removing some unused code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -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);
-
-}

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

@@ -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();
-}

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

@@ -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);
-
-}