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

Class AbstractSpokeExpansion<T extends Interaction,B extends BinaryInteraction>

java.lang.Object

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

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

All Implemented Interfaces:

ComplexExpansionMethod<T,B>

Direct Known Subclasses:

InteractionEvidenceSpokeExpansion, ModelledInteractionSpokeExpansion, SpokeExpansion

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

Abstract class for SpokeExpansion

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
AbstractSpokeExpansion()	Constructor for AbstractSpokeExpansion.

Method Summary

Modifier and Type	Method	Description
protected abstract <P extends Participant> P	collectBestBaitForSpokeExpansion(T interaction)	collectBestBaitForSpokeExpansion
protected Collection<B>	collectBinaryInteractionsFromNary(T interaction)	collectBinaryInteractionsFromNary
protected abstract <P extends Participant> B	createBinaryInteraction(T interaction, P c1, P c2)	createBinaryInteraction

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

AbstractSpokeExpansion

public AbstractSpokeExpansion()

Constructor for AbstractSpokeExpansion.

Method Detail

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 bait

c2 - : the prey

Returns:

the binary interaction

collectBestBaitForSpokeExpansion

protected abstract <P extends Participant> P collectBestBaitForSpokeExpansion(T interaction)

collectBestBaitForSpokeExpansion

Type Parameters:

P - a P object.

Parameters:

interaction - : the interaction to expand

Returns:

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