From 1d2151adcf1bc837a82a768b142d8a881178a975 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 9 Dec 2009 19:34:56 +0000
Subject: [PATCH] Better handling of nulls output by

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2296 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/CommandLineGATK.java    | 8 ++++----
 java/src/org/broadinstitute/sting/gatk/WalkerManager.java | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 88f727fe9..71d7ab733 100755
--- a/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -158,7 +158,7 @@ public class CommandLineGATK extends CommandLineExecutable {
             }
 
             // Dump the walkers into the sorted set.
-            helpText.add(new HelpEntry(packageName, packageDisplayName,packageHelpText,Collections.unmodifiableSortedSet(walkersInPackage)));
+            helpText.add(new HelpEntry(packageName,packageDisplayName,packageHelpText,Collections.unmodifiableSortedSet(walkersInPackage)));
         }
 
         final int headerWidth = Math.max(longestPackageName+PACKAGE_INDENT,longestWalkerName+WALKER_INDENT);
@@ -250,9 +250,9 @@ class HelpEntryComparator implements Comparator<HelpEntry> {
      */
     public int compare(HelpEntry lhs, HelpEntry rhs) {
         if(lhs == null && rhs == null) return 0;
-        if(lhs == null) return 1;
-        if(rhs == null) return -1;
-        return textComparator.compare(lhs.displayName,rhs.displayName);
+        if(lhs == null || lhs.displayName.equals("")) return 1;
+        if(rhs == null || rhs.displayName.equals("")) return -1;
+        return lhs.displayName.equals(rhs.displayName) ? textComparator.compare(lhs.uid,rhs.uid) : textComparator.compare(lhs.displayName,rhs.displayName);
     }
 
 
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 4f5162697..575e8a8df 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -79,7 +79,7 @@ public class WalkerManager extends PluginManager<Walker> {
     public Map<String,Collection<Class<? extends Walker>>> getWalkerNamesByPackage() {
         Map<String,Collection<Class<? extends Walker>>> walkersByPackage = new HashMap<String,Collection<Class<? extends Walker>>>();
         for(Class<? extends Walker> walker: pluginsByName.values()) {
-            String walkerPackage = walker.getPackage().getName();
+            String walkerPackage = walker.getPackage() != null ? walker.getPackage().getName() : "<unpackaged>";
             if(!walkersByPackage.containsKey(walkerPackage))
                 walkersByPackage.put(walkerPackage,new ArrayList<Class<? extends Walker>>());
             walkersByPackage.get(walkerPackage).add(walker);