From 3300ca906ada513f329db07b218da1a25e88f2f6 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 27 Nov 2009 22:25:52 +0000
Subject: [PATCH] An iterator for Eric to use when injecting his new wrapping
 reads -- a stopgap solution for getting additional caching functionality into
 a SAMRecord.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2173 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/SAMDataSource.java      |  4 +-
 .../gatk/iterators/ReadWrappingIterator.java  | 74 +++++++++++++++++++
 2 files changed, 77 insertions(+), 1 deletion(-)
 create mode 100644 java/src/org/broadinstitute/sting/gatk/iterators/ReadWrappingIterator.java

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index 58c1fd461..2dde22630 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -403,7 +403,9 @@ public class SAMDataSource implements SimpleDataSource {
      */
     private StingSAMIterator createIterator( DataStreamSegment segment ) {
         StingSAMIterator iterator = resourcePool.iterator(segment);
-        return new MalformedSAMFilteringIterator( getHeader(), iterator, violations );
+        StingSAMIterator malformedWrappedIterator =  new MalformedSAMFilteringIterator( getHeader(), iterator, violations );
+        StingSAMIterator readWrappingIterator = new ReadWrappingIterator(malformedWrappedIterator);
+        return readWrappingIterator;
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/ReadWrappingIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/ReadWrappingIterator.java
new file mode 100644
index 000000000..0dc92d589
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/ReadWrappingIterator.java
@@ -0,0 +1,74 @@
+package org.broadinstitute.sting.gatk.iterators;
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.Reads;
+
+/**
+ * An iterator which wraps each SAMRecord inside a wrapper class, bringing new functionality to the read while
+ * presenting the original SAMRecord interface.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class ReadWrappingIterator implements StingSAMIterator {
+    /**
+     * Iterator to which to pass
+     */
+    private StingSAMIterator wrappedIterator;
+
+    /**
+     * Decorate the given iterator inside a ReadWrappingIterator.
+     * @param wrappedIterator
+     */
+    public ReadWrappingIterator(StingSAMIterator wrappedIterator) {
+        this.wrappedIterator = wrappedIterator;
+    }
+
+    /**
+     * Get metadata about the reads' sources, etc.
+     * @return Source info about the reads.
+     */
+    public Reads getSourceInfo() {
+        return wrappedIterator.getSourceInfo();
+    }
+
+    /**
+     * Convenience function for use in foreach loops.  Dangerous because it does not actually
+     * reset the iterator.
+     * @return An iterator through the current data stream.
+     */
+    public StingSAMIterator iterator() {
+        // NOTE: this iterator doesn't perform any kind of reset operation; it just returns itself.
+        //       can we do something better?  Do we really have to provide support for the Iterable interface?
+        return this;
+    }
+
+    /**
+     * Close this iterator.
+     */
+    public void close() {
+        wrappedIterator.close();
+    }
+
+    /**
+     * Does the iterator contain more values?
+     * @return True if there are more left to return, false otherwise.
+     */
+    public boolean hasNext() {
+        return wrappedIterator.hasNext();
+    }
+
+    /**
+     * Get the next value in the sequence.
+     * @return Next value in the sequence.  By convention, a NoSuchElementException should be thrown if
+     *         no next exists.
+     */
+    public SAMRecord next() {
+        return wrappedIterator.next();
+    }
+
+    /**
+     * Remove the current element from the list.  Unsupported in this wrapper.
+     */
+    public void remove() { throw new UnsupportedOperationException("Cannot remove from a ReadWrappingIterator"); }
+}