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

Class InteractionEvidenceSpokeExpansion

java.lang.Object

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

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

psidev.psi.mi.jami.binary.expansion.InteractionEvidenceSpokeExpansion

All Implemented Interfaces:

ComplexExpansionMethod<InteractionEvidence,BinaryInteractionEvidence>

public class InteractionEvidenceSpokeExpansion
extends AbstractSpokeExpansion<InteractionEvidence,BinaryInteractionEvidence>

Spoke expansion for interaction evidence

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
InteractionEvidenceSpokeExpansion()

Method Summary

Modifier and Type	Method	Description
protected ParticipantEvidence	collectBestBaitForSpokeExpansion(InteractionEvidence interaction)	collectBestBaitForSpokeExpansion
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 ComplexType	findInteractionCategory(InteractionEvidence 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

InteractionEvidenceSpokeExpansion

public InteractionEvidenceSpokeExpansion()

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

createBinaryInteraction

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

createBinaryInteraction

Specified by:

createBinaryInteraction in class AbstractSpokeExpansion<InteractionEvidence,BinaryInteractionEvidence>

Type Parameters:

P - a P object.

Parameters:

interaction - : the interaction to expand

c1 - : the bait

c2 - : the prey

Returns:

the binary interaction

collectBestBaitForSpokeExpansion

protected ParticipantEvidence collectBestBaitForSpokeExpansion(InteractionEvidence interaction)

collectBestBaitForSpokeExpansion

Specified by:

collectBestBaitForSpokeExpansion in class AbstractSpokeExpansion<InteractionEvidence,BinaryInteractionEvidence>

Parameters:

interaction - : the interaction to expand

Returns:

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