75 lines
2.4 KiB
Java
75 lines
2.4 KiB
Java
package org.broadinstitute.sting.utils.genotype;
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/*
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* Copyright (c) 2009 The Broad Institute
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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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author aaron
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* <p/>
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* Class IndelLikelihood
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* <p/>
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* The representation of an indel allele.
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*/
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// TODO -- DELETE ME GLF
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public class IndelLikelihood {
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protected double loglikelihood;
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protected short lengthOfIndel;
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protected short[] indelSequence;
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/**
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* Create a likelihood object for an indel call
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*
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* @param likelihood the likelihood (represented as a negitive log likelihood,
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* with a ceiling of 255.
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* @param indelSequence the indel sequence, not null terminated
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*/
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public IndelLikelihood( byte likelihood, String indelSequence ) {
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this.loglikelihood = likelihood;
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this.lengthOfIndel = (short)indelSequence.length();
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this.indelSequence = new short[indelSequence.length()];
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for (int tmp = 0; tmp < indelSequence.length(); tmp++) {
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this.indelSequence[tmp] = (short)indelSequence.charAt(tmp);
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}
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}
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/**
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* getter methods
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*/
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public double getLikelihood() {
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return loglikelihood;
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}
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public short getLengthOfIndel() {
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return lengthOfIndel;
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}
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public short[] getIndelSequence() {
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return indelSequence;
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}
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}
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