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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
This commit is contained in:
hanna 2009-05-18 01:31:57 +00:00
parent e6ce80c8e3
commit c10741e9f5
4 changed files with 12 additions and 12 deletions
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6
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
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@ -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.");
}

4
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -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 );

6
java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
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@ -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,

8
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociByReference.java → java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -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!");