Improvements to GATKDocs

-- Now supports a static list of root classes / interfaces that should receive docs.  A complementary approach to documenting features to the DocumentedGATKFeature annotation
-- Tribble codecs are now documented!
-- No longer displayed sub and super classes

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

@@ -30,17 +30,24 @@ package org.broadinstitute.sting.utils.help;
  * @author depristo
  */
 class DocumentedGATKFeatureObject {
-    final boolean enable;
+    private final Class classToDoc;
-    final String groupName, summary;
+    private final boolean enable;
-    final Class[] extraDocs;
+    private final String groupName, summary;
+    private final Class[] extraDocs;
 
-    public DocumentedGATKFeatureObject(final boolean enable, final String groupName, final String summary, final Class[] extraDocs) {
+    public DocumentedGATKFeatureObject(Class classToDoc, final boolean enable, final String groupName, final String summary, final Class[] extraDocs) {
+        this.classToDoc = classToDoc;
         this.enable = enable;
         this.groupName = groupName;
         this.summary = summary;
         this.extraDocs = extraDocs;
     }
 
+    public DocumentedGATKFeatureObject(Class classToDoc, final String groupName, final String summary) {
+        this(classToDoc, true, groupName, summary, new Class[]{});
+    }
+
+    public Class getClassToDoc() { return classToDoc; }
     public boolean enable() { return enable; }
     public String groupName() { return groupName; }
     public String summary() { return summary; }

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

@@ -33,6 +33,7 @@ import freemarker.template.TemplateException;
 import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
+import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
@@ -50,6 +51,14 @@ public class GATKDoclet {
 
     RootDoc rootDoc;
 
+    final static Collection<DocumentedGATKFeatureObject> STATIC_DOCS = new ArrayList<DocumentedGATKFeatureObject>();
+    static {
+        STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class,
+                "Reference ordered data (ROD) codecs",
+                "Tribble codecs for reading reference ordered data such as VCF or BED files"));
+    }
+
+
     /**
      * Extracts the contents of certain types of javadoc and adds them to an XML file.
      * @param rootDoc The documentation root.
@@ -162,12 +171,20 @@ public class GATKDoclet {
 
     private DocumentedGATKFeatureObject getFeatureForClassDoc(ClassDoc doc) {
         Class<? extends Object> docClass = getClassForClassDoc(doc);
-        // todo -- add looked here to static TO DOC collection as well
+
-        if ( docClass != null && docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
+        if ( docClass == null )
-            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
+
+        if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
+            DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class);
+            return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs());
+        } else {
+            for ( DocumentedGATKFeatureObject staticDocs : STATIC_DOCS ) {
+                if ( staticDocs.getClassToDoc().isAssignableFrom(docClass) ) {
+                    return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs());
+                }
+            }
+            return null;
         }
     }
 
@@ -212,16 +229,15 @@ public class GATKDoclet {
 
         Collections.sort(indexData);
 
-        Set<DocumentedGATKFeatureObject> docFeatures = new HashSet<DocumentedGATKFeatureObject>();
+        List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
+        Set<String> seenDocumentationFeatures = new HashSet<String>();
         List<Map<String, String>> data = new ArrayList<Map<String, String>>();
         for ( GATKDocWorkUnit workUnit : indexData ) {
             data.add(workUnit.indexDataMap());
-            docFeatures.add(workUnit.annotation);
+            if ( ! seenDocumentationFeatures.contains(workUnit.annotation.groupName()) ) {
-        }
+                groups.add(toMap(workUnit.annotation));
-
+                seenDocumentationFeatures.add(workUnit.annotation.groupName());
-        List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
+            }
-        for ( DocumentedGATKFeatureObject feature : docFeatures ) {
-            groups.add(toMap(feature));
         }
 
         root.put("data", data);

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

@@ -255,21 +255,21 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
                         put("name", otherUnit.name);}});
 
         }
-
-        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);
         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) {