New uses DocumentedGATKFeatureObject instead of annotation directly

-- Step 1 on the way to creating a static list of additional classes that we want to document.

public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java

@@ -39,6 +39,5 @@ public @interface DocumentedGATKFeature {
     public boolean enable() default true;
     public String groupName();
     public String summary() default "";
-    public Class<? extends DocumentedGATKFeatureHandler> handler() default GenericDocumentationHandler.class;
     public Class[] extraDocs() default {};
 }

public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureObject.java

@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.help;
+
+/**
+ * Documentation unit.  Effectively a class version of the DocumentedGATKFeature
+ *
+ * @author depristo
+ */
+class DocumentedGATKFeatureObject {
+    final boolean enable;
+    final String groupName, summary;
+    final Class[] extraDocs;
+
+    public DocumentedGATKFeatureObject(final boolean enable, final String groupName, final String summary, final Class[] extraDocs) {
+        this.enable = enable;
+        this.groupName = groupName;
+        this.summary = summary;
+        this.extraDocs = extraDocs;
+    }
+
+    public boolean enable() { return enable; }
+    public String groupName() { return groupName; }
+    public String summary() { return summary; }
+    public Class[] extraDocs() { return extraDocs; }
+}

public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java

@@ -51,7 +51,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
     /** The javadoc documentation for clazz */
     final ClassDoc classDoc;
     /** The annotation that lead to this Class being in GATKDoc */
-    final DocumentedGATKFeature annotation;
+    final DocumentedGATKFeatureObject annotation;
     /** When was this walker built, and what's the absolute version number */
     final String buildTimestamp, absoluteVersion;
 
@@ -60,7 +60,7 @@ class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
     Map<String, Object> forTemplate;
 
     public GATKDocWorkUnit(String name, String filename, String group,
-                           DocumentedGATKFeature annotation, DocumentedGATKFeatureHandler handler,
+                           DocumentedGATKFeatureObject annotation, DocumentedGATKFeatureHandler handler,
                            ClassDoc classDoc, Class clazz,
                            String buildTimestamp, String absoluteVersion) {
         this.annotation = annotation;

public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java

@@ -99,7 +99,7 @@ public class GATKDoclet {
             //if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance"))
             //    logger.debug("foo");
 
-            DocumentedGATKFeature feature = getFeatureForClassDoc(doc);
+            DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc);
             DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
             if ( handler != null && handler.includeInDocs(doc) ) {
                 logger.info("Generating documentation for class " + doc);
@@ -146,31 +146,26 @@ public class GATKDoclet {
         }
     }
 
-    private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeature feature) {
+    private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeatureObject feature) {
-        try {
         if ( feature != null ) {
             if ( feature.enable() ) {
-                    DocumentedGATKFeatureHandler handler = feature.handler().newInstance();
+                DocumentedGATKFeatureHandler handler = new GenericDocumentationHandler();
                 handler.setDoclet(this);
                 return handler;
             } else {
                 logger.info("Skipping disabled Documentation for " + doc);
             }
         }
-        } catch ( IllegalAccessException e) {
-            throw new RuntimeException(e); // the constructor is now private -- this is an error
-        } catch ( InstantiationException e) {
-            throw new RuntimeException(e); // the constructor is now private -- this is an error
-        }
 
         return null;
     }
 
-    private DocumentedGATKFeature getFeatureForClassDoc(ClassDoc doc) {
+    private DocumentedGATKFeatureObject getFeatureForClassDoc(ClassDoc doc) {
-        // todo -- what do I need the ? extends Object to pass the compiler?
         Class<? extends Object> docClass = getClassForClassDoc(doc);
+        // todo -- add looked here to static TO DOC collection as well
         if ( docClass != null && docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
-            return docClass.getAnnotation(DocumentedGATKFeature.class);
+            DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class);
+            return new DocumentedGATKFeatureObject(f.enable(), f.groupName(), f.summary(), f.extraDocs());
         } else {
             return null; // not annotated so it shouldn't be documented
         }
@@ -217,7 +212,7 @@ public class GATKDoclet {
 
         Collections.sort(indexData);
 
-        Set<DocumentedGATKFeature> docFeatures = new HashSet<DocumentedGATKFeature>();
+        Set<DocumentedGATKFeatureObject> docFeatures = new HashSet<DocumentedGATKFeatureObject>();
         List<Map<String, String>> data = new ArrayList<Map<String, String>>();
         for ( GATKDocWorkUnit workUnit : indexData ) {
             data.add(workUnit.indexDataMap());
@@ -225,7 +220,7 @@ public class GATKDoclet {
         }
 
         List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
-        for ( DocumentedGATKFeature feature : docFeatures ) {
+        for ( DocumentedGATKFeatureObject feature : docFeatures ) {
             groups.add(toMap(feature));
         }
 
@@ -237,7 +232,7 @@ public class GATKDoclet {
         return root;
     }
 
-    private static final Map<String, String> toMap(DocumentedGATKFeature annotation) {
+    private static final Map<String, String> toMap(DocumentedGATKFeatureObject annotation) {
         Map<String, String> root = new HashMap<String, String>();
         root.put("name", annotation.groupName());
         root.put("summary", annotation.summary());