edu.umn.msi.tropix.proteomics.tools.DTAToMzXML.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.tools.DTAToMzXML.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.tools;

import static java.lang.System.exit;
import static java.lang.System.out;

import java.io.File;
import java.util.ArrayList;
import java.util.Collection;

import net.sourceforge.sashimi.mzxml.v3_0.MzXML;

import org.apache.commons.io.FileUtils;

import edu.umn.msi.tropix.common.io.FileUtilsFactory;
import edu.umn.msi.tropix.proteomics.InMemoryDTAListImpl;
import edu.umn.msi.tropix.proteomics.conversion.DTAToMzXMLConverter;
import edu.umn.msi.tropix.proteomics.conversion.impl.DTAToMzXMLConverterImpl;
import edu.umn.msi.tropix.proteomics.xml.MzXMLUtility;

public class DTAToMzXML {

    public static void main(final String[] args) throws Exception {
        if (args.length < 1) {
            usage();
            System.exit(0);
        }
        Collection<File> files = null;

        if (args[0].equals("-files")) {
            if (args.length < 2) {
                out.println("No files specified.");
                usage();
                exit(-1);
            } else {
                files = new ArrayList<File>(args.length - 1);
                for (int i = 1; i < args.length; i++) {
                    files.add(new File(args[i]));
                }
            }
        } else if (args[0].equals("-directory")) {
            File directory;
            if (args.length < 2) {
                directory = new File(System.getProperty("user.dir"));
            } else {
                directory = new File(args[2]);
            }
            files = FileUtilsFactory.getInstance().listFiles(directory, new String[] { "dta" }, false);
        } else {
            usage();
            exit(-1);
        }

        final InMemoryDTAListImpl dtaList = new InMemoryDTAListImpl();
        File firstFile = null;
        if (files.size() == 0) {
            out.println("No files found.");
            exit(-1);
        } else {
            firstFile = files.iterator().next();
        }
        for (final File file : files) {
            dtaList.add(FileUtils.readFileToByteArray(file), file.getName());
        }

        final DTAToMzXMLConverter dtaToMzXMLConverter = new DTAToMzXMLConverterImpl();
        final MzXML mzxml = dtaToMzXMLConverter.dtaToMzXML(dtaList, null);
        final String mzxmlName = firstFile.getName().substring(0, firstFile.getName().indexOf(".")) + ".mzXML";
        new MzXMLUtility().serialize(mzxml, mzxmlName);
    }

    private static void usage() {
        out.println("Usage: ( -files <dta files> ) or ( -directory [directory]) ");
    }

}