/*
 * Copyright (c) 2010 The Broad Institute
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the ÓSoftwareÓ), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED ÓAS ISÓ, WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */

package org.broadinstitute.sting.gatk.refdata;

import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.text.XReadLines;

import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.io.IOException;
import java.io.File;
import java.io.FileNotFoundException;

public class BeagleROD extends BasicReferenceOrderedDatum {
    GenomeLoc loc;
    List<String> sampleNames = null;
    Map<String, List<String>> sampleGenotypes = new HashMap<String, List<String>>();

    public BeagleROD(String name) {
        super(name);
    }

    public String toString() { return "BeagleRod"; }

    public String delimiterRegex() {
        return " ";
    }

    public GenomeLoc getLocation() {
        return loc;
    }

    public List<String> getSampleNames() {
        return sampleNames;
    }

    public Map<String, List<String>> getGenotypes() {
        return sampleGenotypes;
    }

    public Object initialize(final File source) throws FileNotFoundException {
        String firstLine = new XReadLines(source).next();
        String[] parts = firstLine.split(" ");
        if ( parts[0].equals("I") ) {
            // I id NA12891 NA12891 NA12892 NA12892
            sampleNames = Arrays.asList(parts).subList(2, parts.length);
            return sampleNames;
        } else {
            throw new IllegalStateException("Beagle file " + source + " doesn't have required header line I");
        }
    }

    private static Pattern MARKER_PATTERN = Pattern.compile("c(.+)_p([0-9]+)");

    public static GenomeLoc parseMarkerName(String markerName) {
        Matcher m = MARKER_PATTERN.matcher(markerName);
        if ( m.matches() ) {
            String contig = m.group(1);
            long start = Long.valueOf(m.group(2));
            return GenomeLocParser.createGenomeLoc(contig, start, start);
        } else {
            throw new IllegalArgumentException("Malformatted family structure string: " + markerName + " required format is mom+dad=child");
        }
    }

    public boolean parseLine(final Object header, final String[] parts) throws IOException {
        //System.out.printf("Parsing beagle parts=%s header=%s%n", parts, header);
        List<String> sampleNames = (List<String>)header;

        if ( parts.length == 0 || ! parts[0].equals("M") )
            return false;
        else {
            loc = parseMarkerName(parts[1]);

            for ( int i = 2; i < parts.length; i++ ) {
                String sampleName = sampleNames.get(i-2);
                if ( ! sampleGenotypes.containsKey(sampleName) ) {
                    sampleGenotypes.put(sampleName, new ArrayList<String>());
                }

                sampleGenotypes.get(sampleName).add(parts[i]);
            }

            return true;
        }
    }
}