edu.cornell.med.icb.goby.modes.ReadSetToTextMode.java Source code

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Here is the source code for edu.cornell.med.icb.goby.modes.ReadSetToTextMode.java

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/*
 * Copyright (C) 2009-2010 Institute for Computational Biomedicine,
 *                    Weill Medical College of Cornell University
 *
 *  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 edu.cornell.med.icb.goby.modes;

import com.martiansoftware.jsap.JSAPException;
import com.martiansoftware.jsap.JSAPResult;
import edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl;
import edu.cornell.med.icb.goby.reads.ReadSet;
import org.apache.commons.io.IOUtils;

import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;

/**
 * Converts a compact read sets to plain text.
 *
 * @author Fabien Campagne
 */
public class ReadSetToTextMode extends AbstractGobyMode {
    /**
     * The mode name.
     */
    private static final String MODE_NAME = "set-to-text";

    /**
     * The mode description help text.
     */
    private static final String MODE_DESCRIPTION = "Converts read sets to text format.";

    /**
     * The output file.
     */
    private String outputFilename;

    /**
     * The basename of the compact alignment.
     */
    private String[] basenames;

    private String suffix;

    @Override
    public String getModeName() {
        return MODE_NAME;
    }

    @Override
    public String getModeDescription() {
        return MODE_DESCRIPTION;
    }

    enum OutputFormat {
        PLAIN,

    }

    private OutputFormat outputFormat;

    /**
     * Configure.
     *
     * @param args command line arguments
     * @return this object for chaining
     * @throws java.io.IOException error parsing
     * @throws com.martiansoftware.jsap.JSAPException
     *                             error parsing
     */
    @Override
    public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {
        final JSAPResult jsapResult = parseJsapArguments(args);

        final String[] inputFiles = jsapResult.getStringArray("input");
        basenames = AlignmentReaderImpl.getBasenames(inputFiles);
        outputFilename = jsapResult.getString("output");
        outputFormat = OutputFormat.valueOf(jsapResult.getString("format").toUpperCase());
        suffix = jsapResult.getString("suffix");

        return this;
    }

    /**
     * Display the alignments as text files.
     *
     * @throws java.io.IOException error reading / writing
     */
    @Override
    public void execute() throws IOException {
        PrintStream stream = null;
        try {
            stream = outputFilename == null ? System.out : new PrintStream(new FileOutputStream(outputFilename));
            switch (outputFormat) {
            case PLAIN:
                stream.printf("queryIndex\tmultiplicity%n");
                break;
            default:
                throw new IllegalArgumentException("Unknown output format: " + outputFormat);
            }

            for (final String basename : basenames) {
                final ReadSet set = new ReadSet();
                set.load(basename, suffix);

                for (int queryIndex = 0; queryIndex <= set.getMaxReadIndex(); queryIndex++) {
                    final int multiplicity = set.getMultiplicity(queryIndex);
                    stream.printf("%d\t%d%n", queryIndex,

                            multiplicity);
                }
            }
        } finally {
            if (stream != System.out) {
                IOUtils.closeQuietly(stream);
            }
        }
    }

    /**
     * Main method.
     *
     * @param args command line args.
     * @throws com.martiansoftware.jsap.JSAPException
     *                             error parsing
     * @throws java.io.IOException error parsing or executing.
     */

    public static void main(final String[] args) throws JSAPException, IOException {
        new ReadSetToTextMode().configure(args).execute();
    }
}