Rename TraverseLociByReference to TraverseLoci to represent its new function.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@743 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.executive;
 
-import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
+import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
@@ -42,7 +42,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
      */
     private static final int MAX_OUTSTANDING_OUTPUT_MERGES = 50;
 
-    private TraverseLociByReference traversalEngine = null;
+    private TraverseLoci traversalEngine = null;
 
     /**
      * Manage currently running threads.
@@ -62,7 +62,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Reduce
     protected HierarchicalMicroScheduler( Walker walker, Reads reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse ) {
         super( walker, reads, refFile, rods );
         this.threadPool = Executors.newFixedThreadPool(nThreadsToUse);
-        if( !(traversalEngine instanceof TraverseLociByReference) )
+        if( !(traversalEngine instanceof TraverseLoci) )
             throw new UnsupportedOperationException("Traversal engine supports only traverse loci by reference at this time.");
     }
 

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

@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.traversals.TraverseReads;
-import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
+import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
@@ -72,7 +72,7 @@ public abstract class MicroScheduler {
         if (walker instanceof ReadWalker) {
             traversalEngine = new TraverseReads(reads.getReadsFiles(), refFile, rods);
         } else {
-            traversalEngine = new TraverseLociByReference(reads.getReadsFiles(), refFile, rods);
+            traversalEngine = new TraverseLoci(reads.getReadsFiles(), refFile, rods);
         }
 
         this.reads = getReadsDataSource( reads );

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

@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
-import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
+import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.OutputTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -25,12 +25,12 @@ import java.util.concurrent.Callable;
  */
 public class ShardTraverser implements Callable {
     private Walker walker;
-    private TraverseLociByReference traversalEngine;
+    private TraverseLoci traversalEngine;
     private Shard shard;
     private ShardDataProvider dataProvider;
     private OutputMerger output;
 
-    public ShardTraverser( TraverseLociByReference traversalEngine,
+    public ShardTraverser( TraverseLoci traversalEngine,
                            Walker walker,
                            Shard shard,
                            ShardDataProvider dataProvider,

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

@@ -30,14 +30,14 @@ import java.io.File;
  * mhanna - Added better data source integration.
  * TODO: Gain confidence in this implementation and remove the original.
  */
-public class TraverseLociByReference extends TraversalEngine {
+public class TraverseLoci extends TraversalEngine {
 
     /**
      * our log, which we want to capture anything from this class
      */
     protected static Logger logger = Logger.getLogger(TraversalEngine.class);
 
-    public TraverseLociByReference(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
+    public TraverseLoci(List<File> reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
         super( reads, ref, rods );
     }
 
@@ -45,7 +45,7 @@ public class TraverseLociByReference extends TraversalEngine {
         if ( locations.isEmpty() )
             Utils.scareUser("Requested all locations be processed without providing locations to be processed!");
 
-        throw new UnsupportedOperationException("This traversal type not supported by TraverseLociByReference");
+        throw new UnsupportedOperationException("This traversal type not supported by TraverseLoci");
     }
 
     @Override
@@ -53,7 +53,7 @@ public class TraverseLociByReference extends TraversalEngine {
                              Shard shard,
                              ShardDataProvider dataProvider,
                              T sum ) {
-        logger.debug(String.format("TraverseLociByReference.traverse Genomic interval is %s", shard.getGenomeLoc()));
+        logger.debug(String.format("TraverseLoci.traverse Genomic interval is %s", shard.getGenomeLoc()));
 
         if ( !(walker instanceof LocusWalker) )
             throw new IllegalArgumentException("Walker isn't a loci walker!");