From 04e9a494e9fb69864e6eb7ae1ddd155f7578f854 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 28 Oct 2009 18:08:14 +0000
Subject: [PATCH] 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
---
 .../gatk/walkers/genotyper/GenotypeCall.java  | 15 +++------------
 .../gatk/walkers/CoverageEvalWalker.java      |  2 +-
 .../sting/utils/genotype/GenotypesBacked.java | 19 -------------------
 .../utils/genotype/geli/GeliTextWriter.java   |  2 +-
 .../genotype/tabular/TabularLFWriter.java     |  2 +-
 5 files changed, 6 insertions(+), 34 deletions(-)
 delete mode 100644 java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCall.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCall.java
index 3559de4a2..8cc7e2773 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCall.java
+++ b/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
-     *
-     * @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
      */
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
index 12c843a47..5a3952d33 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
+++ b/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 {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java b/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java
deleted file mode 100644
index 26be15549..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/GenotypesBacked.java
+++ /dev/null
@@ -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);
-}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
index 3f7bc7d9a..34cbe9931 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java
+++ b/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 {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
index 7e518960e..d35f1e965 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java
+++ b/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 {