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A Java API for high-throughput sequencing data (HTS) formats

There is a newer version: 4.1.3

/*
* 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;


/**
 * @author ebanks
 *         
 *         Class VCFFormatHeaderLine
 *         
 *         
 *         A class representing a key=value entry for genotype FORMAT fields in the VCF header
 */
public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {

    public VCFFormatHeaderLine(String name, int count, VCFHeaderLineType type, String description) {
        super(name, count, type, description, SupportedHeaderLineType.FORMAT);
        if (type == VCFHeaderLineType.Flag)
            throw new IllegalArgumentException("Flag is an unsupported type for format fields");
    }

    public VCFFormatHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
        super(name, count, type, description, SupportedHeaderLineType.FORMAT);
    }

    public VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
        super(line, version, SupportedHeaderLineType.FORMAT);
    }

    // format fields do not allow flag values (that wouldn't make much sense, how would you encode this in the genotype).
    @Override
    boolean allowFlagValues() {
        return false;
    }

    @Override
    public boolean shouldBeAddedToDictionary() {
        return true;
    }
}