org.bigwiv.blastgraph.command.RemoveSingleLinkageCommand.java Source code

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Here is the source code for org.bigwiv.blastgraph.command.RemoveSingleLinkageCommand.java

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/*
 * BlastGraph: a comparative genomics tool
 * Copyright (C) 2013  Yanbo Ye (yeyanbo289@gmail.com)
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

/**
 * 
 */
package org.bigwiv.blastgraph.command;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;

import org.apache.commons.collections.CollectionUtils;
import org.bigwiv.blastgraph.BlastGraph;
import org.bigwiv.blastgraph.HitVertex;
import org.bigwiv.blastgraph.ValueEdge;
import org.bigwiv.blastgraph.global.Global;

import edu.uci.ics.jung.graph.util.Pair;

/**
 * @author yeyanbo
 *
 */
public class RemoveSingleLinkageCommand extends Command {
    private Map<ValueEdge, Pair<HitVertex>> removed;

    /**
     * 
     */
    public RemoveSingleLinkageCommand() {
        this.isUndoable = true;
        this.commandName = "RemoveSingleLinkage";
        removed = new HashMap<ValueEdge, Pair<HitVertex>>();
    }

    /* (non-Javadoc)
     * @see org.bigwiv.blastgraph.command.Command#concreteExecute()
     */
    @Override
    public void concreteExecute() {

        ArrayList<ValueEdge> edges = new ArrayList<ValueEdge>(Global.graph.getEdges());

        Collections.sort(edges, new Comparator<ValueEdge>() {
            @Override
            public int compare(ValueEdge arg0, ValueEdge arg1) {
                // from weak to strong
                double evalue = arg0.getExpectValue() - arg1.getExpectValue();
                if (evalue < 0) {
                    return 1;
                } else if (evalue > 0) {
                    return -1;
                } else {
                    double c1 = Global.graph.getCoverage(arg0) - Global.graph.getCoverage(arg1);
                    if (c1 > 0) {
                        return 1;
                    } else if (c1 < 0) {
                        return -1;
                    } else {
                        double c2 = Global.graph.getCoverage2(arg0) - Global.graph.getCoverage2(arg1);
                        if (c2 > 0) {
                            return 1;
                        } else if (c2 < 0) {
                            return -1;
                        } else {
                            return 0;
                        }
                    }
                }
            }
        });

        for (ValueEdge valueEdge : edges) {

            //System.out.println(valueEdge.getExpectValue());
            if (isSingle(valueEdge, Global.graph)) {
                removed.put(valueEdge, Global.graph.getEndpoints(valueEdge));
                Global.graph.removeEdge(valueEdge);
            }
        }

    }

    private boolean isSingle(ValueEdge valueEdge, BlastGraph<HitVertex, ValueEdge> graph) {
        Pair<HitVertex> pair = graph.getEndpoints(valueEdge);

        Collection<HitVertex> vertices1 = graph.getNeighbors(pair.getFirst());
        Collection<HitVertex> vertices2 = graph.getNeighbors(pair.getSecond());

        Collection<HitVertex> union = CollectionUtils.intersection(vertices1, vertices2);
        //System.out.println(vertices1.size() + " " + vertices2.size() + " " + union.size());
        if (union.isEmpty()) {
            return true;
        } else {
            return false;
        }
    }

    /* (non-Javadoc)
     * @see org.bigwiv.blastgraph.command.Command#concreteUnExecute()
     */
    @Override
    public void concreteUnExecute() {

        for (ValueEdge ve : removed.keySet()) {
            Global.graph.addEdge(ve, removed.get(ve));
        }

    }

}