From faa3f8b6f6b8305b21212dc733135b85066c9d78 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 18 Aug 2011 14:04:47 -0400
Subject: [PATCH] Only concrete classes are now documented

---
 .../sting/gatk/CommandLineGATK.java           |  2 +-
 .../help/GenericDocumentationHandler.java     | 28 +++++--------------
 2 files changed, 8 insertions(+), 22 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 60aea9928..b8488dc9a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -50,7 +50,7 @@ import java.util.*;
 @DocumentedGATKFeature(
         groupName = "GATK Engine",
         summary = "Features and arguments for the GATK engine itself, available to all walkers.",
-        extraDocs = { ReadFilter.class, UserException.class })
+        extraDocs = { UserException.class })
 public class CommandLineGATK extends CommandLineExecutable {
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     private String analysisName = null;
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 b4d82f0e8..5b358519e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -52,13 +52,13 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
     @Override
     public boolean includeInDocs(ClassDoc doc) {
-        return true;
-//        try {
-//            Class type = HelpUtils.getClassForDoc(doc);
-//            return JVMUtils.isConcrete(type);
-//        } catch ( ClassNotFoundException e ) {
-//            return false;
-//        }
+//        return true;
+        try {
+            Class type = HelpUtils.getClassForDoc(doc);
+            return JVMUtils.isConcrete(type);
+        } catch ( ClassNotFoundException e ) {
+            return false;
+        }
     }
 
 
@@ -256,20 +256,6 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
 
         }
         root.put("extradocs", extraDocsData);
-
-
-//        List<Map<String, Object>> hierarchyDocs = new ArrayList<Map<String, Object>>();
-//        for (final GATKDocWorkUnit other : all ) {
-//            final String relation = classRelationship(toProcess.clazz, other.clazz);
-//            if ( relation != null )
-//                hierarchyDocs.add(
-//                        new HashMap<String, Object>(){{
-//                            put("filename", other.filename);
-//                            put("relation", relation);
-//                            put("name", other.name);}});
-//
-//        }
-//        root.put("relatedDocs", hierarchyDocs);
     }
 
     private static final String classRelationship(Class me, Class other) {