From faff6e401998ca39ed00553185fcc20e312f3130 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Wed, 21 Sep 2011 18:15:23 -0400
Subject: [PATCH] Failed to commit changes to the GATKReport required for more
 easy access when using the files as data sources (read: histograms) for
 walkers

---
 .../sting/gatk/report/GATKReportColumns.java       | 14 +++++++++++++-
 .../sting/gatk/report/GATKReportTable.java         |  4 ++++
 .../sting/gatk/report/GATKReportVersion.java       |  0
 3 files changed, 17 insertions(+), 1 deletion(-)
 mode change 100644 => 100755 public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java
 mode change 100644 => 100755 public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java
old mode 100644
new mode 100755
index a33631c85..a73123b6c
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java
@@ -24,12 +24,14 @@
 
 package org.broadinstitute.sting.gatk.report;
 
+import org.broadinstitute.sting.utils.collections.Pair;
+
 import java.util.*;
 
 /**
  * Tracks a linked list of GATKReportColumn in order by name.
  */
-public class GATKReportColumns extends LinkedHashMap<String, GATKReportColumn> {
+public class GATKReportColumns extends LinkedHashMap<String, GATKReportColumn> implements Iterable<GATKReportColumn> {
     private List<String> columnNames = new ArrayList<String>();
 
     /**
@@ -52,4 +54,14 @@ public class GATKReportColumns extends LinkedHashMap<String, GATKReportColumn> {
         columnNames.add(key);
         return super.put(key, value);
     }
+
+    @Override
+    public Iterator<GATKReportColumn> iterator() {
+        return new Iterator<GATKReportColumn>() {
+            int offset = 0;
+            public boolean hasNext() { return offset < columnNames.size() ; }
+            public GATKReportColumn next() { return getByIndex(offset++); }
+            public void remove() { throw new UnsupportedOperationException("Cannot remove from a GATKReportColumn iterator"); }
+        };
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
index 3e3aa29a7..2fd5ad7e3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
@@ -286,6 +286,10 @@ public class GATKReportTable {
         }
     }
 
+    public boolean containsKey(Object primaryKey) {
+        return primaryKeyColumn.contains(primaryKey);
+    }
+
     /**
      * Set the value for a given position in the table
      *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
old mode 100644
new mode 100755