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Better handling of nulls output by 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2296 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-09 19:34:56 +00:00
parent 40c2d7a4bc
commit 1d2151adcf
2 changed files with 5 additions and 5 deletions
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8
java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -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);
}

2
java/src/org/broadinstitute/sting/gatk/WalkerManager.java
View File

@ -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);