141 lines
4.0 KiB
Java
141 lines
4.0 KiB
Java
/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broad.tribble.vcf;
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import org.broadinstitute.sting.utils.StingException;
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import java.util.Map;
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/**
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* @author ebanks
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* <p/>
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* Class VCFHeaderLine
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* <p/>
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* A class representing a key=value entry in the VCF header
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*/
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public class VCFHeaderLine implements Comparable {
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private String stringRep = null;
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private String mKey = null;
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private String mValue = null;
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/**
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* create a VCF header line
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*
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* @param key the key for this header line
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* @param value the value for this header line
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*/
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public VCFHeaderLine(String key, String value) {
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mKey = key;
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mValue = value;
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}
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/**
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* Get the key
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*
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* @return the key
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*/
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public String getKey() {
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return mKey;
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}
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/**
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* Set the key
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*
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* @param key the key for this header line
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*/
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public void setKey(String key) {
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mKey = key;
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stringRep = null;
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}
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/**
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* Get the value
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*
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* @return the value
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*/
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public String getValue() {
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return mValue;
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}
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/**
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* Set the value
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*
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* @param value the value for this header line
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*/
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public void setValue(String value) {
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mValue = value;
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stringRep = null;
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}
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public String toString() {
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if ( stringRep == null )
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stringRep = toStringEncoding();
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return stringRep;
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}
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protected String toStringEncoding() {
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return mKey + "=" + mValue;
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}
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public boolean equals(Object o) {
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if ( !(o instanceof VCFHeaderLine) )
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return false;
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return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue());
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}
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public int compareTo(Object other) {
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return toString().compareTo(other.toString());
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}
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/**
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* create a string of a mapping pair for the target VCF version
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* @param keyValues a mapping of the key->value pairs to output
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* @return a string, correctly formatted
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*/
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public static String toStringEncoding(Map<String, ? extends Object> keyValues) {
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StringBuilder builder = new StringBuilder();
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builder.append("<");
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boolean start = true;
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for (Map.Entry<String,?> entry : keyValues.entrySet()) {
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if (start) start = false;
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else builder.append(",");
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if ( entry.getValue() == null ) throw new StingException("Header problem: unbound value at " + entry + " from " + keyValues);
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builder.append(entry.getKey());
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builder.append("=");
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builder.append(entry.getValue().toString().contains(",") ||
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entry.getValue().toString().contains(" ") ||
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entry.getKey().equals("Description") ? "\""+ entry.getValue() + "\"" : entry.getValue());
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}
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builder.append(">");
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return builder.toString();
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}
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} |