From 7a9cfe1f75d8c354e553192360ceffa129d50bbf Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 8 May 2009 13:46:28 +0000
Subject: [PATCH] Push reduceInit down a level so that the walker can call into
 it without weird casts.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@638 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/executive/LinearMicroScheduler.java |  2 +-
 .../sting/gatk/walkers/LocusWalker.java            |  4 ----
 .../sting/gatk/walkers/ReadWalker.java             |  4 ----
 .../broadinstitute/sting/gatk/walkers/Walker.java  | 14 ++++++++++++++
 4 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index 8744221af..0be399f48 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -55,7 +55,7 @@ public class LinearMicroScheduler extends MicroScheduler {
         SAMDataSource dataSource = getReadsDataSource();
 
         walker.initialize();
-        Object accumulator = ((LocusWalker<?, ?>) walker).reduceInit();
+        Object accumulator = walker.reduceInit();
 
         for (Shard shard : shardStrategy) {
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
index 42fee73df..2c186534b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
@@ -28,8 +28,4 @@ public abstract class LocusWalker<MapType, ReduceType> extends Walker<MapType, R
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
     public abstract MapType map(RefMetaDataTracker tracker, char ref, LocusContext context);
-
-    // Given result of map function
-    public abstract ReduceType reduceInit();
-    public abstract ReduceType reduce(MapType value, ReduceType sum);
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
index a19dd8970..8d6443a56 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
@@ -24,8 +24,4 @@ public abstract class ReadWalker<MapType, ReduceType> extends Walker<MapType, Re
 
     // Map over the org.broadinstitute.sting.gatk.LocusContext
     public abstract MapType map(LocusContext context, SAMRecord read);
-
-    // Given result of map function
-    public abstract ReduceType reduceInit();
-    public abstract ReduceType reduce(MapType value, ReduceType sum);
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index e347c944a..aceb10672 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -56,6 +56,20 @@ public abstract class Walker<MapType, ReduceType> {
 
     public void initialize() { }
 
+    /**
+     * Provide an initial value for reduce computations.
+     * @return Initial value of reduce.
+     */
+    public abstract ReduceType reduceInit();
+
+    /**
+     * Reduces a single map with the accumulator provided as the ReduceType.
+     * @param value result of the map.
+     * @param sum accumulator for the reduce.
+     * @return accumulator with result of the map taken into account.
+     */
+    public abstract ReduceType reduce(MapType value, ReduceType sum);    
+
     public void onTraversalDone(ReduceType result) {
         out.println("[REDUCE RESULT] Traversal result is: " + result);
     }