From 7e5e4225914fa50875a55c8414757d7a82d4973a Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 May 2009 15:23:22 +0000
Subject: [PATCH] ReferenceOrdereData now inspects the ROD class using
 reflection. If the ROD declares a static Iterator<ROD> createIterator(String
 rodName, File rodFile) factory method, it is wrapped and used by the
 ReferenceOrderedData to read records from rodFile. If the ROD does not
 provide such factory method, the old behavior is the default:
 ReferenceOrderedData uses its own simple default iterator to read the file
 line by line (assuming there is only one line per record/position).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@768 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/refdata/ReferenceOrderedData.java    | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index 50138e8fc..921193ce1 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -7,6 +7,7 @@ import java.io.FileNotFoundException;
 import java.util.*;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -150,8 +151,25 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
     }
 
     public RODIterator iterator() {
-        return new RODIterator(new SimpleRODIterator());
-    }
+    	Iterator<ROD> it;
+        try {
+            Method m = type.getDeclaredMethod("createIterator", String.class,java.io.File.class);
+            it = (Iterator<ROD>) m.invoke(null, name, file);
+        } catch ( java.lang.NoSuchMethodException e ) {
+            it = new SimpleRODIterator();
+        } catch ( java.lang.NullPointerException e ) {
+            throw new RuntimeException(e);
+        } catch ( java.lang.SecurityException e ) {
+            throw new RuntimeException(e);
+        }  catch ( java.lang.IllegalAccessException e ) {
+        	throw new RuntimeException(e);
+        }  catch ( java.lang.IllegalArgumentException e ) {
+        	throw new RuntimeException(e);
+        }  catch ( java.lang.reflect.InvocationTargetException e ) {
+        	throw new RuntimeException(e);
+        }        
+        return new RODIterator(it); 	
+   }
 
     // ----------------------------------------------------------------------
     //
@@ -275,7 +293,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         private PushbackIterator<ROD> it;
         private ROD prev = null;
         
-        public RODIterator(SimpleRODIterator it) {
+        public RODIterator(Iterator<ROD> it) {
             this.it = new PushbackIterator<ROD>(it);
         }