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made some private member/methods protected to allow for subclassing 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2836 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2010-02-12 21:16:00 +00:00
parent 232d884578
commit 28f24ca2ae
1 changed files with 11 additions and 11 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
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@ -53,9 +53,9 @@ public class GenotypeLikelihoods implements Cloneable {
protected double[] log10Likelihoods = null; protected double[] log10Likelihoods = null;
protected double[] log10Posteriors = null; protected double[] log10Posteriors = null;
private DiploidGenotypePriors priors = null; protected DiploidGenotypePriors priors = null;
private FourBaseProbabilities fourBaseLikelihoods = null; protected FourBaseProbabilities fourBaseLikelihoods = null;
/** /**
* Create a new GenotypeLikelhoods object with flat priors for each diploid genotype * Create a new GenotypeLikelhoods object with flat priors for each diploid genotype
@ -115,12 +115,12 @@ public class GenotypeLikelihoods implements Cloneable {
return c; return c;
} }
private void initialize(BaseMismatchModel m, EmpiricalSubstitutionProbabilities.SequencerPlatform pl) { protected void initialize(BaseMismatchModel m, EmpiricalSubstitutionProbabilities.SequencerPlatform pl) {
fourBaseLikelihoods = FourBaseProbabilitiesFactory.makeFourBaseLikelihoods(m, pl); fourBaseLikelihoods = FourBaseProbabilitiesFactory.makeFourBaseLikelihoods(m, pl);
setToZero(); setToZero();
} }
private void setToZero() { protected void setToZero() {
log10Likelihoods = zeros.clone(); // likelihoods are all zeros log10Likelihoods = zeros.clone(); // likelihoods are all zeros
log10Posteriors = priors.getPriors().clone(); // posteriors are all the priors log10Posteriors = priors.getPriors().clone(); // posteriors are all the priors
} }
@ -330,11 +330,11 @@ public class GenotypeLikelihoods implements Cloneable {
static GenotypeLikelihoods[][][][][][] CACHE = new GenotypeLikelihoods[BaseMismatchModel.values().length][EmpiricalSubstitutionProbabilities.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE+1][MAX_PLOIDY][2]; static GenotypeLikelihoods[][][][][][] CACHE = new GenotypeLikelihoods[BaseMismatchModel.values().length][EmpiricalSubstitutionProbabilities.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE+1][MAX_PLOIDY][2];
private boolean inCache( char observedBase, byte qualityScore, int ploidy, SAMRecord read) { protected boolean inCache( char observedBase, byte qualityScore, int ploidy, SAMRecord read) {
return getCache(CACHE, observedBase, qualityScore, ploidy, read) != null; return getCache(CACHE, observedBase, qualityScore, ploidy, read) != null;
} }
private GenotypeLikelihoods getCachedGenotypeLikelihoods( char observedBase, byte qualityScore, int ploidy, SAMRecord read) { protected GenotypeLikelihoods getCachedGenotypeLikelihoods( char observedBase, byte qualityScore, int ploidy, SAMRecord read) {
GenotypeLikelihoods gl = getCache(CACHE, observedBase, qualityScore, ploidy, read); GenotypeLikelihoods gl = getCache(CACHE, observedBase, qualityScore, ploidy, read);
if ( gl == null ) if ( gl == null )
throw new RuntimeException(String.format("BUG: trying to fetch an unset cached genotype likelihood at base=%c, qual=%d, ploidy=%d, read=%s", throw new RuntimeException(String.format("BUG: trying to fetch an unset cached genotype likelihood at base=%c, qual=%d, ploidy=%d, read=%s",
@ -342,7 +342,7 @@ public class GenotypeLikelihoods implements Cloneable {
return gl; return gl;
} }
private GenotypeLikelihoods calculateCachedGenotypeLikelihoods(char observedBase, byte qualityScore, int ploidy, SAMRecord read, int offset) { protected GenotypeLikelihoods calculateCachedGenotypeLikelihoods(char observedBase, byte qualityScore, int ploidy, SAMRecord read, int offset) {
GenotypeLikelihoods gl = calculateGenotypeLikelihoods(observedBase, qualityScore, read, offset); GenotypeLikelihoods gl = calculateGenotypeLikelihoods(observedBase, qualityScore, read, offset);
setCache(CACHE, observedBase, qualityScore, ploidy, read, gl); setCache(CACHE, observedBase, qualityScore, ploidy, read, gl);
return gl; return gl;
@ -372,7 +372,7 @@ public class GenotypeLikelihoods implements Cloneable {
return cache[m][a][i][j][k][x]; return cache[m][a][i][j][k][x];
} }
private GenotypeLikelihoods calculateGenotypeLikelihoods(char observedBase, byte qualityScore, SAMRecord read, int offset) { protected GenotypeLikelihoods calculateGenotypeLikelihoods(char observedBase, byte qualityScore, SAMRecord read, int offset) {
FourBaseProbabilities fbl = fourBaseLikelihoods.computeLog10Likelihoods(observedBase, qualityScore, read, offset); FourBaseProbabilities fbl = fourBaseLikelihoods.computeLog10Likelihoods(observedBase, qualityScore, read, offset);
if ( fbl == null ) if ( fbl == null )
return null; return null;
@ -434,7 +434,7 @@ public class GenotypeLikelihoods implements Cloneable {
* @param observedBase observed base * @param observedBase observed base
* @return true if the base is a bad base * @return true if the base is a bad base
*/ */
private boolean badBase(char observedBase) { protected boolean badBase(char observedBase) {
return BaseUtils.simpleBaseToBaseIndex(observedBase) == -1; return BaseUtils.simpleBaseToBaseIndex(observedBase) == -1;
} }
@ -497,11 +497,11 @@ public class GenotypeLikelihoods implements Cloneable {
// //
// Constant static data // Constant static data
// //
private final static double[] zeros = new double[DiploidGenotype.values().length]; protected final static double[] zeros = new double[DiploidGenotype.values().length];
static { static {
for ( DiploidGenotype g : DiploidGenotype.values() ) { for ( DiploidGenotype g : DiploidGenotype.values() ) {
zeros[g.ordinal()] = 0.0; zeros[g.ordinal()] = 0.0;
} }
} }
} }