Merge branch 'master' into help

Conflicts:
	public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java

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

@@ -180,7 +180,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         formatter.format("%n");
 
         formatter.format("For a full description of this walker, see its GATKdocs at:%n");
-        formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType));
+        formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
 
         return additionalHelp.toString();
     }

public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java

@@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.help.GATKDocUtils;
 import org.broadinstitute.sting.utils.help.HelpUtils;
 
 import javax.mail.Header;
@@ -225,7 +226,7 @@ public class FeatureManager  {
                 String oneDoc = String.format(format,
                         descriptor.getName(),
                         descriptor.getSimpleFeatureName(),
-                        HelpUtils.helpLinksToGATKDocs(descriptor.getCodecClass()));
+                        GATKDocUtils.helpLinksToGATKDocs(descriptor.getCodecClass()));
                 docs.append(oneDoc);
             }
         }

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 HelpUtils.htmlFilenameForClass(clazz);
+        return GATKDocUtils.htmlFilenameForClass(clazz);
     }
 
     /**

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

@@ -0,0 +1,44 @@
+/*
+ * 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;
+
+public class GATKDocUtils {
+    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/";
+
+    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(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath);
+        //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

@@ -32,9 +32,6 @@ 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)
@@ -79,16 +76,4 @@ public class HelpUtils {
                 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(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath);
-        //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();
-    }
 }