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

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Here is the source code for edu.umn.msi.tropix.proteomics.tools.ITraqQuantification.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.out;

import java.io.File;
import java.util.List;

import org.springframework.context.support.ClassPathXmlApplicationContext;

import com.google.common.collect.Lists;

import edu.umn.msi.tropix.common.collect.Closure;
import edu.umn.msi.tropix.proteomics.itraqquantitation.QuantitationOptions;
import edu.umn.msi.tropix.proteomics.itraqquantitation.impl.InputReport;
import edu.umn.msi.tropix.proteomics.itraqquantitation.impl.ReportExtractor.ReportType;

public class ITraqQuantification {

    public static void main(final String[] args) throws Exception {
        if (args.length < 2) {
            usage();
            System.exit(-1);
        }

        final List<File> mzxmlFiles = Lists.newArrayListWithCapacity(args.length - 1);
        for (int i = 0; i < args.length - 2; i++) {
            mzxmlFiles.add(new File(args[i]));
        }
        final File scaffoldFile = new File(args[args.length - 2]);
        final File outFile = new File(args[args.length - 1]);
        // TODO: Take in type some how
        final QuantitationOptions options = QuantitationOptions
                .forInput(mzxmlFiles, new InputReport(scaffoldFile, ReportType.SCAFFOLD)).withOutput(outFile)
                .is4Plex().get();

        final ClassPathXmlApplicationContext context = new ClassPathXmlApplicationContext(
                "edu/umn/msi/tropix/proteomics/itraqquantitation/applicationContext.xml");
        @SuppressWarnings("unchecked")
        final Closure<QuantitationOptions> closure = (Closure<QuantitationOptions>) context
                .getBean("quantitationClosure");
        closure.apply(options);
    }

    private static void usage() {
        out.println("Usage: mzxmlfile(s) xlsfile outfile");
    }
}