Add a getFormat() method to get the output format from the writer. The need for

this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2418 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/io/storage/GenotypeWriterStorage.java

@@ -45,6 +45,7 @@ import edu.mit.broad.picard.genotype.geli.GeliFileReader;
  * @version 0.1
  */
 public class GenotypeWriterStorage implements GenotypeWriter, Storage<GenotypeWriter> {
+    private final GenotypeWriterFactory.GENOTYPE_FORMAT format;
     private final File file;
     private final GenotypeWriter writer;
 
@@ -53,12 +54,23 @@ public class GenotypeWriterStorage implements GenotypeWriter, Storage<GenotypeWr
     }
 
     public GenotypeWriterStorage( GenotypeWriterStub stub, File file ) {
+        this.format = stub.getFormat();
         this.file = file;
         writer = GenotypeWriterFactory.create(stub.getFormat(), file);
         Set<String> samples = SampleUtils.getSAMFileSamples(stub.getSAMFileHeader());
         GenotypeWriterFactory.writeHeader(writer, stub.getSAMFileHeader(), samples, new HashSet<VCFHeaderLine>());
     }
 
+    /**
+     * Reports the format of the given genotyping data, taken directly from the stub.
+     * @return The format of the genotyping file.
+     */
+    @Override
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat() {
+        return format;
+    }
+    
+
     public void mergeInto( GenotypeWriter targetStream ) {
 
         // TODO -- This is ugly, but there is no GenotypeWriter interface since

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

@@ -36,6 +36,13 @@ import java.util.List;
  */
 public interface GenotypeWriter {
 
+    /**
+     * Gets the file format of this genotype writer, to disambiguate
+     * between different forms of data required.
+     * @return Type of this GenotypeWriter.
+     */
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat();
+
     /**
      * Add a genotype, given a genotype locus
      * @param call the locus to add

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

@@ -61,6 +61,15 @@ public class GeliAdapter implements GenotypeWriter {
         this.writeTo = writeTo;
     }
 
+    /**
+     * Indicates that this is a binary-format geli writer.
+     * @return GENOTYPE_FORMAT.GELI_BINARY always.
+     */
+    @Override
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat() {
+        return GenotypeWriterFactory.GENOTYPE_FORMAT.GELI_BINARY;
+    }
+
     /**
      * wrap a GeliFileWriter in the Genotype writer interface
      *

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

@@ -44,6 +44,15 @@ public class GeliTextWriter implements GenotypeWriter {
         mWriter.println(headerLine);
     }
 
+    /**
+     * Indicates that this is a geli writer.
+     * @return GENOTYPE_FORMAT.GELI always.
+     */
+    @Override
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat() {
+        return GenotypeWriterFactory.GENOTYPE_FORMAT.GELI;
+    }
+
     public final static String headerLine = "#Sequence       Position        ReferenceBase   NumberOfReads   MaxMappingQuality       BestGenotype    BtrLod  BtnbLod    AA      AC      AG      AT      CC      CG      CT      GG      GT      TT";
 
     /**

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

@@ -83,6 +83,15 @@ public class GLFWriter implements GenotypeWriter {
         outputBinaryCodec.setOutputFileName(writeTo.toString());
     }
 
+    /**
+     * Indicates that this is a GLF writer.
+     * @return GENOTYPE_FORMAT.GLF always.
+     */
+    @Override
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat() {
+        return GenotypeWriterFactory.GENOTYPE_FORMAT.GLF;
+    }
+
     /**
      * Write out the header information for the GLF file.  The header contains
      * the magic number, the length of the header text, the text itself, the reference

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

@@ -38,6 +38,16 @@ public class TabularLFWriter implements GenotypeWriter {
         outStream.println("location sample_name ref alt genotype qhat qstar lodVsRef lodVsNextBest depth bases");
     }
 
+    /**
+     * Indicates that this is a tabular genotype writer.
+     * @return GENOTYPE_FORMAT.TABULAR always.
+     */
+    @Override
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat() {
+        return GenotypeWriterFactory.GENOTYPE_FORMAT.TABULAR;
+    }
+    
+
     /**
      * Add a genotype, given a genotype locus
      *

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

@@ -35,6 +35,15 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
         mWriter = new VCFWriter(writeTo);
     }
 
+    /**
+     * Indicates that this is a VCF writer.
+     * @return GENOTYPE_FORMAT.VCF always.
+     */
+    @Override
+    public GenotypeWriterFactory.GENOTYPE_FORMAT getFormat() {
+        return GenotypeWriterFactory.GENOTYPE_FORMAT.VCF;
+    }
+
     /**
      * initialize this VCF header
      *