edu.umn.msi.tropix.proteomics.conversion.impl.MzXMLToDTAConverterStreamingImplTest.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.conversion.impl.MzXMLToDTAConverterStreamingImplTest.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.conversion.impl;

import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Scanner;

import org.apache.commons.math.util.MathUtils;
import org.testng.annotations.Test;

import edu.umn.msi.tropix.common.io.IOUtils;
import edu.umn.msi.tropix.common.io.IOUtilsFactory;
import edu.umn.msi.tropix.proteomics.DTAList;
import edu.umn.msi.tropix.proteomics.conversion.MzXMLToDTAOptions;
import edu.umn.msi.tropix.proteomics.test.ProteomicsTests;
import edu.umn.msi.tropix.proteomics.test.VerifyUtils;
import edu.umn.msi.tropix.proteomics.utils.DTAUtils;

public class MzXMLToDTAConverterStreamingImplTest {
    private static final IOUtils IO_UTILS = IOUtilsFactory.getInstance();

    @Test(groups = "unit")
    public void structureDefaultOptions() throws Exception {
        testStructure(null);
    }

    @Test(groups = "unit")
    public void structure() throws Exception {
        final MzXMLToDTAOptions options = new MzXMLToDTAOptions();
        testStructure(options);
    }

    @Test(groups = "unit")
    public void readw() {
        /*
        final Random random = new Random();
        int count = 5000;
        double[] peaks = new double[count];
        for(int i =0; i < count; i++) {
          peaks[i] = random.nextDouble();
        }
            
        System.out.println(new String(Base64.encodeBase64(ConversionUtils.doubles2bytes(peaks))));
        */
        final MzXMLToDTAConverterStreamingImpl converter = new MzXMLToDTAConverterStreamingImpl();
        DTAList dtaList;
        InputStream mzxmlStream;
        mzxmlStream = ProteomicsTests.getResourceAsStream("readw.mzXML");
        try {
            dtaList = converter.mzxmlToDTA(mzxmlStream, null);
            double[] contents78charge2 = null, contents78charge3 = null;
            for (DTAList.Entry entry : dtaList) {
                if (entry.getName().matches(".*0*78\\.0*78\\.2\\.dta$")) {
                    assert contents78charge2 == null;
                    contents78charge2 = DTAUtils.readDtaDoublePairs(entry.getContents());
                }
                if (entry.getName().matches(".*0*78\\.0*78\\.3\\.dta$")) {
                    assert contents78charge3 == null;
                    contents78charge3 = DTAUtils.readDtaDoublePairs(entry.getContents());
                }
                if (entry.getName().matches(".*0*1993\\.0*1993\\.1\\.dta$")) {
                    final double[] values = DTAUtils.readDtaDoublePairs(entry.getContents());
                    final Scanner scanner = new Scanner(new ByteArrayInputStream(entry.getContents()));
                    assert MathUtils.equals(scanner.nextDouble(), 1515.390000);
                    assert scanner.nextInt() == 1;
                    assert Math.abs(662.267334 - values[0]) < .01 : values[0];
                    assert Math.abs(4.004042 - values[values.length - 1]) < .01;
                }
            }
            assert contents78charge2 != null;
            assert contents78charge3 != null;
            assert contents78charge2.length == contents78charge3.length;
            for (int i = 2; i < contents78charge2.length; i++) {
                assert MathUtils.equals(contents78charge2[i], contents78charge3[i]);
            }
        } finally {
            IO_UTILS.closeQuietly(mzxmlStream);
        }
    }

    private void testStructure(final MzXMLToDTAOptions options) throws Exception {
        final MzXMLToDTAConverterStreamingImpl converter = new MzXMLToDTAConverterStreamingImpl();
        DTAList dtaList;
        InputStream mzxmlStream;
        mzxmlStream = ProteomicsTests.getResourceAsStream("validMzXML.mzxml");
        try {
            dtaList = converter.mzxmlToDTA(mzxmlStream, options);
            VerifyUtils.verifyDTAList(dtaList);
        } finally {
            IO_UTILS.closeQuietly(mzxmlStream);
        }

        mzxmlStream = ProteomicsTests.getResourceAsStream("validMzXML.mzxml");
        try {
            dtaList = converter.mzxmlToDTA(mzxmlStream, options);
            final HashSet<String> originalNames = new HashSet<String>();
            originalNames.addAll(Arrays.asList(new String[] { "mrr.103.106.1.dta", "mrr.1105.1106.2.dta",
                    "mrr.1105.1106.3.dta", "mrr.2025.2026.2.dta", "mrr.2025.2026.3.dta", "mrr.3009.3011.1.dta" }));

            final HashSet<String> mzxmlNames = new HashSet<String>();
            for (final DTAList.Entry entry : dtaList) {
                mzxmlNames.add(entry.getName());
            }
            assert mzxmlNames.equals(originalNames);
        } finally {
            IO_UTILS.closeQuietly(mzxmlStream);
        }

    }

}