/*
* 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.tribble.TribbleException;
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 {
protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
private String mKey = null;
private String mValue = 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) {
if ( key == null )
throw new IllegalArgumentException("VCFHeaderLine: key cannot be null");
if ( key.contains("<") || key.contains(">") )
throw new IllegalArgumentException("VCFHeaderLine: key cannot contain angle brackets");
if ( key.contains("=") )
throw new IllegalArgumentException("VCFHeaderLine: key cannot contain an equals sign");
mKey = key;
mValue = value;
}
/**
* Get the key
*
* @return the key
*/
public String getKey() {
return mKey;
}
/**
* Get the value
*
* @return the value
*/
public String getValue() {
return mValue;
}
/**
* By default the header lines won't be added to the dictionary, unless this method will be override (for example in FORMAT, INFO or FILTER header lines)
*
* @return false
*/
public boolean shouldBeAddedToDictionary() {
return false;
}
public String toString() {
return toStringEncoding();
}
/**
* Should be overloaded in sub classes to do subclass specific
*
* @return the string encoding
*/
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());
}
/**
* @param line the line
* @return true if the line is a VCF meta data line, or false if it is not
*/
public static boolean isHeaderLine(String line) {
return line != null && line.length() > 0 && VCFHeader.HEADER_INDICATOR.equals(line.substring(0,1));
}
/**
* 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 TribbleException.InternalCodecException("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();
}
}