htsjdk.variant.vcf.VCFContigHeaderLine Maven / Gradle / Ivy

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/*
* 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 htsjdk.variant.vcf;

import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.tribble.TribbleException;

import java.util.LinkedHashMap;
import java.util.Map;

/**
 * A special class representing a contig VCF header line.  Knows the true contig order and sorts on that
 *
 * Note: this class has a natural ordering that is inconsistent with equals()
 *
 * @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, final int contigIndex) {
        super(line, version, key, null);
	    if (contigIndex < 0) throw new TribbleException("The contig index is less than zero.");
        this.contigIndex = contigIndex;
    }

    public VCFContigHeaderLine(final Map mapping, final int contigIndex) {
        super(VCFHeader.CONTIG_KEY, mapping);
	    if (contigIndex < 0) throw new TribbleException("The contig index is less than zero.");
        this.contigIndex = contigIndex;
    }

	VCFContigHeaderLine(final SAMSequenceRecord sequenceRecord, final String assembly) {
        // Using LinkedHashMap to preserve order of keys in contig line (ID, length, assembly)
        super(VCFHeader.CONTIG_KEY, new LinkedHashMap() {{
			// Now inside an init block in an anon HashMap subclass
			this.put("ID", sequenceRecord.getSequenceName());
			this.put("length", Integer.toString(sequenceRecord.getSequenceLength()));
			if ( assembly != null ) this.put("assembly", assembly);
		}});
		this.contigIndex = sequenceRecord.getSequenceIndex();
	}

    public Integer getContigIndex() {
        return contigIndex;
    }

	public SAMSequenceRecord getSAMSequenceRecord() {
		final String lengthString = this.getGenericFieldValue("length");
		if (lengthString == null) throw new TribbleException("Contig " + this.getID() + " does not have a length field.");
		final SAMSequenceRecord record = new SAMSequenceRecord(this.getID(), Integer.valueOf(lengthString));
        record.setAssembly(this.getGenericFieldValue("assembly"));
		record.setSequenceIndex(this.contigIndex);
		return record;
	}

    @Override
    public boolean equals(final Object o) {
        if ( this == o ) {
            return true;
        }
        if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
            return false;
        }

        final VCFContigHeaderLine that = (VCFContigHeaderLine) o;
        return contigIndex.equals(that.contigIndex);
    }

    @Override
    public int hashCode() {
        int result = super.hashCode();
        result = 31 * result + contigIndex.hashCode();
        return result;
    }

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