From df7e7921cefc9fe7f60ef40a64062bc4d1b20417 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 5 Apr 2010 19:30:08 +0000
Subject: [PATCH] removing some unused code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/GenotypeCall.java    | 31 ---------------
 .../sting/utils/genotype/ReadBacked.java      | 30 --------------
 .../sting/utils/genotype/VariationCall.java   | 39 -------------------
 3 files changed, 100 deletions(-)
 delete mode 100755 java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java
 delete mode 100644 java/src/org/broadinstitute/sting/utils/genotype/ReadBacked.java
 delete mode 100755 java/src/org/broadinstitute/sting/utils/genotype/VariationCall.java

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java
deleted file mode 100755
index cd65bac39..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/GenotypeCall.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-
-/**
- * @author ebanks
- *         <p/>
- *         Class GenotypeCall
- *         <p/>
- *         represents the genotype-specific data associated with a genotype call.
- */
-public interface GenotypeCall extends Genotype {
-
-    /**
-     *
-     * @param   variation   the Variation object associated with this genotype
-     */
-    public void setVariation(Variation variation);
-
-    /**
-     *
-     * @param   genotype    the genotype
-     */
-    public void setGenotype(DiploidGenotype genotype);
-
-    /**
-     *
-     * @param   value       -log10PEror
-     */
-    public void setNegLog10PError(double value);
-
-}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/ReadBacked.java b/java/src/org/broadinstitute/sting/utils/genotype/ReadBacked.java
deleted file mode 100644
index 015dbd8eb..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/ReadBacked.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-
-/**
- * @author ebanks
- *
- * Interface ReadBacked
- *
- * This interface indicates that a genotype or variant is backed by reads
- */
-public interface ReadBacked {
-    /**
-     * get the pileup that backs this genotype call
-     * @return a pileup
-     */
-    public ReadBackedPileup getPileup();
-
-    /**
-     *
-     * @param   pileup    the pileup for this genotype
-     */
-    public void setPileup(ReadBackedPileup pileup);
-
-    /**
-     * get the count of reads
-     * @return the number of reads we're backed by
-     */
-    public int getReadCount();
-}
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/VariationCall.java b/java/src/org/broadinstitute/sting/utils/genotype/VariationCall.java
deleted file mode 100755
index 18bf7a7b1..000000000
--- a/java/src/org/broadinstitute/sting/utils/genotype/VariationCall.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.broadinstitute.sting.utils.genotype;
-
-
-import java.util.List;
-
-/**
- * @author ebanks
- *         <p/>
- *         Class VariationCall
- *         <p/>
- *         represents locus specific (non-genotype) data associated with a call plus the ability to set genotypes.
- */
-public interface VariationCall extends Variation {
-
-    /**
-     *
-     * @param   alt    the alternate allele base for this variation
-     */
-    public void addAlternateAllele(String alt);
-
-    /**
-     *
-     * @return true if the allele frequency has been set
-     */
-    public boolean hasNonRefAlleleFrequency();
-
-    /**
-     *
-     * @param   frequency    the allele frequency for this variation
-     */
-    public void setNonRefAlleleFrequency(double frequency);
-
-    /**
-     *
-     * @param   calls    the Genotypes for this variation
-     */
-    public void setGenotypeCalls(List<Genotype> calls);
-
-}
\ No newline at end of file