From 65b98470f3dc3b9c8356d2a1e4ab880eb4293f35 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 23 Oct 2009 16:00:12 +0000
Subject: [PATCH] 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
---
 .../ManagingReferenceOrderedView.java         | 32 ++++++++-----------
 .../datasources/providers/RodLocusView.java   | 10 ++++++
 2 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
index d17dc06ce..653b90e52 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
@@ -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;
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
index e5a8831b4..5e438b559 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
@@ -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;
     }