Generalized handler to allow it to be used with any arbitrary class structure.

DocumentedGATKFeature now includes a field for the group name.
Build.xml works with public / private now.

build.xml

@@ -457,8 +457,9 @@
         </javadoc>
     </target>
 
-    <target name="walkerdocs" unless="uptodate.extracthelp"
+    <target name="gatkdocs" unless="uptodate.extracthelp" depends="gatk.compile"
 	        description="Extract help key/value pair file from the JavaDoc tags.">
+        <property name="gatk.target" value="private"/>
         <path id="doclet.classpath">
             <path refid="external.dependencies" />
             <pathelement location="${java.classes}" />

public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.WalkerDocumentationHandler;
+import org.broadinstitute.sting.utils.help.GenericDocumentationHandler;
 
 import java.util.List;
 
@@ -46,7 +46,7 @@ import java.util.List;
 @ReadFilters(MalformedReadFilter.class)
 @PartitionBy(PartitionType.NONE)
 @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@DocumentedGATKFeature( handler = WalkerDocumentationHandler.class )
+@DocumentedGATKFeature( groupName = "GATK walkers" )
 public abstract class Walker<MapType, ReduceType> {
     final protected static Logger logger = Logger.getLogger(Walker.class);
     private GenomeAnalysisEngine toolkit;

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

@@ -36,5 +36,6 @@ import java.lang.annotation.*;
 @Retention(RetentionPolicy.RUNTIME)
 @Target(ElementType.TYPE)
 public @interface DocumentedGATKFeature {
-    Class<? extends DocumentedGATKFeatureHandler> handler();
+    String groupName();
+    Class<? extends DocumentedGATKFeatureHandler> handler() default GenericDocumentationHandler.class;
 }

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

@@ -49,6 +49,7 @@ import java.util.Map;
  */
 public abstract class DocumentedGATKFeatureHandler {
     private GATKDoclet doclet;
+    private String groupName;
 
     protected RootDoc getRootDoc() {
         return this.doclet.rootDoc;
@@ -64,7 +65,14 @@ public abstract class DocumentedGATKFeatureHandler {
         return ResourceBundleExtractorDoclet.getClassName(doc).replace(".", "_") + ".html";
     }
 
-    public abstract String getGroupName();
+    final public String getGroupName() {
+        return groupName;
+    }
+
+    final public void setGroupName(String groupName) {
+        this.groupName = groupName;
+    }
+
     public abstract String getTemplateName(ClassDoc doc) throws IOException;
     public abstract GATKDoclet.DocumentationData processOne(ClassDoc doc);
 }

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

@@ -110,6 +110,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
 
             List<DocumentationData> indexData = new ArrayList<DocumentationData>();
             for ( ClassDoc doc : rootDoc.classes() ) {
+                System.out.printf("Considering %s%n", doc);
                 DocumentedGATKFeatureHandler handler = getHandlerForClassDoc(doc);
                 if ( handler != null && handler.shouldBeProcessed(doc) ) {
                     DocumentationData docData = processDocumentationWithHandler(cfg, handler, doc);
@@ -132,6 +133,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
             if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
                 DocumentedGATKFeature feature = docClass.getAnnotation(DocumentedGATKFeature.class);
                 DocumentedGATKFeatureHandler handler = feature.handler().newInstance();
+                handler.setGroupName(feature.groupName());
                 handler.setDoclet(this);
                 return handler;
             } else {
@@ -152,7 +154,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
 
     private void processIndex(Configuration cfg, List<DocumentationData> indexData) throws IOException {
         /* Get or create a template */
-        Template temp = cfg.getTemplate("walker.index.template.html");
+        Template temp = cfg.getTemplate("generic.index.template.html");
 
         /* Merge data-model with template */
         Writer out = new OutputStreamWriter(new FileOutputStream(new File("testdoc/index.html")));

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

@@ -48,7 +48,7 @@ import java.util.Map;
 /**
  *
  */
-public class WalkerDocumentationHandler extends DocumentedGATKFeatureHandler {
+public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     @Override
     public boolean shouldBeProcessed(ClassDoc doc) {
         try {
@@ -59,17 +59,14 @@ public class WalkerDocumentationHandler extends DocumentedGATKFeatureHandler {
         }
     }
 
-    @Override
-    public String getGroupName() { return "GATK Walkers"; }
-
     @Override
     public String getTemplateName(ClassDoc doc) throws IOException {
-        return "walker.template.html";
+        return "generic.template.html";
     }
 
     @Override
     public GATKDoclet.DocumentationData processOne(ClassDoc doc) {
-        System.out.printf("Walker class %s%n", doc);
+        System.out.printf("%s class %s%n", getGroupName(), doc);
         Map<String, Object> root = buildWalkerDataModel(doc); // Create the root hash
         return new GATKDoclet.DocumentationData(doc.name(), (String)root.get("summary"), root);
     }
@@ -136,9 +133,9 @@ public class WalkerDocumentationHandler extends DocumentedGATKFeatureHandler {
     }
 
     private FieldDoc getFieldDoc(ClassDoc classDoc, String name, boolean primary) {
-        System.out.printf("Looking for %s in %s%n", name, classDoc.name());
+        //System.out.printf("Looking for %s in %s%n", name, classDoc.name());
         for ( FieldDoc fieldDoc : classDoc.fields(false) ) {
-            System.out.printf("fieldDoc " + fieldDoc + " name " + fieldDoc.name());
+            //System.out.printf("fieldDoc " + fieldDoc + " name " + fieldDoc.name());
             if ( fieldDoc.name().equals(name) )
                 return fieldDoc;