From dfce301bebd62275ad55d326dd2801cbbce47d81 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 23 Sep 2011 09:03:04 -0400
Subject: [PATCH] Looks for @Hidden annotation on all classes and excludes them
 from the docs

---
 .../sting/utils/help/GenericDocumentationHandler.java          | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index 4f1e95499..7ea77a939 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -66,7 +66,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     public boolean includeInDocs(ClassDoc doc) {
         try {
             Class type = HelpUtils.getClassForDoc(doc);
-            return JVMUtils.isConcrete(type);
+            boolean hidden = ! getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class);
+            return ! hidden && JVMUtils.isConcrete(type);
         } catch ( ClassNotFoundException e ) {
             return false;
         }