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

Class MatrixExpansion

java.lang.Object

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

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

psidev.psi.mi.jami.binary.expansion.MatrixExpansion

All Implemented Interfaces:

ComplexExpansionMethod<Interaction,BinaryInteraction>

public class MatrixExpansion
extends AbstractMatrixExpansion<Interaction,BinaryInteraction>

The matrix Expansion method. Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other.

Since:

04/06/13

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
MatrixExpansion()	Constructor for MatrixExpansion.

Method Summary

Modifier and Type	Method	Description
protected <P extends Participant> BinaryInteraction	createBinaryInteraction(Interaction interaction, P c1, P c2)	createBinaryInteraction
protected Participant[]	createParticipantsArray(Interaction interaction)	createParticipantsArray
Collection<BinaryInteraction>	expand(Interaction interaction)	expand
void	setBinaryInteractionFactory(BinaryInteractionFactory factory)	Sets the binary interaction factory

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

collectBinaryInteractionsFromNary

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

MatrixExpansion

public MatrixExpansion()

Constructor for MatrixExpansion.

Method Detail

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

createBinaryInteraction

protected <P extends Participant> BinaryInteraction createBinaryInteraction(Interaction interaction,
                                                                            P c1,
                                                                            P c2)

createBinaryInteraction

Specified by:

createBinaryInteraction in class AbstractMatrixExpansion<Interaction,BinaryInteraction>

Type Parameters:

P - a P object.

Parameters:

interaction - : the interaction to expand

c1 - : participant A

c2 - : participant B

Returns:

the binary interaction

createParticipantsArray

protected Participant[] createParticipantsArray(Interaction interaction)

createParticipantsArray

Specified by:

createParticipantsArray in class AbstractMatrixExpansion<Interaction,BinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

the array of participants involved in this interaction

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.