From c10741e9f5cbd060fc97b2680ff1beef27ef217b Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 18 May 2009 01:31:57 +0000 Subject: [PATCH] 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 --- .../sting/gatk/executive/HierarchicalMicroScheduler.java | 6 +++--- .../sting/gatk/executive/MicroScheduler.java | 4 ++-- .../sting/gatk/executive/ShardTraverser.java | 6 +++--- .../{TraverseLociByReference.java => TraverseLoci.java} | 8 ++++---- 4 files changed, 12 insertions(+), 12 deletions(-) rename java/src/org/broadinstitute/sting/gatk/traversals/{TraverseLociByReference.java => TraverseLoci.java} (92%) diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index c419ba84c..4a4d6075c 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/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> 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."); } diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 5a198e416..e147efb21 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/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 ); diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 93d8f3236..19e2a5f99 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/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, diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociByReference.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java similarity index 92% rename from java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociByReference.java rename to java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 84a9efeb5..8c08b83ae 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociByReference.java +++ b/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 reads, File ref, List> rods) { + public TraverseLoci(List reads, File ref, List> 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!");