From 826781a760fbaf530ee27a58915669eb8fc9cc4a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 27 Mar 2009 13:44:46 +0000
Subject: [PATCH] The traversal engine now passes the reduce result to
 OnTraversalDone() in the walker base class

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@210 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/TraversalEngine.java | 4 ++--
 java/src/org/broadinstitute/sting/gatk/WalkerManager.java  | 2 +-
 .../org/broadinstitute/sting/gatk/walkers/LocusWalker.java | 2 +-
 .../org/broadinstitute/sting/gatk/walkers/ReadWalker.java  | 2 +-
 java/src/org/broadinstitute/sting/gatk/walkers/Walker.java | 7 +++++--
 5 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
index 46ef0b546..e77471aee 100755
--- a/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
@@ -616,7 +616,7 @@ public class TraversalEngine {
         }
 
         printOnTraversalDone("loci", sum);
-        walker.onTraversalDone();
+        walker.onTraversalDone(sum);
         return 0;
     }
 
@@ -738,7 +738,7 @@ public class TraversalEngine {
         }
 
         printOnTraversalDone("reads", sum);
-        walker.onTraversalDone();
+        walker.onTraversalDone(sum);
         return 0;
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 360f1d435..030f39e9e 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -338,7 +338,7 @@ public class WalkerManager {
 
         for (Class<Walker> walkerClass : walkerClasses) {
             String walkerName = getWalkerName(walkerClass);
-            logger.info(String.format("* Adding module %s%n", walkerName));
+            logger.info(String.format("* Adding module %s", walkerName));
             walkers.put(walkerName, walkerClass);
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
index 83d4f102f..a7e371cbb 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
@@ -12,7 +12,7 @@ import java.util.List;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-public abstract class LocusWalker<MapType, ReduceType> extends Walker {
+public abstract class LocusWalker<MapType, ReduceType> extends Walker<ReduceType> {
     // Do we actually want to operate on the context?
     public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
         return true;    // We are keeping all the reads
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
index dbc073eb7..093d55916 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
@@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
  * Time: 2:52:28 PM
  * To change this template use File | Settings | File Templates.
  */
-public abstract class ReadWalker<MapType, ReduceType> extends Walker {
+public abstract class ReadWalker<MapType, ReduceType> extends Walker<ReduceType> {
     public boolean requiresOrderedReads() { return false; }
     
     // Do we actually want to operate on the context?
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index dc69ab344..101595a1c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
  * Time: 1:53:31 PM
  * To change this template use File | Settings | File Templates.
  */
-public abstract class Walker {
+public abstract class Walker<ReduceType> {
     // TODO: Can a walker be templatized so that map and reduce live here?
 
     protected Walker() {
@@ -27,5 +27,8 @@ public abstract class Walker {
     }
 
     public void initialize() { }
-    public void onTraversalDone() { }
+    public void onTraversalDone(ReduceType result) {
+        // TODO: replace with the correct output stream
+        System.out.println("[REDUCE RESULT] Traversal result is: " + result);
+    }
 }