now that the design is stable, pull the setReference and setLocation methods back out of Genotype and stick them into constructors of implementing classes

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1931 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -54,12 +54,8 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
         for ( String sample : GLs.keySet() ) {
 
             // create the call
-            Genotype call = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT);
-            call.setReference(ref);
-
-            // get the context
             AlignmentContext context = contexts.get(sample).getContext(StratifiedContext.OVERALL);
-            call.setLocation(context.getLocation());
+            Genotype call = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT, ref, context.getLocation());
 
             if ( call instanceof ReadBacked ) {
                 ((ReadBacked)call).setReads(context.getReads());

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

@@ -321,11 +321,8 @@ public class JointEstimateGenotypeCalculationModel extends GenotypeCalculationMo
             for ( String sample : GLs.keySet() ) {
 
                 // create the call
-                Genotype call = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT);
-                call.setReference(ref);
-
                 AlignmentContext context = contexts.get(sample).getContext(StratifiedContext.OVERALL);
-                call.setLocation(context.getLocation());
+                Genotype call = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT, ref, context.getLocation());
 
                 if ( call instanceof ReadBacked ) {
                     ((ReadBacked)call).setReads(context.getReads());

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

@@ -44,9 +44,7 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
 
             // create the genotype call object
             // create the call
-            Genotype call = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT);
+            Genotype call = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT, ref, context.getLocation());
-            call.setReference(ref);
-            call.setLocation(context.getLocation());
 
             Pair<ReadBackedPileup, GenotypeLikelihoods> discoveryGL = getSingleSampleLikelihoods(ref, sampleContext, priors, StratifiedContext.OVERALL);
 

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

@@ -113,11 +113,6 @@ public class BasicGenotype implements Genotype {
         return mLocation;
     }
 
-    // set the location
-    public void setLocation(GenomeLoc loc) {
-        mLocation = loc;
-    }
-
     /**
      * returns true if the genotype is a point genotype, false if it's a indel / deletion
      *
@@ -150,11 +145,6 @@ public class BasicGenotype implements Genotype {
         return mRef;
     }
 
-    // set the reference base
-    public void setReference(char refBase) {
-        mRef = Character.toUpperCase(refBase);
-    }
-
     /**
      * return this genotype as a variant
      *

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

@@ -52,12 +52,6 @@ public interface Genotype {
      */
     public GenomeLoc getLocation();
 
-    /**
-     * set the location.
-     * @param loc the location
-     */
-    public void setLocation(GenomeLoc loc);
-
     /**
      * returns true if the genotype is a point genotype, false if it's a indel / deletion
      *
@@ -80,12 +74,6 @@ public interface Genotype {
      */
     public char getReference();
 
-    /**
-     * set the reference base.
-     * @param ref the ref base
-     */
-    public void setReference(char ref);
-
     /**
      * return this genotype as a variant
      *

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.genotype;
 
 import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.geli.*;
 import org.broadinstitute.sting.utils.genotype.glf.*;
@@ -74,15 +75,15 @@ public class GenotypeWriterFactory {
      * @param format the format
      * @return an unpopulated genotype call object
      */
-    public static Genotype createSupportedCall(GENOTYPE_FORMAT format) {
+    public static Genotype createSupportedCall(GENOTYPE_FORMAT format, char ref, GenomeLoc loc) {
         switch (format) {
             case VCF:
-                return new VCFGenotypeCall();
+                return new VCFGenotypeCall(ref, loc);
             case GELI:
             case GELI_BINARY:
-                return new GeliGenotypeCall();
+                return new GeliGenotypeCall(ref, loc);
             case GLF:
-                return new GLFGenotypeCall();
+                return new GLFGenotypeCall(ref, loc);
             default:
                 throw new StingException("Genotype format " + format.toString() + " is not implemented");
         }

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

@@ -34,22 +34,16 @@ public class GeliGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked
      * Generate a single sample genotype object
      *
      */
-    public GeliGenotypeCall() {
+    public GeliGenotypeCall(char ref, GenomeLoc loc) {
+        mRefBase = ref;
+        mLocation = loc;
+
         // fill in empty data
-        mRefBase = 'N';
         mPosteriors = new double[10];
         Arrays.fill(mPosteriors, Double.MIN_VALUE);
         mReads = new ArrayList<SAMRecord>();
     }
 
-    public void setReference(char refBase) {
-        mRefBase = Character.toUpperCase(refBase);
-    }
-
-    public void setLocation(GenomeLoc loc) {
-        mLocation = loc;
-    }
-
     public void setReads(List<SAMRecord> reads) {
         mReads = new ArrayList<SAMRecord>(reads);
     }

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java

@@ -31,24 +31,18 @@ public class GLFGenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked
      * Generate a single sample genotype object, containing everything we need to represent calls out of a genotyper object
      *
      */
-    public GLFGenotypeCall() {
+    public GLFGenotypeCall(char ref, GenomeLoc loc) {
+        mRefBase = ref;
+        mGenotype = Utils.dupString(ref, 2);
+
         // fill in empty data
-        mRefBase = 'N';
+        mLocation = loc;
-        mGenotype = "NN";
         mLikelihoods = new double[10];
         Arrays.fill(mLikelihoods, Double.MIN_VALUE);
         mReads = new ArrayList<SAMRecord>();
         mNegLog10PError = Double.MIN_VALUE;
     }
 
-    public void setReference(char refBase) {
-        mRefBase = Character.toUpperCase(refBase);
-    }
-
-    public void setLocation(GenomeLoc loc) {
-        mLocation = loc;
-    }
-
     public void setReads(List<SAMRecord> reads) {
         mReads = new ArrayList<SAMRecord>(reads);
     }

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java

@@ -37,23 +37,17 @@ public class VCFGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked,
      * Generate a single sample genotype object
      *
      */
-    public VCFGenotypeCall() {
+    public VCFGenotypeCall(char ref, GenomeLoc loc) {
+        mRefBase = ref;
+        mLocation = loc;
+
         // fill in empty data
-        mRefBase = 'N';
         mPosteriors = new double[10];
         Arrays.fill(mPosteriors, Double.MIN_VALUE);
         mSampleName = "";
         mReads = new ArrayList<SAMRecord>();
     }
 
-    public void setReference(char refBase) {
-        mRefBase = Character.toUpperCase(refBase);
-    }
-
-    public void setLocation(GenomeLoc loc) {
-        mLocation = loc;
-    }
-
     public void setReads(List<SAMRecord> reads) {
         mReads = new ArrayList<SAMRecord>(reads);
     }

java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java

@@ -145,8 +145,7 @@ class FakeGenotype extends GLFGenotypeCall implements Comparable<FakeGenotype> {
      * @param negLog10PError the confidence score
      */
     public FakeGenotype(GenomeLoc location, String genotype, char ref, double negLog10PError, double likelihoods[]) {
-        setLocation(location);
+        super(ref, location);
-        setReference(ref);
         setLikelihoods(likelihoods);
         setGenotype(genotype);
         setNegLog10PError(negLog10PError);