More cleanup -- pushing shared functions down into the traversal engine.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@639 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReferenceProvider.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.dataSources.providers;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
 
@@ -16,7 +17,8 @@ public class ReferenceProvider {
     private ReferenceSequence referenceSequence;
     private GenomeLoc referenceInterval;
 
-    public ReferenceProvider( IndexedFastaSequenceFile sequenceFile, GenomeLoc position ) {
+    public ReferenceProvider( IndexedFastaSequenceFile sequenceFile, Shard shard ) {
+        GenomeLoc position = shard.getGenomeLoc();
         this.referenceSequence = sequenceFile.getSubsequenceAt( position.getContig(),
                                                                 position.getStart(),
                                                                 position.getStop() );

java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -117,7 +117,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
             throw new StingException("Unable to retrieve result", ex );
         }
         
-        traversalEngine.printOnTraversalDone("loci", result);
+        traversalEngine.printOnTraversalDone(result);
         walker.onTraversalDone(result);
     }
 

java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java

@@ -5,12 +5,10 @@ import org.broadinstitute.sting.gatk.dataSources.providers.ReferenceProvider;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
 import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
-import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSourceLoadException;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.traversals.TraverseByReads;
 import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
 import org.broadinstitute.sting.gatk.traversals.TraverseReads;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
@@ -61,7 +59,7 @@ public class LinearMicroScheduler extends MicroScheduler {
 
             StingSAMIterator readShard = dataSource.seek(shard);
 
-            ReferenceProvider referenceProvider = new ReferenceProvider(reference, shard.getGenomeLoc());
+            ReferenceProvider referenceProvider = new ReferenceProvider(reference, shard);
             LocusContextProvider locusProvider = new LocusContextProvider(readShard);
 
             if (!isAReadWalker) {
@@ -73,8 +71,7 @@ public class LinearMicroScheduler extends MicroScheduler {
             readShard.close();
         }
 
-        String type = (isAReadWalker) ? "read" : "loci";
+        traversalEngine.printOnTraversalDone(accumulator);
-        traversalEngine.printOnTraversalDone(type, accumulator);
 
         walker.onTraversalDone(accumulator);
     }

java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -53,12 +53,12 @@ public class ShardTraverser implements Callable {
     }
 
     public Object call() {
-        Object accumulator = ((LocusWalker<?,?>)walker).reduceInit();
+        Object accumulator = walker.reduceInit();
 
         CloseableIterator<SAMRecord> readShard = null;
         readShard = reads.seek( shard );
 
-        ReferenceProvider referenceProvider = new ReferenceProvider( reference, shard.getGenomeLoc() );
+        ReferenceProvider referenceProvider = new ReferenceProvider( reference, shard );
         LocusContextProvider locusProvider = new LocusContextProvider( readShard );
 
         OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker();

java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -280,6 +280,16 @@ public abstract class TraversalEngine {
         }
     }
 
+    /**
+     * A passthrough method so that subclasses can report which types of traversals they're using.
+     * TODO: Make this method abstract once all traversals support it.
+     * @param sum Result of the computation.
+     * @param <T> Type of the computation.
+     */
+    public <T> void printOnTraversalDone( T sum ) {
+        throw new UnsupportedOperationException( "This method should be overridden." );
+    }
+
     /**
      * Called after a traversal to print out information about the traversal process
      *
@@ -287,7 +297,7 @@ public abstract class TraversalEngine {
      * @param sum  The reduce result of the traversal
      * @param <T>  ReduceType of the traversal
      */
-    public <T> void printOnTraversalDone(final String type, T sum) {
+    protected <T> void printOnTraversalDone(final String type, T sum) {
         printProgress(true, type, null);
         logger.info("Traversal reduce result is " + sum);
         final long curTime = System.currentTimeMillis();

java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociByReference.java

@@ -90,4 +90,14 @@ public class TraverseLociByReference extends TraversalEngine {
 
         return sum;
     }
+
+    /**
+     * Temporary override of printOnTraversalDone.
+     * TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
+     * @param sum Result of the computation.
+     * @param <T> Type of the result.
+     */
+    public <T> void printOnTraversalDone( T sum ) {
+        printOnTraversalDone( "loci", sum );
+    }
 }

java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java

@@ -119,4 +119,13 @@ public class TraverseReads extends TraversalEngine {
         return sum;
     }
 
+    /**
+     * Temporary override of printOnTraversalDone.
+     * TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
+     * @param sum Result of the computation.
+     * @param <T> Type of the result.
+     */
+    public <T> void printOnTraversalDone( T sum ) {
+        printOnTraversalDone( "reads", sum );
+    }    
 }