/*
* The MIT License
*
* Copyright (c) 2009 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 picard.fingerprint;
import java.util.HashMap;
import java.util.Map;
import picard.PicardException;
import htsjdk.samtools.util.StringUtil;
/**
* A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
* DO NOT ADD TO OR REORDER THIS ENUM AS THAT WOULD BREAK THE GELI FILE FORMAT.
*/
public enum DiploidGenotype {
AA('A','A'),
AC('A','C'),
AG('A','G'),
AT('A','T'),
CC('C','C'),
CG('C','G'),
CT('C','T'),
GG('G','G'),
GT('G','T'),
TT('T','T');
private static final Map<Integer, DiploidGenotype> genotypes = new HashMap<Integer, DiploidGenotype>();
static {
for (final DiploidGenotype genotype : values()) {
// this relies on the fact that the integer sum of allele1 and allele2 is unique
if (genotypes.put(genotype.allele1 + genotype.allele2, genotype) != null) {
// this check is just for safety, this should never happen
throw new PicardException("sum of allele values are not unique!!!");
}
}
}
/** Converts a pair of bases into a DiploidGenotype regardless of base order or case */
public static DiploidGenotype fromBases(final byte[] bases) {
if (bases.length != 2) {
throw new IllegalArgumentException("bases must contain 2 and only 2 bases, it actually contained " + bases.length);
}
return fromBases(bases[0], bases[1]);
}
/** Converts a pair of bases into a DiploidGenotype regardless of base order or case */
public static DiploidGenotype fromBases(final byte base1, final byte base2) {
final byte first = StringUtil.toUpperCase(base1);
final byte second = StringUtil.toUpperCase(base2);
final DiploidGenotype genotype = genotypes.get(first + second);
if (genotype == null) {
throw new IllegalArgumentException("Unknown genotype string [" +
StringUtil.bytesToString(new byte[] {base1, base2}) +
"], any pair of ACTG case insensitive is acceptable");
}
return genotype;
}
/**
* @return true if this is a valid base, i.e. one of [ACGTacgt]
*/
public static boolean isValidBase(final byte base) {
switch(StringUtil.toUpperCase(base)) {
case 'A':
case 'C':
case 'G':
case 'T':
return true;
default:
return false;
}
}
private final byte allele1;
private final byte allele2;
private DiploidGenotype(final char allele1, final char allele2) {
this.allele1 = (byte)(allele1 & 0xff);
this.allele2 = (byte)(allele2 & 0xff);
}
public byte getAllele1() { return allele1; }
public byte getAllele2() { return allele2; }
public boolean isHeterozygous() { return this.allele1 != this.allele2; }
public boolean isHomomozygous() { return this.allele1 == this.allele2; }
}