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

Class SpokeExpansion

java.lang.Object

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

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

psidev.psi.mi.jami.binary.expansion.SpokeExpansion

All Implemented Interfaces:

ComplexExpansionMethod<Interaction,BinaryInteraction>

public class SpokeExpansion
extends AbstractSpokeExpansion<Interaction,BinaryInteraction>

The spoke expansion Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait.

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
SpokeExpansion()	Constructor for SpokeExpansion.

Method Summary

Modifier and Type	Method	Description
protected Participant	collectBestBaitForSpokeExpansion(Interaction interaction)	collectBestBaitForSpokeExpansion
protected BinaryInteraction	createBinaryInteraction(Interaction interaction, Participant c1, Participant c2)	createBinaryInteraction
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.AbstractSpokeExpansion

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

SpokeExpansion

public SpokeExpansion()

Constructor for SpokeExpansion.

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

createBinaryInteraction

Specified by:

createBinaryInteraction in class AbstractSpokeExpansion<Interaction,BinaryInteraction>

Parameters:

interaction - : the interaction to expand

c1 - : the bait

c2 - : the prey

Returns:

the binary interaction

collectBestBaitForSpokeExpansion

protected Participant collectBestBaitForSpokeExpansion(Interaction interaction)

collectBestBaitForSpokeExpansion

Specified by:

collectBestBaitForSpokeExpansion in class AbstractSpokeExpansion<Interaction,BinaryInteraction>

Parameters:

interaction - : the interaction to expand

Returns:

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