a little bit more clean-up
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3122 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
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package org.broadinstitute.sting.utils.genotype;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.util.*;
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/**
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* @author ebanks
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* <p/>
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* Class BasicGenotypeBackedVariation
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* <p/>
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* represents a genotype-backed Variation.
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*/
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public class BasicGenotypeBackedVariation implements Variation, VariantBackedByGenotype {
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// the discovery lod score
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private double mConfidence = 0.0;
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// the location
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private GenomeLoc mLoc;
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// the ref base and alt bases
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private char mRefBase;
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private List<String> mAltBases = new ArrayList<String>();
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// the variant type
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private final VARIANT_TYPE mType = VARIANT_TYPE.SNP;
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// the genotypes
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private List<Genotype> mGenotypes = null;
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/**
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* create a basic genotype-backed variation bject, given the following fields
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*
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* @param ref the reference base
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* @param loc the locus
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* @param type the variant type
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*/
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public BasicGenotypeBackedVariation(char ref, GenomeLoc loc, VARIANT_TYPE type) {
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if ( type != VARIANT_TYPE.SNP && type != VARIANT_TYPE.REFERENCE )
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throw new IllegalArgumentException("Only SNPs and REFs are supported in the Geli format");
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mRefBase = ref;
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mLoc = loc;
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}
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/**
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* get the reference base.
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* @return a character, representing the reference base
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*/
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public String getReference() {
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return String.valueOf(mRefBase);
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}
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/**
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* get the genotype's location
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*
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* @return a GenomeLoc representing the location
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*/
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public GenomeLoc getLocation() {
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return mLoc;
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}
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public boolean isBiallelic() {
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return true;
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}
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public boolean isSNP() {
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return mType == VARIANT_TYPE.SNP;
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}
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public boolean isInsertion() {
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return false;
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}
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public boolean isIndel() {
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return false;
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}
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public boolean isDeletion() {
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return false;
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}
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public boolean isReference() {
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return mType == VARIANT_TYPE.REFERENCE;
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}
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public VARIANT_TYPE getType() {
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return mType;
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}
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public double getNegLog10PError() {
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return mConfidence / 10.0;
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}
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public double getNonRefAlleleFrequency() {
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return 0.0;
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}
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public List<String> getAlternateAlleleList() {
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return mAltBases;
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}
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public void addAlternateAllele(String alt) {
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mAltBases.add(alt);
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}
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public List<String> getAlleleList() {
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LinkedList<String> alleles = new LinkedList<String>(mAltBases);
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alleles.addFirst(getReference());
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return alleles;
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}
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public char getAlternativeBaseForSNP() {
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if ( !isSNP() )
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throw new IllegalStateException("This variant is not a SNP");
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if ( mAltBases.size() == 0 )
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throw new IllegalStateException("No alternate alleles have been set");
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return mAltBases.get(0).charAt(0);
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}
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public char getReferenceForSNP() {
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if ( !isSNP() )
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throw new IllegalStateException("This variant is not a SNP");
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return mRefBase;
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}
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/**
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* get the confidence
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*
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* @return the confidence
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*/
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public double getConfidence() {
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return mConfidence;
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}
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/**
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*
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* @param confidence the confidence for this genotype
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*/
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public void setConfidence(double confidence) {
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mConfidence = confidence;
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}
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/**
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*
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* @param calls the GenotypeCalls for this variation
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*/
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public void setGenotypeCalls(List<Genotype> calls) {
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mGenotypes = calls;
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}
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/**
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* @return a specific genotype that represents the called genotype
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*/
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public Genotype getCalledGenotype() {
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if ( mGenotypes == null || mGenotypes.size() != 1 )
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throw new IllegalStateException("There is not one and only one Genotype associated with this Variation");
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return mGenotypes.get(0);
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}
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/**
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* @return a list of all the genotypes
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*/
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public List<Genotype> getGenotypes() {
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return mGenotypes;
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}
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/**
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* do we have the specified genotype? not all backedByGenotypes
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* have all the genotype data.
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*
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* @param x the genotype
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*
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* @return true if available, false otherwise
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*/
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public boolean hasGenotype(DiploidGenotype x) {
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if ( mGenotypes == null )
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return false;
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for ( Genotype g : mGenotypes ) {
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if ( DiploidGenotype.valueOf(g.getBases()).equals(x) )
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return true;
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}
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return false;
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}
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}
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@ -1,22 +0,0 @@
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package org.broadinstitute.sting.utils.genotype;
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import java.util.Comparator;
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/**
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*
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* @author aaron
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*
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* Class LexigraphicalComparator
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*
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class LexigraphicalComparator implements Comparator<Genotype> {
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private final Double EPSILON = 1.0e-15;
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@Override
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public int compare(Genotype genotype, Genotype genotype1) {
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return genotype.getBases().compareTo(genotype1.getBases());
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}
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}
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