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Fixed method override issue with old-style traversals. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@660 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-12 01:22:18 +00:00
parent 862b8a6787
commit 32696b13f5
7 changed files with 17 additions and 13 deletions
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2
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -203,7 +203,7 @@ public abstract class TraversalEngine {
public boolean hasLocations() {
return this.locs != null;
return this.locs != null && !this.locs.isEmpty();
}
// --------------------------------------------------------------------------------------------------------------

5
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
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@ -34,7 +34,8 @@ public class TraverseByLoci extends TraversalEngine {
super(reads, ref, rods);
}
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
@Override
public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
if ( walker instanceof LocusWalker ) {
LocusWalker<M, T> locusWalker = (LocusWalker<M, T>)walker;
T sum = traverseByLoci(locusWalker, locations);
@ -54,7 +55,7 @@ public class TraverseByLoci extends TraversalEngine {
* @param <T> ReduceType -- the result of calling reduce() on the walker
* @return 0 on success
*/
protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, List<GenomeLoc> locations) {
logger.debug("Entering traverseByLoci");
if(readsFiles.size() > 1)

9
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
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@ -32,7 +32,8 @@ public class TraverseByLocusWindows extends TraversalEngine {
super(reads, ref, rods);
}
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
@Override
public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
if ( walker instanceof LocusWindowWalker ) {
LocusWindowWalker<M, T> locusWindowWalker = (LocusWindowWalker<M, T>)walker;
T sum = traverseByIntervals(locusWindowWalker, locations);
@ -52,7 +53,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
* @param <T> ReduceType -- the result of calling reduce() on the walker
* @return 0 on success
*/
protected <M, T> T traverseByIntervals(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
protected <M, T> T traverseByIntervals(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations) {
logger.debug("Entering traverseByIntervals");
if(readsFiles.size() > 1)
@ -83,7 +84,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
return sum;
}
protected <M, T> T strictIntervalTraversal(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations, T sum) {
protected <M, T> T strictIntervalTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
for ( GenomeLoc interval : locations ) {
logger.debug(String.format("Processing interval %s", interval.toString()));
@ -98,7 +99,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
return sum;
}
protected <M, T> T fullInputTraversal(LocusWindowWalker<M, T> walker, ArrayList<GenomeLoc> locations, T sum) {
protected <M, T> T fullInputTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
// set everything up
GenomeLoc currentInterval = (locations.size() > 0 ? locations.get(0) : null);

5
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
View File

@ -32,7 +32,8 @@ public class TraverseByReads extends TraversalEngine {
super(reads, ref, rods);
}
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
@Override
public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
if ( walker instanceof ReadWalker ) {
Walker x = walker;
ReadWalker<?, ?> readWalker = (ReadWalker<?, ?>)x;
@ -53,7 +54,7 @@ public class TraverseByReads extends TraversalEngine {
* @param <> ReduceType -- the result of calling reduce() on the walker
* @return 0 on success
*/
public <M, T> Object traverseByRead(ReadWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
public <M, T> Object traverseByRead(ReadWalker<M, T> walker, List<GenomeLoc> locations) {
samReadIter = initializeReads();
if ( refFileName != null && !locations.isEmpty() )
GenomeLoc.setupRefContigOrdering(new FastaSequenceFile2(refFileName));

2
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReference.java
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@ -42,7 +42,7 @@ public class TraverseByReference extends TraverseByLoci {
* @param <T> ReduceType -- the result of calling reduce() on the walker
* @return 0 on success
*/
protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
protected <M, T> T traverseByLoci(LocusWalker<M, T> walker, List<GenomeLoc> locations) {
logger.debug("Entering traverseByReference");
// initialize the walker object

5
java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
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@ -256,7 +256,8 @@ public class TraverseDuplicates extends TraversalEngine {
// old style interface to the system
//
// --------------------------------------------------------------------------------------------------------------
public <M,T> T traverse(Walker<M,T> walker, ArrayList<GenomeLoc> locations) {
@Override
public <M,T> T traverse(Walker<M,T> walker, List<GenomeLoc> locations) {
if ( walker instanceof DuplicateWalker) {
Walker x = walker;
DuplicateWalker<?, ?> dupWalker = (DuplicateWalker<?, ?>)x;
@ -269,7 +270,7 @@ public class TraverseDuplicates extends TraversalEngine {
/**
* Should we deleted at the soonist possible opportunity
*/
public <M, T> Object traverseByRead(DuplicateWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
public <M, T> Object traverseByRead(DuplicateWalker<M, T> walker, List<GenomeLoc> locations) {
samReadIter = initializeReads();
// Initialize the walker

2
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -275,7 +275,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
* @param curr Current genome Location
* @return true if we are past the last location to process
*/
public static boolean pastFinalLocation(GenomeLoc curr, ArrayList<GenomeLoc> locs) {
public static boolean pastFinalLocation(GenomeLoc curr, List<GenomeLoc> locs) {
return (locs.size() > 0 && curr.isPast(locs.get(locs.size() - 1)));
}