/*
 * Copyright (c) 2012, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), 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 "AS IS", 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.utils.codecs.vcf;

import java.util.Map;

/**
 * A special class representing a contig VCF header line.  Nows the true contig order and sorts on that
 *
 * @author mdepristo
 */
public class VCFContigHeaderLine extends VCFSimpleHeaderLine {
    final Integer contigIndex;


    /**
     * create a VCF contig header line
     *
     * @param line      the header line
     * @param version   the vcf header version
     * @param key            the key for this header line
     */
    public VCFContigHeaderLine(final String line, final VCFHeaderVersion version, final String key, int contigIndex) {
        super(line, version, key, null);
        this.contigIndex = contigIndex;
    }

    public VCFContigHeaderLine(final String key, final Map<String, String> mapping, int contigIndex) {
        super(key, mapping, null);
        this.contigIndex = contigIndex;
    }

    public Integer getContigIndex() {
        return contigIndex;
    }

    /**
     * IT IS CRITIAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
     *
     * @param other
     * @return
     */
    @Override
    public int compareTo(final Object other) {
        if ( other instanceof VCFContigHeaderLine )
            return contigIndex.compareTo(((VCFContigHeaderLine) other).contigIndex);
        else {
            return super.compareTo(other);
        }
    }
}