From a46e22ed13eccbd142fac40e3c5aa2db06a3ea97 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 30 Jun 2010 18:55:57 +0000
Subject: [PATCH] Refactored ArgumentDefinition to absorb functionality from
 ArgumentDefinition and ArgumentTypeDescriptor.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3689 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/queue/function/CommandLineFunction.scala       | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
index 0935ff6f7..d94ac998b 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.queue.function
 import org.broadinstitute.sting.queue.util._
 import java.lang.reflect.Field
 import java.lang.annotation.Annotation
-import org.broadinstitute.sting.commandline.{Input, Output, ArgumentDescription}
+import org.broadinstitute.sting.commandline.{Input, Output}
 
 trait CommandLineFunction extends InputOutputFunction with DispatchFunction {
   var properties = Map.empty[String, String]
@@ -49,8 +49,11 @@ trait CommandLineFunction extends InputOutputFunction with DispatchFunction {
     missing
   }
 
-  private def isRequired(field: Field, annotation: Class[_ <: Annotation]) =
-    new ArgumentDescription(field.getAnnotation(annotation)).required
+  private def isRequired(field: Field, annotationClass: Class[_ <: Annotation]) =
+    getAnnotationValue(field.getAnnotation(annotationClass), "required").asInstanceOf[Boolean]
+
+  private def getAnnotationValue(annotation: Annotation, method: String) =
+    annotation.getClass.getMethod(method).invoke(annotation)
 
   protected def hasFieldValue(field: Field) = hasValue(this.getFieldValue(field))