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removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1924 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-10-28 18:08:14 +00:00
parent e3b9114664
commit 04e9a494e9
5 changed files with 6 additions and 34 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCall.java
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@ -18,7 +18,7 @@ import java.util.List;
* The implementation of the genotype interface, which contains
* extra information for the various genotype outputs
*/
public class GenotypeCall implements Genotype, ReadBacked, GenotypesBacked, LikelihoodsBacked, PosteriorsBacked, SampleBacked {
public class GenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked, PosteriorsBacked, SampleBacked {
private final char mRefBase;
private final GenotypeLikelihoods mGenotypeLikelihoods;
@ -265,16 +265,7 @@ public class GenotypeCall implements Genotype, ReadBacked, GenotypesBacked, Like
}
/**
* get the likelihoods
*
* @return an array in lexigraphical order of the likelihoods
*/
public Genotype getGenotype(DiploidGenotype x) {
return new GenotypeCall(mSampleName, mLocation, mRefBase, mGenotypeLikelihoods, mPileup, x);
}
/**
* get the likelihood information for this
* get the likelihood information for this call
*
* @return
*/
@ -284,7 +275,7 @@ public class GenotypeCall implements Genotype, ReadBacked, GenotypesBacked, Like
/**
* get the likelihood information for this
* get the posteriors information for this call
*
* @return
*/

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
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@ -121,7 +121,7 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
if (locus instanceof ReadBacked) {
readDepth = ((ReadBacked)locus).getReadCount();
}
if (!(locus instanceof GenotypesBacked)) {
if (!(locus instanceof PosteriorsBacked)) {
posteriors = new double[10];
Arrays.fill(posteriors, 0.0);
} else {

19
java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java
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@ -1,19 +0,0 @@
package org.broadinstitute.sting.utils.genotype;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
/**
* @author aaron
*
* Interface LikelihoodsBacked
*
* indicate that this genotype was called, and contains the other genotypes with their
* associtated information.
*/
public interface GenotypesBacked {
/**
* get the likelihoods
* @return an array in lexigraphical order of the likelihoods
*/
public Genotype getGenotype(DiploidGenotype x);
}

2
java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
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@ -59,7 +59,7 @@ public class GeliTextWriter implements GenotypeWriter {
char ref = locus.getReference();
if (!(locus instanceof GenotypesBacked)) {
if (!(locus instanceof PosteriorsBacked)) {
posteriors = new double[10];
Arrays.fill(posteriors, 0.0);
} else {

2
java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
View File

@ -49,7 +49,7 @@ public class TabularLFWriter implements GenotypeWriter {
int readDepth = -1;
double nextVrsBest = 0;
double nextVrsRef = 0;
if (!(locus instanceof GenotypesBacked)) {
if (!(locus instanceof LikelihoodsBacked)) {
likelihoods = new double[10];
Arrays.fill(likelihoods, Double.MIN_VALUE);
} else {