Moving HelpConstants out of HelpUtils so that we stop getting these ProgramElementDoc errors when com.sun.javadoc cannot load on a user's system.

public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java

@@ -32,8 +32,8 @@ import org.apache.log4j.PatternLayout;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
+import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
-import org.broadinstitute.sting.utils.help.HelpUtils;
 
 import java.io.IOException;
 import java.util.*;
@@ -289,7 +289,7 @@ public abstract class CommandLineProgram {
      */
     private static void printDocumentationReference() {
         errorPrintf("Visit our website and forum for extensive documentation and answers to %n");
-        errorPrintf("commonly asked questions " + HelpUtils.BASE_GATK_URL + "%n");
+        errorPrintf("commonly asked questions " + HelpConstants.BASE_GATK_URL + "%n");
     }
 
 

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

@@ -36,10 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
 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.HelpUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
@@ -161,7 +158,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         List<String> header = new ArrayList<String>();
         header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
         header.add("Copyright (c) 2010 The Broad Institute");
-        header.add("For support and documentation go to " + HelpUtils.BASE_GATK_URL);
+        header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL);
         return header;
     }
 

public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java

@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.filters;
 
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.help.GATKDocUtils;
-import org.broadinstitute.sting.utils.help.HelpUtils;
+import org.broadinstitute.sting.utils.help.HelpConstants;
 
 import java.util.Collection;
 import java.util.List;
@@ -71,7 +71,7 @@ public class FilterManager extends PluginManager<ReadFilter> {
 
         return String.format("Read filter %s not found. Available read filters:%n%n%s%n%n%s",pluginName,
                 userFriendlyListofReadFilters(availableFilters),
-                "Please consult the GATK Documentation (" + HelpUtils.GATK_DOCS_URL + ") for more information.");
+                "Please consult the GATK Documentation (" + HelpConstants.GATK_DOCS_URL + ") for more information.");
     }
 
     private String userFriendlyListofReadFilters(List<Class<? extends ReadFilter>> filters) {

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.help.HelpUtils;
+import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -81,7 +81,7 @@ public class VariantDataManager {
             final double theSTD = standardDeviation(theMean, iii);
             logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) );
             if( Double.isNaN(theMean) ) {
-                throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpUtils.forumPost("discussion/49/using-variant-annotator"));
+                throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpConstants.forumPost("discussion/49/using-variant-annotator"));
             }
 
             foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-6);

public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java

@@ -30,7 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpUtils;
+import org.broadinstitute.sting.utils.help.HelpConstants;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
@@ -278,7 +278,7 @@ public class UserException extends ReviewedStingException {
 
     public static class ReadMissingReadGroup extends MalformedBAM {
         public ReadMissingReadGroup(SAMRecord read) {
-            super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use " + HelpUtils.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
+            super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK.  Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
         }
     }
 
@@ -354,7 +354,7 @@ public class UserException extends ReviewedStingException {
             super(String.format("Lexicographically sorted human genome sequence detected in %s."
                     + "\nFor safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs."
                     + "\nThis is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files."
-                    + "\nYou can use the ReorderSam utility to fix this problem: " + HelpUtils.forumPost("discussion/58/companion-utilities-reordersam")
+                    + "\nYou can use the ReorderSam utility to fix this problem: " + HelpConstants.forumPost("discussion/58/companion-utilities-reordersam")
                     + "\n  %s contigs = %s",
                     name, name, ReadUtils.prettyPrintSequenceRecords(dict)));
         }

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

@@ -50,7 +50,7 @@ public class ForumAPIUtils {
         Gson gson = new Gson();
         List<String> output = new ArrayList<String>();
 
-        String text = httpGet(HelpUtils.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
+        String text = httpGet(HelpConstants.GATK_FORUM_API_URL + "categories.json?CategoryIdentifier=tool-bulletin&page=1-100000&" + ACCESS_TOKEN + forumKey);
 
         APIQuery details = gson.fromJson(text, APIQuery.class);
         ForumDiscussion[] discussions = details.Discussions;
@@ -158,7 +158,7 @@ public class ForumAPIUtils {
         Gson gson = new Gson();
 
         String data = gson.toJson(post.getPostData());
-        httpPost(data, HelpUtils.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
+        httpPost(data, HelpConstants.GATK_FORUM_API_URL + "post/discussion.json?" + ACCESS_TOKEN + forumKey);
 
 
     }

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

@@ -28,7 +28,7 @@ public class GATKDocUtils {
     /**
      * The URL root for RELEASED GATKDOC units
      */
-    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpUtils.GATK_DOCS_URL;
+    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpConstants.GATK_DOCS_URL;
     /**
      * The URL root for STABLE GATKDOC units
      */

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

@@ -0,0 +1,81 @@
+/*
+ * 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;
+
+import com.sun.javadoc.FieldDoc;
+import com.sun.javadoc.PackageDoc;
+import com.sun.javadoc.ProgramElementDoc;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+
+import java.lang.reflect.Field;
+
+public class HelpConstants {
+
+    public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
+    public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
+    public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
+    public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
+
+    public static String forumPost(String post) {
+    	return GATK_FORUM_URL + post;
+    }
+
+    protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
+        try {
+            Class type = getClassForDoc(classDoc);
+            return lhsClass.isAssignableFrom(type) && (!requireConcrete || JVMUtils.isConcrete(type));
+        } catch (Throwable t) {
+            // Ignore errors.
+            return false;
+        }
+    }
+
+    protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException {
+        return Class.forName(getClassName(doc));
+    }
+
+    protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) {
+        try {
+            Class clazz = getClassForDoc(fieldDoc.containingClass());
+            return JVMUtils.findField(clazz, fieldDoc.name());
+        } catch (ClassNotFoundException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    /**
+     * Reconstitute the class name from the given class JavaDoc object.
+     *
+     * @param doc the Javadoc model for the given class.
+     * @return The (string) class name of the given class.
+     */
+    protected static String getClassName(ProgramElementDoc doc) {
+        PackageDoc containingPackage = doc.containingPackage();
+        return containingPackage.name().length() > 0 ?
+                String.format("%s.%s", containingPackage.name(), doc.name()) :
+                String.format("%s", doc.name());
+    }
+
+}

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

@@ -33,15 +33,6 @@ import java.lang.reflect.Field;
 
 public class HelpUtils {
 
-    public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk";
-    public final static String GATK_DOCS_URL = BASE_GATK_URL + "/gatkdocs/";
-    public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/";
-    public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
-
-    public static String forumPost(String post) {
-    	return GATK_FORUM_URL + post;
-    }
-
     protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
         try {
             Class type = getClassForDoc(classDoc);