gatk-3.8/java/src/org/broad/tribble/vcf/VCFHeaderLine.java

/*
 * Copyright (c) 2010.
 *
 * 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.broad.tribble.vcf;

import org.broadinstitute.sting.utils.StingException;

import java.util.Map;


/**
 * @author ebanks
 *         <p/>
 *         Class VCFHeaderLine
 *         <p/>
 *         A class representing a key=value entry in the VCF header
 */
public class VCFHeaderLine implements Comparable {

    private String stringRep = null;
    private String mKey = null;
    private String mValue = null;
    protected VCFHeaderVersion mVersion = null;

    /**
     * create a VCF header line
     *
     * @param key     the key for this header line
     * @param value   the value for this header line
     */
    public VCFHeaderLine(String key, String value, VCFHeaderVersion version) {
        mKey = key;
        mValue = value;
        mVersion = version;
    }

    /**
     * create a VCF header line
     *
     * @param key     the key for this header line
     * @param value   the value for this header line
     */
    public VCFHeaderLine(String key, String value) {
        mKey = key;
        mValue = value;
        mVersion = VCFHeaderVersion.VCF3_3;
    }

    /**
     * Get the key
     *
     * @return the key
     */
    public String getKey() {
        return mKey;
    }

    /**
     * Set the key
     *
     * @param key     the key for this header line
     */
    public void setKey(String key) {
        mKey = key;
        stringRep = null;
    }

    /**
     * Get the value
     *
     * @return the value
     */
    public String getValue() {
        return mValue;
    }

    /**
     * Set the value
     *
     * @param value     the value for this header line
     */
    public void setValue(String value) {
        mValue = value;
        stringRep = null;
    }

    public String toString() {
        if ( stringRep == null )
            stringRep = toStringEncoding();
        return stringRep;
    }

    protected String toStringEncoding() {
        return mKey + "=" + mValue;
    }

    public boolean equals(Object o) {
        if ( !(o instanceof VCFHeaderLine) )
            return false;
        return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue());
    }

    public int compareTo(Object other) {
        return toString().compareTo(other.toString());
    }

    /**
     * set the version string, which resets the current stored string representation if the version changed
     * @param version
     */
    public void setVersion(VCFHeaderVersion version) {
        if (!version.equals(this.mVersion)) this.stringRep = null;
        this.mVersion = version;
    }

    /**
     * create a string of a mapping pair for the target VCF version
     * @param keyValues a mapping of the key->value pairs to output
     * @return a string, correctly formatted
     */
    public static String toStringEncoding(Map<String, ? extends Object> keyValues) {
        StringBuilder builder = new StringBuilder();
        builder.append("<");
        boolean start = true;
        for (Map.Entry<String,?> entry : keyValues.entrySet()) {
            if (start) start = false;
            else builder.append(",");

            if ( entry.getValue() == null ) throw new StingException("Header problem: unbound value at " + entry + " from " + keyValues);

            builder.append(entry.getKey());
            builder.append("=");
            builder.append(entry.getValue().toString().contains(",") ||
                           entry.getValue().toString().contains(" ") ||
                           entry.getKey().equals("Description") ? "\""+ entry.getValue() + "\"" : entry.getValue());
        }
        builder.append(">");
        return builder.toString();
    }
}