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Temporary fix: have RodLocusView manage and close its RODs. Really the 

relationship between these two classes needs to be rethought; see JIRA
GSA-207.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1904 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-23 16:00:12 +00:00
parent ad1fc511b1
commit 65b98470f3
2 changed files with 23 additions and 19 deletions
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32
java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
View File

@ -26,11 +26,6 @@ import java.util.Collections;
* A view into the reference-ordered data in the provider.
*/
public class ManagingReferenceOrderedView implements ReferenceOrderedView {
/**
* The provider that's supplying our backing data.
*/
//private final ShardDataProvider provider;
/**
* The data sources along with their current states.
*/
@ -41,7 +36,6 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
* @param provider
*/
public ManagingReferenceOrderedView( ShardDataProvider provider ) {
//this.provider = provider;
for( ReferenceOrderedDataSource dataSource: provider.getReferenceOrderedData() )
states.add( new ReferenceOrderedDataState( dataSource, (SeekableRODIterator)dataSource.seek(provider.getShard()) ) );
@ -72,17 +66,17 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
// Clear out the existing data so that post-close() accesses to this data will fail-fast.
states = null;
}
/**
* Models the traversal state of a given ROD lane.
*/
private class ReferenceOrderedDataState {
public final ReferenceOrderedDataSource dataSource;
public final SeekableRODIterator iterator;
public ReferenceOrderedDataState( ReferenceOrderedDataSource dataSource, SeekableRODIterator iterator ) {
this.dataSource = dataSource;
this.iterator = iterator;
}
}
}
/**
* Models the traversal state of a given ROD lane.
*/
class ReferenceOrderedDataState {
public final ReferenceOrderedDataSource dataSource;
public final SeekableRODIterator iterator;
public ReferenceOrderedDataState( ReferenceOrderedDataSource dataSource, SeekableRODIterator iterator ) {
this.dataSource = dataSource;
this.iterator = iterator;
}
}

10
java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
View File

@ -39,6 +39,11 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
// broken support for multi-locus rods
//List<ReferenceOrderedDatum> multiLocusRODs = new LinkedList<ReferenceOrderedDatum>();
/**
* The data sources along with their current states.
*/
private List<ReferenceOrderedDataState> states = new ArrayList<ReferenceOrderedDataState>();
/**
* Enable debugging output -- todo remove me
*/
@ -67,6 +72,8 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
GenomeLoc shardLoc = provider.getShard().getGenomeLoc();
it.seekForward(GenomeLocParser.createGenomeLoc(shardLoc.getContigIndex(), shardLoc.getStart()-1, shardLoc.getStart()-1));
states.add(new ReferenceOrderedDataState(dataSource,it));
// we need to special case the interval so we don't always think there's a rod at the first location
if ( dataSource.getName().equals(INTERVAL_ROD_NAME) ) {
if ( interval != null )
@ -202,6 +209,9 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
* Closes the current view.
*/
public void close() {
for( ReferenceOrderedDataState state: states )
state.dataSource.close( state.iterator );
rodQueue = null;
tracker = null;
}