118 lines
3.7 KiB
Java
Executable File
118 lines
3.7 KiB
Java
Executable File
package org.broad.tribble.vcf;
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import org.broad.tribble.util.ParsingUtils;
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import java.util.Arrays;
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import java.util.LinkedHashMap;
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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 VCFFormatHeaderLine
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* <p/>
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* A class representing a key=value entry for genotype FORMAT fields in the VCF header
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*/
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public class VCFFormatHeaderLine extends VCFHeaderLine {
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// the format field types
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public enum FORMAT_TYPE {
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Integer, Float, String;
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public Object convert(String value) {
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switch (this) {
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case Integer:
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return java.lang.Integer.valueOf(value); // the java.lang is needed since we use Integer as a enum name
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case Float:
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return java.lang.Float.valueOf(value);
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case String:
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return value;
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default:
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throw new IllegalStateException("field." + this + " doesn't have a set conversion approach");
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}
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}
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}
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private String mName;
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private int mCount;
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private String mDescription;
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private FORMAT_TYPE mType;
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/**
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* create a VCF format header line
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*
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* @param name the name for this header line
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* @param count the count for this header line
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* @param type the type for this header line
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* @param description the description for this header line
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*/
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public VCFFormatHeaderLine(String name, int count, FORMAT_TYPE type, String description) {
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super("FORMAT", "");
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mName = name;
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mCount = count;
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mType = type;
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mDescription = description;
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}
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/**
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* create a VCF format header line
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*
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* @param line the header line
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* @param version the VCF header version
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*
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*/
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protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {
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super("FORMAT", "", version);
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Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
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mName = mapping.get("ID");
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mCount = Integer.valueOf(mapping.get("Number"));
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mType = FORMAT_TYPE.valueOf(mapping.get("Type"));
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mDescription = mapping.get("Description");
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}
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protected String makeStringRep() {
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if (mVersion == VCFHeaderVersion.VCF3_3 || mVersion == VCFHeaderVersion.VCF3_2)
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return String.format("FORMAT=%s,%d,%s,\"%s\"", mName, mCount, mType.toString(), mDescription);
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else if (mVersion == VCFHeaderVersion.VCF4_0) {
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Map<String,Object> map = new LinkedHashMap<String,Object>();
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map.put("ID",mName);
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map.put("Number",mCount);
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map.put("Type",mType);
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map.put("Description",mDescription);
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return "FORMAT=" + VCFHeaderLineTranslator.toValue(this.mVersion,map);
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}
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else throw new RuntimeException("Unsupported VCFVersion " + mVersion);
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}
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public String getName() { return mName; }
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public int getCount() { return mCount; }
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public String getDescription() { return mDescription; }
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public FORMAT_TYPE getType() { return mType; }
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public boolean equals(Object o) {
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if ( !(o instanceof VCFFormatHeaderLine) )
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return false;
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VCFFormatHeaderLine other = (VCFFormatHeaderLine)o;
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return mName.equals(other.mName) &&
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mCount == other.mCount &&
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mDescription.equals(other.mDescription) &&
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mType == other.mType;
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}
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public String getmName() {
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return mName;
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}
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public int getmCount() {
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return mCount;
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}
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public String getmDescription() {
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return mDescription;
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}
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public FORMAT_TYPE getmType() {
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return mType;
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}
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} |