From f7097c8ee71f79d91a81ab529e3e5f147952efcd Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 26 Mar 2009 21:24:12 +0000
Subject: [PATCH] Cleanup.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@205 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/cmdLine/ArgumentParser.java   | 36 ++++++++++++-------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
index eabe3f3b5..37cc4f749 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
@@ -356,7 +356,7 @@ public class ArgumentParser {
      * will be alone a set.  Every option should appear in exactly one set.
      * WARNING: Has no concept of nested dependencies.
      * @param fields list of fields for which to check options.
-     * @return
+     * @return groupings of mutually exclusive options.
      */
     private List<Set<Field>> groupExclusiveOptions( Field[] fields ) {
         List<Set<Field>> optionGroups = new ArrayList<Set<Field>>();
@@ -414,30 +414,42 @@ public class ArgumentParser {
         String shortName = (argument.shortName().length() != 0) ? argument.shortName() : fullName.substring(0,1);
         if(shortName.length() != 1)
             throw new IllegalArgumentException("Invalid short name: " + shortName);
+        String description = argument.doc();
+        boolean isRequired = argument.required();
         boolean isFlag = (field.getType() == Boolean.class) || (field.getType() == Boolean.TYPE);
         boolean isCollection = field.getType().isArray() || Collection.class.isAssignableFrom(field.getType());
 
         if( isFlag && isCollection )
             throw new IllegalArgumentException("Can't have an array of flags.");
 
-        String description = String.format("[%s] %s", sourceName, argument.doc());
-
-        OptionBuilder ob = OptionBuilder.withLongOpt(fullName);
+        OptionBuilder.withLongOpt(fullName);
         if( !isFlag ) {
-            ob = ob.withArgName(fullName);
-            ob = isCollection ? ob.hasArgs() : ob.hasArg();
+            OptionBuilder.withArgName(fullName);
+            if( isCollection )
+                OptionBuilder.hasArgs();
+            else
+                OptionBuilder.hasArg();
         }
-        if( argument.required() ) {
-            ob = ob.isRequired();
-            description = String.format("[%s] (Required Option) %s", sourceName, argument.doc());
+        if( isRequired ) {
+            OptionBuilder.isRequired();
+            description = String.format("(Required Option) %s", description);
         }
-        if( description.length() != 0 ) ob = ob.withDescription( description );
 
-        Option option = ob.create( shortName );
+        sourceName = sourceName.trim();
+        if( sourceName.length() > 0 )
+            description = String.format("[%s] %s", sourceName, description );
 
-        return option;
+        if( description.length() != 0 ) OptionBuilder.withDescription( description );
+
+        return OptionBuilder.create( shortName );
     }
 
+    /**
+     * Constructs a command-line argument given a string and field.
+     * @param f Field type from which to infer the type.
+     * @param strs Collection of parameter strings to parse.
+     * @return Parsed object of the inferred type.
+     */
     private Object constructFromString(Field f, String[] strs) {
         Class type = f.getType();