edu.umn.msi.tropix.proteomics.itraqquantitation.impl.QuantitationClosureImpl.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.itraqquantitation.impl.QuantitationClosureImpl.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.itraqquantitation.impl;

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

import org.apache.commons.io.FilenameUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Function;

import edu.umn.msi.tropix.common.collect.Closure;
import edu.umn.msi.tropix.common.io.FileUtils;
import edu.umn.msi.tropix.common.io.FileUtilsFactory;
import edu.umn.msi.tropix.common.io.IOUtils;
import edu.umn.msi.tropix.common.io.IOUtilsFactory;
import edu.umn.msi.tropix.common.xml.XMLUtility;
import edu.umn.msi.tropix.proteomics.itraqquantitation.QuantificationResultsExporter;
import edu.umn.msi.tropix.proteomics.itraqquantitation.QuantitationOptions;
import edu.umn.msi.tropix.proteomics.itraqquantitation.impl.ITraqLabels.ITraqRatio;
import edu.umn.msi.tropix.proteomics.itraqquantitation.results.QuantificationResults;

class QuantitationClosureImpl implements Closure<QuantitationOptions> {
    private static final Log LOG = LogFactory.getLog(QuantitationClosureImpl.class);
    private static final FileUtils FILE_UTILS = FileUtilsFactory.getInstance();
    private static final IOUtils IO_UTILS = IOUtilsFactory.getInstance();

    private ITraqMatchBuilder iTraqMatchBuilder;
    private Quantifier quantifier = new QuantifierImpl();

    public void setItraqMatchBuilder(final ITraqMatchBuilder iTraqMatchBuilder) {
        this.iTraqMatchBuilder = iTraqMatchBuilder;
    }

    @VisibleForTesting
    public void setQuantifier(final Quantifier quantifier) {
        this.quantifier = quantifier;
    }

    public void apply(final QuantitationOptions options) {
        final List<ITraqLabel> labels = ITraqLabels.getLabels(options.getQuantificationType());

        LOG.info("Building data entries for quantitation analysis");
        final List<ITraqMatch> iTraqMatchs = iTraqMatchBuilder.buildDataEntries(options.getInputMzxmlFiles(),
                options.getInputReport(), new ITraqMatchBuilder.ITraqMatchBuilderOptions(labels,
                        options.getGroupType(), options.getThreads()));

        Function<Double, Double> trainingFunction = null;
        if (options.getWeights() != null) {
            LOG.info("Building iTraq matches for training data");
            // final List<ITraqMatch> trainingMatches = iTraqMatchBuilder.buildDataEntries(options.getInputMzxmlFiles(), options.getInputScaffoldReport(),
            // new ITraqMatchBuilder.ITraqMatchBuilderOptions(labels));
            trainingFunction = new TrainingWeightFunctionImpl(options.getWeights());
        }

        LOG.info("Building report summary for quantitation analysis");
        final ReportSummary summary = new ReportSummary(iTraqMatchs, labels, options.getGroupType());

        final Collection<ITraqRatio> iTraqRatios = ITraqLabels.buildRatios(labels);

        LOG.info("Running quantitation analysis.");
        final QuantificationResults results = quantifier.quantify(iTraqRatios, summary, trainingFunction,
                options.includeNormalized());

        final File outputFile = options.getOutputFile();
        if (FilenameUtils.getExtension(outputFile.getName()).toLowerCase().equals("xml")) {
            final XMLUtility<QuantificationResults> resultXmlUtility = new XMLUtility<QuantificationResults>(
                    QuantificationResults.class);

            LOG.info("Writing XML resluts");
            resultXmlUtility.serialize(results, outputFile);
        } else {
            final OutputStream outputStream = FILE_UTILS.getFileOutputStream(outputFile);
            try {
                QuantificationResultsExporter.writeAsSpreadsheet(results, outputStream, options.getGroupType());
            } finally {
                IO_UTILS.closeQuietly(outputStream);
            }
        }

    }

}