : the prey

Returns:

the binary interaction

collectBestBaitForSpokeExpansion

protected ModelledParticipant collectBestBaitForSpokeExpansion(ModelledInteraction interaction)

collectBestBaitForSpokeExpansion

Specified by:

collectBestBaitForSpokeExpansion in class AbstractSpokeExpansion<ModelledInteraction,ModelledBinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

the best bait to use for complex expansion among all participants of this interaction