logicProteinHypernetwork.analysis.complexes.Complex.java Source code

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Here is the source code for logicProteinHypernetwork.analysis.complexes.Complex.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 java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import org.apache.commons.collections15.SetUtils;
import proteinHypernetwork.proteins.Protein;

/**
 * Class Complex models a list of proteins that are in one complex.
 * 
 * @author Johannes Kster <johannes.koester@tu-dortmund.de>
 */
public class Complex extends ArrayList<Protein> implements Collection<Protein>, Comparable<Complex> {

    private ProteinSubnetwork subnetwork;
    private int hashCode = -1;

    /**
     * Construct an empty complex.
     */
    public Complex() {
    }

    /**
     * Construct a complex out of an iterable of proteins.
     *
     * @param c the proteins
     */
    public Complex(Iterable<? extends Protein> c) {
        for (Protein p : c)
            add(p);
    }

    /**
     * Add a protein to the complex.
     *
     * @param p the protein
     * @return true
     */
    @Override
    public boolean add(Protein p) {
        boolean b = super.add(p);
        hashCode = -1;
        return b;
    }

    /**
     * Returns the protein subnetwork corresponding to this complex.
     *
     * @return the protein subnetwork
     */
    public ProteinSubnetwork getSubnetwork() {
        return subnetwork;
    }

    /**
     * Sets the protein subnetwork.
     *
     * @param subnetwork the subnetwork
     */
    public void setSubnetwork(ProteinSubnetwork subnetwork) {
        this.subnetwork = subnetwork;
    }

    public int compareTo(Complex o) {
        return o.size() - size();
    }

    @Override
    public int hashCode() {
        if (hashCode == -1) {
            hashCode = 0;
            for (Protein p : this) {
                hashCode += p.hashCode(); // the sum of hashcodes as specified in the set interface
            }
        }
        return hashCode;
    }

    @Override
    public boolean equals(Object obj) {
        if (obj == null) {
            return false;
        }
        if (getClass() != obj.getClass()) {
            return false;
        }
        final Complex other = (Complex) obj;

        return SetUtils.isEqualSet(this, other);
    }

    @Override
    public String toString() {
        String s = "";
        for (int i = 0; i < this.size(); i++) {
            s += this.get(i);
            if (i < this.size() - 1) {
                s += ", ";
            }
        }
        return s;
    }

    /**
     * Comparator that compares complexes by their density.
     */
    public static class DensityComparator implements Comparator<Complex> {

        private ProteinSubnetwork.DensityComparator subcomp = new ProteinSubnetwork.DensityComparator();

        public int compare(Complex c, Complex c1) {
            return subcomp.compare(c.subnetwork, c1.subnetwork);
        }
    }
}