edu.umn.msi.tropix.proteomics.conversion.DtaNameUtils.java Source code

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

import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.commons.io.FilenameUtils;

public class DtaNameUtils {
    private static final Pattern DTA_PATTERN = Pattern
            .compile("(.*)\\.(\\d+)\\.(\\d+)\\.(\\d+)(\\.[dD][tT][aA])?$");

    public static final class DtaNameSummary {
        private final String basename;
        private final int start, end;
        private final short charge;

        public DtaNameSummary(final String basename, final int start, final int end, final short charge) {
            this.basename = basename;
            this.start = start;
            this.end = end;
            this.charge = charge;
        }

        public String getBasename() {
            return basename;
        }

        public int getStart() {
            return start;
        }

        public int getEnd() {
            return end;
        }

        public short getCharge() {
            return charge;
        }

    }

    public static boolean isDtaName(final String filename) {
        return DTA_PATTERN.matcher(FilenameUtils.getName(filename)).matches();
    }

    public static DtaNameSummary getDtaNameSummary(final String filename) {
        final Matcher matcher = DTA_PATTERN.matcher(FilenameUtils.getName(filename));
        matcher.matches();
        final String basename = matcher.group(1);
        final int start = Integer.parseInt(matcher.group(2));
        final int end = Integer.parseInt(matcher.group(3));
        final short charge = Short.parseShort(matcher.group(4));
        return new DtaNameSummary(basename, start, end, charge);
    }

}