Help now points to GATKDocs instead of spitting out full, garbled description

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.help.GATKDoclet;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
@@ -175,12 +176,8 @@ public class CommandLineGATK extends CommandLineExecutable {
         StringBuilder additionalHelp = new StringBuilder();
         Formatter formatter = new Formatter(additionalHelp);
 
-        formatter.format("Description:%n");
+        formatter.format("For a full description of this walker, see its GATKdocs at:%n");
-
+        formatter.format("%s%n", GATKDoclet.helpLinksToGATKDocs(walkerType));
-        WalkerManager walkerManager = engine.getWalkerManager();
-        String walkerHelpText = walkerManager.getWalkerDescriptionText(walkerType);
-
-        printDescriptorLine(formatter,WALKER_INDENT,"",WALKER_INDENT,FIELD_SEPARATOR,walkerHelpText,TextFormattingUtils.DEFAULT_LINE_WIDTH);
 
         return additionalHelp.toString();
     }
@@ -194,8 +191,6 @@ public class CommandLineGATK extends CommandLineExecutable {
         StringBuilder additionalHelp = new StringBuilder();
         Formatter formatter = new Formatter(additionalHelp);
 
-        formatter.format("Available analyses:%n");
-
         // Get the list of walker names from the walker manager.
         WalkerManager walkerManager = engine.getWalkerManager();
 

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

@@ -50,8 +50,8 @@ public abstract class DocumentedGATKFeatureHandler {
 
     public boolean shouldBeProcessed(ClassDoc doc) { return true; }
 
-    public String getDestinationFilename(ClassDoc doc) {
+    public String getDestinationFilename(ClassDoc doc, Class clazz) {
-        return HelpUtils.getClassName(doc).replace(".", "_") + ".html";
+        return GATKDoclet.htmlFilenameForClass(clazz);
     }
 
     public abstract String getTemplateName(ClassDoc doc) throws IOException;

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

@@ -30,19 +30,29 @@ import java.util.HashMap;
 import java.util.Map;
 
 /**
-* Created by IntelliJ IDEA.
+ * Simple collection of all relevant information about something the GATKDoclet can document
-* User: depristo
+ *
-* Date: 7/24/11
+ * Created by IntelliJ IDEA.
-* Time: 7:59 PM
+ * User: depristo
-* To change this template use File | Settings | File Templates.
+ * Date: 7/24/11
-*/
+ * Time: 7:59 PM
-public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
+ */
-    // known at the start
+class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
-    final String name, filename, group;
+    /** The class that's being documented */
-    final DocumentedGATKFeatureHandler handler;
-    final ClassDoc classDoc;
     final Class clazz;
+    /** The name of the thing we are documenting */
+    final String name;
+    /** the filename where we will be writing the docs for this class */
+    final String filename;
+    /** The name of the documentation group (e.g., walkers, read filters) class belongs to */
+    final String group;
+    /** The documentation handler for this class */
+    final DocumentedGATKFeatureHandler handler;
+    /** The javadoc documentation for clazz */
+    final ClassDoc classDoc;
+    /** The annotation that lead to this Class being in GATKDoc */
     final DocumentedGATKFeature annotation;
+    /** When was this walker built, and what's the absolute version number */
     final String buildTimestamp, absoluteVersion;
 
     // set by the handler
@@ -64,12 +74,21 @@ public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
         this.absoluteVersion = absoluteVersion;
     }
 
+    /**
+     * Called by the GATKDoclet to set handler provided context for this work unit
+     * @param summary
+     * @param forTemplate
+     */
     public void setHandlerContent(String summary, Map<String, Object> forTemplate) {
         this.summary = summary;
         this.forTemplate = forTemplate;
     }
 
-    public Map<String, String> toMap() {
+    /**
+     * Return a String -> String map suitable for FreeMarker to create an index to this WorkUnit
+     * @return
+     */
+    public Map<String, String> indexDataMap() {
         Map<String, String> data = new HashMap<String, String>();
         data.put("name", name);
         data.put("summary", summary);
@@ -78,6 +97,11 @@ public class GATKDocWorkUnit implements Comparable<GATKDocWorkUnit> {
         return data;
     }
 
+    /**
+     * Sort in order of the name of this WorkUnit
+     * @param other
+     * @return
+     */
     public int compareTo(GATKDocWorkUnit other) {
         return this.name.compareTo(other.name);
     }

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

@@ -42,6 +42,9 @@ import java.util.*;
  *
  */
 public class GATKDoclet {
+    private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
+    private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
+    private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
     final protected static File SETTINGS_DIR = new File("settings/helpTemplates");
     final protected static File DESTINATION_DIR = new File("gatkdocs");
     final protected static Logger logger = Logger.getLogger(GATKDoclet.class);
@@ -89,6 +92,19 @@ public class GATKDoclet {
         return showHiddenFeatures;
     }
 
+    public static String htmlFilenameForClass(Class c) {
+        return c.getName().replace(".", "_") + ".html";
+    }
+
+    public static String helpLinksToGATKDocs(Class c) {
+        String classPath = htmlFilenameForClass(c);
+        StringBuilder b = new StringBuilder();
+        b.append("release  version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
+        b.append("stable   version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
+        b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
+        return b.toString();
+    }
+
     public Set<GATKDocWorkUnit> workUnits() {
         TreeSet<GATKDocWorkUnit> m = new TreeSet<GATKDocWorkUnit>();
 
@@ -103,7 +119,7 @@ public class GATKDoclet {
             DocumentedGATKFeatureHandler handler = createHandler(doc, feature);
             if ( handler != null && handler.shouldBeProcessed(doc) ) {
                 logger.info("Going to generate documentation for class " + doc);
-                String filename = handler.getDestinationFilename(doc);
+                String filename = handler.getDestinationFilename(doc, clazz);
                 GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(),
                         filename, feature.groupName(),
                         feature, handler, doc, clazz,
@@ -220,7 +236,7 @@ public class GATKDoclet {
         Set<DocumentedGATKFeature> docFeatures = new HashSet<DocumentedGATKFeature>();
         List<Map<String, String>> data = new ArrayList<Map<String, String>>();
         for ( GATKDocWorkUnit workUnit : indexData ) {
-            data.add(workUnit.toMap());
+            data.add(workUnit.indexDataMap());
             docFeatures.add(workUnit.annotation);
         }