logicProteinHypernetwork.analysis.complexes.ComplexToMinimalNetworkStates.java Source code

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Here is the source code for logicProteinHypernetwork.analysis.complexes.ComplexToMinimalNetworkStates.java

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/* Copyright (c) 2010, Johannes Kster <johannes.koester@tu-dortmund.de>
 * All rights reserved.
 *
 * This software is open-source under the BSD license; see "license.txt"
 * for a description.
 */
package logicProteinHypernetwork.analysis.complexes;

import edu.uci.ics.jung.algorithms.filters.FilterUtils;
import java.util.ArrayList;
import java.util.Collection;
import logicProteinHypernetwork.networkStates.MinimalNetworkState;
import logicProteinHypernetwork.networkStates.MinimalNetworkStates;
import org.apache.commons.collections15.Transformer;
import proteinHypernetwork.interactions.Interaction;

/**
 * Transforms complexes to sets of minimal network states.
 * 
 * @author Johannes Kster <johannes.koester@tu-dortmund.de>
 */
public class ComplexToMinimalNetworkStates implements Transformer<Complex, Collection<MinimalNetworkState>> {

    private ProteinSubnetwork ppin;
    private MinimalNetworkStates minimalNetworkStates;

    /**
     * Constructor of class ComplexToMinimalNetworkStates.
     * @param ppin the protein network
     * @param minimalNetworkStates the minimal network states
     */
    public ComplexToMinimalNetworkStates(ProteinSubnetwork ppin, MinimalNetworkStates minimalNetworkStates) {
        this.ppin = ppin;
        this.minimalNetworkStates = minimalNetworkStates;
    }

    /**
     * Returns all minimal network states belonging to given complex.
     * 
     * @param c the complex
     * @return the minimal network states
     */
    public Collection<MinimalNetworkState> transform(Complex c) {
        ProteinSubnetwork naiveComplex = FilterUtils.createInducedSubgraph(c, ppin);

        Collection<MinimalNetworkState> mns = new ArrayList<MinimalNetworkState>();

        for (Interaction i : naiveComplex.getEdges()) {
            try {
                mns.addAll(minimalNetworkStates.getMinimalNetworkStates(i));
            } catch (NullPointerException ex) {
                // happens if artificially inserted interactions occur. These do not hurt since they won't have any competitors.
            }
        }

        return mns;
    }
}