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The tagger was automatically combining identical tags, but this is a problem 

for the ROD system.  Eliminate tag combine operation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4121 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-08-25 22:01:32 +00:00
parent 39da567d48
commit bdb3a7ebe6
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -230,11 +230,11 @@ public abstract class ArgumentTypeDescriptor {
* @return The value of the argument if available, or null if not present. * @return The value of the argument if available, or null if not present.
*/ */
protected List<String> getArgumentTags(ArgumentMatches matches) { protected List<String> getArgumentTags(ArgumentMatches matches) {
Set<String> tags = new LinkedHashSet<String>(); List<String> tags = new ArrayList<String>();
for( ArgumentMatch match: matches ) { for( ArgumentMatch match: matches ) {
tags.addAll(match.tags); tags.addAll(match.tags);
} }
return new ArrayList<String>(tags); return tags;
} }
/** /**
@ -395,7 +395,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
public Object parse(ParsingEngine parsingEngine,ArgumentSource source, Class type, ArgumentMatches matches) { public Object parse(ParsingEngine parsingEngine,ArgumentSource source, Class type, ArgumentMatches matches) {
Class componentType; Class componentType;
Object result; Object result;
Set<String> tags = new LinkedHashSet<String>(); List<String> tags = new ArrayList<String>();
if( Collection.class.isAssignableFrom(type) ) { if( Collection.class.isAssignableFrom(type) ) {
@ -456,7 +456,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
throw new StingException("Unsupported compound argument type: " + type); throw new StingException("Unsupported compound argument type: " + type);
// WARNING: Side effect! // WARNING: Side effect!
parsingEngine.addTags(result,new ArrayList<String>(tags)); parsingEngine.addTags(result,tags);
return result; return result;
} }