getBoundRods() convenience method

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1595 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java

@@ -4,6 +4,7 @@ import org.apache.log4j.Logger;
 
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.LinkedList;
 
 /**
  * This class represents the Reference Metadata available at a particular site in the genome.  It can be
@@ -85,6 +86,22 @@ public class RefMetaDataTracker {
         return map.values();
     }
 
+    /**
+     * Get all of the RODs at the current site
+     *
+     * @return
+     */
+    public Collection<ReferenceOrderedDatum> getBoundRods() {
+        LinkedList<ReferenceOrderedDatum> bound = new LinkedList<ReferenceOrderedDatum>();
+        
+        for ( ReferenceOrderedDatum value : map.values() ) {
+            if ( value != null )
+            bound.add(value);
+        }
+
+        return bound;
+    }
+
     /**
      * Binds the reference ordered datum ROD to name at this site.  Should be used only but the traversal
      * system to provide access to RODs in a structured way to the walkers.