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

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCall.java

@@ -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
+     * get the likelihood information for this call
-     *
-     * @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
      *
      * @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
      */

java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java

@@ -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 {

java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java

@@ -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);
-}

java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java

@@ -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 {

java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java

@@ -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 {