Implemented see also and version header

build.xml

@@ -479,7 +479,7 @@
                  docletpathref="doclet.classpath"
                  classpathref="external.dependencies"
                  classpath="${java.classes}"
-                 additionalparam="-private -build-timestamp "${build.timestamp}" -absolute-version ${build.version} -out ${basedir}/${resource.path} -quiet -J-Xdebug -J-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005">
+                 additionalparam="-private -build-timestamp "${build.timestamp}" -absolute-version ${build.version} -quiet -J-Xdebug -J-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005">
             <sourcefiles>
                 <union>
                     <fileset refid="all.java.source.files"/>

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

@@ -48,18 +48,21 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
 
     public static class DocWorkUnit implements Comparable<DocWorkUnit> {
         // known at the start
-        String name, filename, group;
+        final String name, filename, group;
-        DocumentedGATKFeatureHandler handler;
+        final DocumentedGATKFeatureHandler handler;
-        ClassDoc classDoc;
+        final ClassDoc classDoc;
-        Class clazz;
+        final Class clazz;
-        DocumentedGATKFeature annotation;
+        final DocumentedGATKFeature annotation;
+        final String buildTimestamp, absoluteVersion;
 
         // set by the handler
         String summary;
         Map<String, Object> forTemplate;
 
-        public DocWorkUnit(DocumentedGATKFeature annotation, String name, String filename, String group,
+        public DocWorkUnit(String name, String filename, String group,
-                           DocumentedGATKFeatureHandler handler, ClassDoc classDoc, Class clazz) {
+                           DocumentedGATKFeature annotation, DocumentedGATKFeatureHandler handler,
+                           ClassDoc classDoc, Class clazz,
+                           String buildTimestamp, String absoluteVersion) {
             this.annotation = annotation;
             this.name = name;
             this.filename = filename;
@@ -67,6 +70,8 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
             this.handler = handler;
             this.classDoc = classDoc;
             this.clazz = clazz;
+            this.buildTimestamp = buildTimestamp;
+            this.absoluteVersion = absoluteVersion;
         }
 
         public void setHandlerContent(String summary, Map<String, Object> forTemplate) {
@@ -116,9 +121,10 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
             DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
             if ( handler != null && handler.shouldBeProcessed(doc) ) {
                 String filename = handler.getDestinationFilename(doc);
-                DocWorkUnit unit = new DocWorkUnit(feature,
+                DocWorkUnit unit = new DocWorkUnit(doc.name(),
-                        doc.name(), filename, feature.groupName(),
+                        filename, feature.groupName(),
-                        handler, doc, clazz );
+                        feature, handler, doc, clazz,
+                        buildTimestamp, absoluteVersion);
                 m.add(unit);
             }
         }
@@ -130,6 +136,7 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
     protected void processDocs(RootDoc rootDoc, PrintStream ignore) {
         // setup the global access to the root
         this.rootDoc = rootDoc;
+        super.loadData(rootDoc, false);
 
         try {
             // basic setup
@@ -239,6 +246,8 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
 
         root.put("data", data);
         root.put("groups", groups);
+        root.put("timestamp", buildTimestamp);
+        root.put("version", absoluteVersion);
 
         return root;
     }

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

@@ -88,6 +88,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
              summaryBuilder.append(tag.text());
         root.put("summary", summaryBuilder.toString());
         root.put("description", classdoc.commentText());
+        root.put("timestamp", toProcess.buildTimestamp);
+        root.put("version", toProcess.absoluteVersion);
 
         for(Tag tag: classdoc.tags()) {
             root.put(tag.name(), tag.text());

settings/helpTemplates/common.html

@@ -4,3 +4,12 @@
     <link href="style.css" type="text/css" rel="stylesheet"> 
   </head>
 </#macro>
+
+<#macro headerInfo>
+    <p class="see-also">See also <a href="index.html">Main index</a> | <a href="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit">GATK wiki</a> | <a href="http://getsatisfaction.com/gsa">GATK support forum</a></p>
+    <p class="version">GATK version ${version} built at ${timestamp}.</p>
+</#macro>
+
+<#macro footerInfo>
+</#macro>
+

settings/helpTemplates/generic.index.template.html

@@ -25,9 +25,12 @@
 <@makeHeader title="GATK documentation index"/>
 <body>
   <h1>GATK documentation index</h1>
+  <@headerInfo />
   <#list groups as group>
     <@emitGroup group=group/>
   </#list>
+  
+  <@footerInfo />
 </body>
 </html>
 

settings/helpTemplates/generic.template.html

@@ -45,7 +45,8 @@
 <html>
 <@makeHeader title="${name} documentation"/>
 <body>
-  <h1>${name}<h1>
+  <h1>${name}</h1>
+  <@headerInfo />
   <h2>Brief summary</h2>
   ${summary}
   <#if author??>
@@ -104,5 +105,7 @@
         <@argumentDetails arg=arg/>
       </#list>
   </#if>
+  
+  <@footerInfo />
 </body>
 </html>

settings/helpTemplates/style.css

@@ -14,6 +14,11 @@ p, ul, ol, dl, dt, dd, td
 	font-size: 12pt;
 }
 
+p.version, p.see-also
+{
+	font-size: 6pt;
+}
+
 dt
 { 
 	padding-bottom: 6pt;
@@ -35,7 +40,7 @@ a:visited
 h1, h2, h3
 {
 	font-family: Corbel, Arial, Helvetica, Sans-Serif;
-	font-weight: lighter;
+	font-weight: bold;
 	text-align: left;
 	color: #bac8da;
 }