From c43b5981f2507f2cdd8f1c59155a22e20f0d85d8 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 24 Jul 2011 20:52:44 -0400
Subject: [PATCH] Hidden variables are hidden by default.  Settable by command
 line option

DiffObjectsWalker test arguments removed.
Minor refactoring of GATKDoclet
---
 .../walkers/diffengine/DiffObjectsWalker.java  | 15 ---------------
 .../help/DocumentedGATKFeatureHandler.java     |  4 ++++
 .../sting/utils/help/GATKDoclet.java           |  9 ++++++++-
 .../help/GenericDocumentationHandler.java      | 18 +++++++++++-------
 4 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index c660bda36..fb7e6b579 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -182,21 +182,6 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @Argument(fullName="showItemizedDifferences", shortName="SID", doc="Should we enumerate all differences between the files?", required=false)
     boolean showItemizedDifferences = false;
 
-    @Hidden
-    @Argument(fullName="testEnum", doc="X", required=false)
-    TestEnum testEnum = TestEnum.ONE;
-
-    @Deprecated
-    @Argument(fullName="testDepreciates", doc="Y", required=false)
-    int dontUseMe = 1;
-
-    public enum TestEnum {
-        /** Docs for ONE */
-        ONE,
-        /** Docs for TWO */
-        TWO
-    };
-
     final DiffEngine diffEngine = new DiffEngine();
 
     @Override
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
index 2227f9aba..366df0c3a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
@@ -44,6 +44,10 @@ public abstract class DocumentedGATKFeatureHandler {
         this.doclet = doclet;
     }
 
+    public GATKDoclet getDoclet() {
+        return doclet;
+    }
+
     public boolean shouldBeProcessed(ClassDoc doc) { return true; }
 
     public String getDestinationFilename(ClassDoc doc) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
index 2c8746f61..b4ab3b98e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
@@ -45,6 +45,7 @@ public class GATKDoclet {
     final protected static File DESTINATION_DIR = new File("gatkdocs");
     final protected static Logger logger = Logger.getLogger(GATKDoclet.class);
     protected static String buildTimestamp = null, absoluteVersion = null;
+    protected static boolean showHiddenFeatures = false;
 
     RootDoc rootDoc;
 
@@ -61,6 +62,8 @@ public class GATKDoclet {
                 buildTimestamp = options[1];
             if (options[0].equals("-absolute-version"))
                 absoluteVersion = options[1];
+            if (options[0].equals("-include-hidden"))
+                showHiddenFeatures = true;
         }
 
         GATKDoclet doclet = new GATKDoclet();
@@ -74,12 +77,16 @@ public class GATKDoclet {
      * @return Number of potential parameters; 0 if not supported.
      */
     public static int optionLength(String option) {
-        if(option.equals("-build-timestamp") || option.equals("-absolute-version") ) {
+        if(option.equals("-build-timestamp") || option.equals("-absolute-version") || option.equals("-include-hidden")) {
             return 2;
         }
         return 0;
     }
 
+    public boolean showHiddenFeatures() {
+        return showHiddenFeatures;
+    }
+
     public Set<GATKDocWorkUnit> workUnits() {
         TreeSet<GATKDocWorkUnit> m = new TreeSet<GATKDocWorkUnit>();
 
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 1aef110eb..8773fc4f8 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -113,13 +113,17 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
                 ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
                 FieldDoc fieldDoc = getFieldDoc(classdoc, argumentSource.field.getName());
                 Map<String, Object> argBindings = docForArgument(fieldDoc, argumentSource, argDef); // todo -- why can you have multiple ones?
-                String kind = "optional";
-                if ( argumentSource.isRequired() ) kind = "required";
-                else if ( argumentSource.isHidden() ) kind = "hidden";
-                else if ( argumentSource.isDeprecated() ) kind = "depreciated";
-                args.get(kind).add(argBindings);
-                args.get("all").add(argBindings);
-                System.out.printf("Processing %s%n", argumentSource);
+                if ( ! argumentSource.isHidden() || getDoclet().showHiddenFeatures() ) {
+                    System.out.printf("Processing %s%n", argumentSource);
+                    String kind = "optional";
+                    if ( argumentSource.isRequired() ) kind = "required";
+                    else if ( argumentSource.isHidden() ) kind = "hidden";
+                    else if ( argumentSource.isDeprecated() ) kind = "depreciated";
+                    args.get(kind).add(argBindings);
+                    args.get("all").add(argBindings);
+                } else {
+                    System.out.printf("Skipping hidden feature %s%n", argumentSource);
+                }
             }
         } catch ( ClassNotFoundException e ) {
             throw new RuntimeException(e);