edu.umn.msi.tropix.proteomics.test.VerifyUtils.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.test.VerifyUtils.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.test;

import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.util.List;

import net.sourceforge.sashimi.mzxml.v3_0.MsRun;
import net.sourceforge.sashimi.mzxml.v3_0.MsRun.ParentFile;
import net.sourceforge.sashimi.mzxml.v3_0.MzXML;
import net.sourceforge.sashimi.mzxml.v3_0.Scan;
import net.sourceforge.sashimi.mzxml.v3_0.Scan.Peaks;
import net.sourceforge.sashimi.mzxml.v3_0.Scan.ScanOrigin;

import org.apache.commons.io.IOUtils;
import org.apache.commons.io.LineIterator;

import com.google.common.base.Function;

import edu.umn.msi.tropix.common.collect.Collections;
import edu.umn.msi.tropix.proteomics.DTAList;

public class VerifyUtils {

    public static void verifyMGF(final InputStream stream) {
        final LineIterator lineIterator = IOUtils.lineIterator(new InputStreamReader(stream));
        assert lineIterator.hasNext();
        String line = lineIterator.nextLine();
        assert line.startsWith("COM=");
        assert lineIterator.hasNext();
        line = lineIterator.nextLine();
        assert line.startsWith("CHARGE=");
        while (true) {
            if (!lineIterator.hasNext()) {
                break;
            }
            line = lineIterator.nextLine();
            assert line.equals("BEGIN IONS") : line;
            line = lineIterator.nextLine();
            assert line.matches(
                    "PEPMASS=(\\d*\\.?\\d*)( (\\d*\\.?\\d*))?") : "Does not appear to be a peptide mass line "
                            + line;
            line = lineIterator.nextLine();
            assert line.matches("CHARGE=[\\d, \\+]+") : line;
            line = lineIterator.nextLine();
            assert line.startsWith("SCANS=") : line;
            line = lineIterator.nextLine();
            assert line.startsWith("TITLE=") : line;
            while (true) {
                line = lineIterator.nextLine();

                if (line.equals("END IONS")) {
                    break;
                } else if (line
                        .matches(RegexUtils.FLOATING_POINT_LITERAL + "\\s+" + RegexUtils.FLOATING_POINT_LITERAL)) {
                    continue;
                } else {
                    assert false : "MGF contains invalid line " + line;
                }
            }
        }
    }

    private static final Function<ParentFile, String> GET_PARENT_ID_FUNCTION = new Function<ParentFile, String>() {

        public String apply(final ParentFile parentFile) {
            return parentFile.getFileSha1();
        }

    };

    public static void verifyMzXML(final MzXML mzxml) {
        final MsRun run = mzxml.getMsRun();
        final List<ParentFile> parentFiles = run.getParentFile();
        for (final Scan scan : run.getScan()) {

            for (final ScanOrigin scanOrigin : scan.getScanOrigin()) {
                final String parentFileId = scanOrigin.getParentFileID();
                assert Collections.transform(parentFiles, GET_PARENT_ID_FUNCTION).contains(parentFileId);
            }
            assert scan.getNum() != null;
            assert scan.getPeaks() != null;
            for (final Peaks peaks : scan.getPeaks()) {
                final int len = peaks.getCompressedLen();
                assert len == (peaks.getValue().length * 4 / 3);
            }
        }
    }

    public static void verifyDTAList(final DTAList dtaList) {
        for (final DTAList.Entry entry : dtaList) {
            final byte[] bytes = entry.getContents();
            final LineIterator lineIterator = IOUtils.lineIterator(new StringReader(new String(bytes)));
            final String firstLine = lineIterator.nextLine();
            assert firstLine.matches("^\\d+\\.\\d+\\s+\\d+\\s*$");
            while (lineIterator.hasNext()) {
                final String line = lineIterator.nextLine();
                assert line.matches(RegexUtils.FLOATING_POINT_LITERAL + "\\s+" + RegexUtils.FLOATING_POINT_LITERAL
                        + "\\s*") : "Line is not of form -- <double> <double>";
            }
            final String name = entry.getName();
            assert name.matches("^.*\\.\\d+\\.\\d+\\.\\d+\\.[dD][tT][aA]$");
        }
    }

}