Package psidev.psi.mi.jami.analysis.graph

Class BindingSiteCliqueFinder<I extends Interaction,F extends Feature>

java.lang.Object

psidev.psi.mi.jami.analysis.graph.BindingSiteCliqueFinder<I,F>

public class BindingSiteCliqueFinder<I extends Interaction,F extends Feature>
extends Object

The BindingSiteClique finder is an extension of BronKerboschCliqueFinder. It can find all maximal cliques in a graph of binding feature pairs (can retrieve complete graph of binding sites). This BronKerboschCliqueFinder implements Bron-Kerbosch clique detection algorithm as it is described in [Samudrala R.,Moult J.:A Graph-theoretic Algorithm for comparative Modeling of Protein Structure; J.Mol. Biol. (1998); vol 279; pp. 287-302]

Since:

14/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
BindingSiteCliqueFinder(I interaction)	Constructor for BindingSiteCliqueFinder.
BindingSiteCliqueFinder(I interaction, MIComparator<F> featureComparator)	Constructor for BindingSiteCliqueFinder.
BindingSiteCliqueFinder(Collection<I> interaction)	Constructor for BindingSiteCliqueFinder.
BindingSiteCliqueFinder(Collection<I> interaction, MIComparator<F> featureComparator)	Constructor for BindingSiteCliqueFinder.
BindingSiteCliqueFinder(Iterator<I> interaction)	Constructor for BindingSiteCliqueFinder.
BindingSiteCliqueFinder(Iterator<I> interaction, MIComparator<F> featureComparator)	Constructor for BindingSiteCliqueFinder.
BindingSiteCliqueFinder(BindingFeatureGraph<F> graph)	Creates a new clique finder.

Method Summary

Modifier and Type	Method	Description
Collection<Set<F>>	getAllMaximalCliques()	getAllMaximalCliques
Collection<Set<F>>	getBiggestMaximalCliques()	getBiggestMaximalCliques

Methods inherited from class java.lang.Object

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

Constructor Detail

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(BindingFeatureGraph<F> graph)

Creates a new clique finder.

Parameters:

graph - the graph in which cliques are to be found; graph must be simple

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(I interaction)

Constructor for BindingSiteCliqueFinder.

Parameters:

interaction - a I object.

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(Collection<I> interaction)

Constructor for BindingSiteCliqueFinder.

Parameters:

interaction - a Collection object.

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(Iterator<I> interaction)

Constructor for BindingSiteCliqueFinder.

Parameters:

interaction - a Iterator object.

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(I interaction,
                               MIComparator<F> featureComparator)

Constructor for BindingSiteCliqueFinder.

Parameters:

interaction - a I object.

featureComparator - a MIComparator object.

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(Collection<I> interaction,
                               MIComparator<F> featureComparator)

Constructor for BindingSiteCliqueFinder.

Parameters:

interaction - a Collection object.

featureComparator - a MIComparator object.

BindingSiteCliqueFinder

public BindingSiteCliqueFinder(Iterator<I> interaction,
                               MIComparator<F> featureComparator)

Constructor for BindingSiteCliqueFinder.

Parameters:

interaction - a Iterator object.

featureComparator - a MIComparator object.

Method Detail

getAllMaximalCliques

public Collection<Set<F>> getAllMaximalCliques()

getAllMaximalCliques

Returns:

a Collection object.

getBiggestMaximalCliques

public Collection<Set<F>> getBiggestMaximalCliques()

getBiggestMaximalCliques

Returns:

a Collection object.