Improved header and argument details

Argument detail structure cleaned up. Only relevant pieces of information are shown now, and in a cleaner layout.
Misc. cleanup in the code.

public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java

@@ -186,6 +186,10 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
     @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 { ONE, TWO };
 
     final DiffEngine diffEngine = new DiffEngine();

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

@@ -75,7 +75,6 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         addArgumentBindings(root);
         addRelatedBindings(root);
 
-        //System.out.printf("Root is %s%n", root);
         toProcess.setHandlerContent((String)root.get("summary"), root);
     }
 
@@ -110,7 +109,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             for ( ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(classdoc)) ) {
                 ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
                 FieldDoc fieldDoc = getFieldDoc(classdoc, argumentSource.field.getName());
-                GATKDoc doc = docForArgument(fieldDoc, argDef); // todo -- why can you have multiple ones?
+                GATKDoc doc = 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";
@@ -216,7 +215,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             return null;
     }
 
-    protected GATKDoc docForArgument(FieldDoc fieldDoc, ArgumentDefinition def) {
+    protected GATKDoc docForArgument(FieldDoc fieldDoc, ArgumentSource source, ArgumentDefinition def) {
         final String name = def.fullName != null ? "--" + def.fullName : "-" + def.shortName;
         GATKDoc doc = new GATKDoc(GATKDoc.DocType.WALKER_ARG, name);
 
@@ -228,17 +227,23 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         if ( def.doc != null ) doc.setSummary(def.doc);
 
         List<String> attributes = new ArrayList<String>();
-        attributes.add(def.ioType.annotationClass.getSimpleName());
+        // this one below is just too much.
+        //attributes.add(def.ioType.annotationClass.getSimpleName());
         if ( def.required ) attributes.add("required");
-        if ( def.isFlag ) attributes.add("flag");
+        // flag is just boolean, not interesting
+        //if ( def.isFlag ) attributes.add("flag");
         if ( def.isHidden ) attributes.add("hidden");
-        doc.addTag("attributes", Utils.join(",", attributes));
+        if ( source.isDeprecated() ) attributes.add("depreciated");
+        if ( attributes.size() > 0 )
+            doc.addTag("attributes", Utils.join(", ", attributes));
 
-        // todo -- need depreciated value
+        if ( def.validOptions != null ) {
+            //source.field.getType().isEnum();
+            // todo -- what's the best way to link to these docs?  Maybe a separate section on enums?
+            doc.addTag("options", Utils.join(", ", def.validOptions));
+        }
 
-        doc.addTag("options", def.validOptions == null ? GATKDoc.NA_STRING : Utils.join(",", def.validOptions));
+        doc.setFulltext(fieldDoc.commentText().equals("") ? GATKDoc.NA_STRING : fieldDoc.commentText());
-
-        doc.setFulltext(fieldDoc.commentText());
 
         return doc;
     }

settings/helpTemplates/generic.template.html

@@ -18,12 +18,10 @@
 </#macro>    
    
 <#macro argumentDetails arg>
-    <h3><a name="${arg.name}">${arg.name} / ${arg.synonyms}</a></h3>
+    <h3><a name="${arg.name}">${arg.name} / ${arg.synonyms}</a>
-    Summary: ${arg.summary}<br>
+    (<#if arg.attributes??>${arg.attributes} </#if>${arg.type})</h3>
-    Attributes: ${arg.attributes}<br>
+    ${arg.summary}. ${arg.fulltext}<br>
-    Type: ${arg.type}<br> 
+    <#if arg.options??>TODO: document enum in line here.  Possible values ${arg.options}</#if>
-    Options: ${arg.options}<br> 
-    Details: ${arg.fulltext}<br>
 </#macro>     
    
 <#macro relatedByType name type>

settings/helpTemplates/style.css

@@ -16,7 +16,7 @@ p, ul, ol, dl, dt, dd, td
 
 p.version, p.see-also
 {
-	font-size: 6pt;
+	font-size: 8pt;
 }
 
 dt