logicProteinHypernetwork.analysis.complexes.offline.ComplexPredictionCommand.java Source code

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Here is the source code for logicProteinHypernetwork.analysis.complexes.offline.ComplexPredictionCommand.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.offline;

import edu.uci.ics.jung.graph.UndirectedGraph;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Scanner;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
import logicProteinHypernetwork.analysis.complexes.Complex;
import org.apache.commons.collections15.Transformer;
import proteinHypernetwork.ProteinHypernetwork;
import proteinHypernetwork.interactions.Interaction;
import proteinHypernetwork.proteins.Protein;

/**
 * Predict complexes with external command.
 *
 * @author Johannes Kster <johannes.koester@tu-dortmund.de>
 */
public class ComplexPredictionCommand
        implements Transformer<UndirectedGraph<Protein, Interaction>, Collection<Complex>> {

    private String command;
    private ProteinHypernetwork hypernetwork;

    /**
     * Constructor of ComplexPredictionCommand.
     *
     * @param command the external command
     * @param hypernetwork the protein hypernetwork
     */
    public ComplexPredictionCommand(String command, ProteinHypernetwork hypernetwork) {
        this.command = command;
        this.hypernetwork = hypernetwork;
    }

    /**
     * Returns predicted complexes for a given undirected graph of proteins.
     *
     * @param g the graph
     * @return the predicted complexes
     */
    public Collection<Complex> transform(UndirectedGraph<Protein, Interaction> g) {
        try {
            Process p = Runtime.getRuntime().exec(command);
            BufferedOutputStream outputStream = new BufferedOutputStream(p.getOutputStream());
            BufferedInputStream inputStream = new BufferedInputStream(p.getInputStream());

            for (Interaction i : g.getEdges()) {
                String out = i.first() + " pp " + i.second();
                outputStream.write(out.getBytes());
            }
            outputStream.close();
            p.waitFor();

            if (!hypernetwork.getProteins().hasIndex()) {
                hypernetwork.getProteins().buildIndex();
            }

            Collection<Complex> complexes = new ArrayList<Complex>();
            Scanner s = new Scanner(inputStream);
            Pattern rowPattern = Pattern.compile(".*?\\n");
            Pattern proteinPattern = Pattern.compile(".*?\\s");
            while (s.hasNext(rowPattern)) {
                Complex c = new Complex();
                while (s.hasNext(proteinPattern)) {
                    c.add(hypernetwork.getProteins().getProteinById(s.next(proteinPattern).trim()));
                }
                complexes.add(c);
            }
            inputStream.close();

            return complexes;

        } catch (InterruptedException ex) {
            Logger.getLogger(ComplexPredictionCommand.class.getName()).log(Level.SEVERE, null, ex);
        } catch (IOException ex) {
            Logger.getLogger(ComplexPredictionCommand.class.getName()).log(Level.SEVERE, null, ex);
        }
        return null;
    }
}