VCFContigHeaderLine.java

/*
* 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
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* 
* The above copyright notice and this permission notice shall be
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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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
 *
 * @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<String, String> 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<String, String>() {{
			// 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;
	}

    /**
     * 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);
        }
    }
}