Better location for help utils

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

@@ -34,10 +34,7 @@ import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.walkers.Attribution;
 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.*;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.GATKDocUtils;
-import org.broadinstitute.sting.utils.help.GATKDoclet;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
@@ -178,7 +175,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         Formatter formatter = new Formatter(additionalHelp);
 
         formatter.format("For a full description of this walker, see its GATKdocs at:%n");
-        formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
+        formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType));
 
         return additionalHelp.toString();
     }

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

@@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler {
      * @return
      */
     public String getDestinationFilename(ClassDoc doc, Class clazz) {
-        return GATKDocUtils.htmlFilenameForClass(clazz);
+        return HelpUtils.htmlFilenameForClass(clazz);
     }
 
     /**

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

@@ -1,48 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.help;
-
-/**
- * @author depristo
- * @since 8/8/11
- */
-public class GATKDocUtils {
-    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/";
-
-    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/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java

@@ -32,6 +32,10 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import java.lang.reflect.Field;
 
 public class HelpUtils {
+    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
+    public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
+    public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
+
     protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
         for (Class interfaceClass : interfaceClasses)
             if (assignableToClass(classDoc, interfaceClass, false))
@@ -74,4 +78,17 @@ public class HelpUtils {
                 String.format("%s.%s", containingPackage.name(), doc.name()) :
                 String.format("%s", doc.name());
     }
+
+    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();
+    }
 }