From 907c1832428766b44963b9f09eec7be8b3bd8076 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 31 Mar 2009 15:05:33 +0000
Subject: [PATCH] update walkers so that onTraversalDone works (it now takes an
 arg)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@235 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/AlignedReadsHistoWalker.java    | 2 +-
 .../gatk/walkers/AlleleFrequencyMetricsWalker.java          | 2 +-
 .../playground/gatk/walkers/BaseQualityDumpWalker.java      | 6 ------
 .../playground/gatk/walkers/BaseQualityHistoWalker.java     | 2 +-
 .../sting/playground/gatk/walkers/MismatchHistoWalker.java  | 2 +-
 5 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
index 7657d71b7..10bd5ad3c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
@@ -45,7 +45,7 @@ public class AlignedReadsHistoWalker extends ReadWalker<Integer, Integer> {
         return value + sum;
     }
 
-    public void onTraversalDone() {
+    public void onTraversalDone(Integer result) {
         int curTotal = 0;
         for ( int i = 0; i < alignCounts.length; i++ ) {
             curTotal += alignCounts[i];
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
index 2c0c9b42d..5ef12ef87 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
@@ -159,7 +159,7 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
         out.println();
     }
 
-    public void onTraversalDone() 
+    public void onTraversalDone(String result) 
     {
         printMetrics();
     }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
index 27461a63e..1ad6cb7fa 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
@@ -4,12 +4,6 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import org.broadinstitute.sting.utils.Utils;
-import edu.mit.broad.picard.reference.ReferenceSequence;
-
-import java.util.Iterator;
-import java.util.List;
-import static java.lang.reflect.Array.*;
 
 @WalkerName("Base_Quality_Dump")
 public class BaseQualityDumpWalker extends ReadWalker<Integer, Integer> {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
index 74c4358b4..f0767bbdb 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
@@ -43,7 +43,7 @@ public class BaseQualityHistoWalker extends ReadWalker<Integer, Integer> {
         return value + sum;
     }
 
-    public void onTraversalDone() {
+    public void onTraversalDone(Integer result) {
         int lastNonZero = -1;
         for ( int i = this.qualCounts.length-1; i >= 0; i-- ) {
             if ( this.qualCounts[i] > 0 ) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
index 4a5c8051a..9165ac8cd 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
@@ -70,7 +70,7 @@ public class MismatchHistoWalker extends ReadWalker<Integer, Integer> {
         return value + sum;
     }
 
-    public void onTraversalDone() {
+    public void onTraversalDone(Integer result) {
         for ( int i = 0; i < mismatchCounts.length; i++ )
             out.println((i+1) + "\t" + mismatchCounts[i]);
     }