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

Class BipartiteExpansion

java.lang.Object

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

psidev.psi.mi.jami.binary.expansion.AbstractBipartiteExpansion<Interaction,BinaryInteraction>

psidev.psi.mi.jami.binary.expansion.BipartiteExpansion

All Implemented Interfaces:

ComplexExpansionMethod<Interaction,BinaryInteraction>

public class BipartiteExpansion
extends AbstractBipartiteExpansion<Interaction,BinaryInteraction>

The bipartite expansion. Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity.

Since:

05/06/13

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
BipartiteExpansion()	Constructor for BipartiteExpansion.

Method Summary

Modifier and Type	Method	Description
protected BinaryInteraction	createBinaryInteraction(Interaction interaction, Participant c1, Participant c2)	createBinaryInteraction
protected Participant	createParticipantForComplexEntity(Complex complexEntity)	createParticipantForComplexEntity
Collection<BinaryInteraction>	expand(Interaction interaction)	expand
void	setBinaryInteractionFactory(BinaryInteractionFactory factory)	Sets the binary interaction factory
void	setInteractorFactory(InteractorFactory interactorFactory)	Setter for the field interactorFactory.

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

collectBinaryInteractionsFromNary, createComplexEntity, generateComplexName, getInteractorFactory

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

createBinaryInteractionWrappersFrom, createNewSelfBinaryInteractionsFrom, findInteractionCategory, getBinaryInteractionFactory, getMethod, isInteractionExpandable

Methods inherited from class java.lang.Object

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

Constructor Detail

BipartiteExpansion

public BipartiteExpansion()

Constructor for BipartiteExpansion.

Method Detail

createBinaryInteraction

protected BinaryInteraction createBinaryInteraction(Interaction interaction,
                                                    Participant c1,
                                                    Participant c2)

createBinaryInteraction

Specified by:

createBinaryInteraction in class AbstractBipartiteExpansion<Interaction,BinaryInteraction>

Parameters:

interaction - : the interaction to expand

c1 - : the participant with the created complex

c2 - : the original participant

Returns:

the binary interaction

createParticipantForComplexEntity

protected Participant createParticipantForComplexEntity(Complex complexEntity)

createParticipantForComplexEntity

Specified by:

createParticipantForComplexEntity in class AbstractBipartiteExpansion<Interaction,BinaryInteraction>

Parameters:

complexEntity - : the generated complex

Returns:

the participant generated for the generated complex

expand

public Collection<BinaryInteraction> expand(Interaction interaction)
                                     throws ComplexExpansionException

expand

Specified by:

expand in interface ComplexExpansionMethod<Interaction,BinaryInteraction>

Overrides:

expand in class AbstractComplexExpansionMethod<Interaction,BinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

the collection of binary interactions generated from the given interaction.

Throws:

ComplexExpansionException - : when the interaction is not expandable by this method

setInteractorFactory

public void setInteractorFactory(InteractorFactory interactorFactory)

Setter for the field interactorFactory.

Overrides:

setInteractorFactory in class AbstractBipartiteExpansion<Interaction,BinaryInteraction>

Parameters:

interactorFactory - : the interactor factory we want to use to create the complex for bipartite expansion

setBinaryInteractionFactory

public void setBinaryInteractionFactory(BinaryInteractionFactory factory)

Sets the binary interaction factory

Specified by:

setBinaryInteractionFactory in interface ComplexExpansionMethod<Interaction,BinaryInteraction>

Overrides:

setBinaryInteractionFactory in class AbstractComplexExpansionMethod<Interaction,BinaryInteraction>

Parameters:

factory - a BinaryInteractionFactory object.