Docs for read filters, the engine, and the UserExceptions.

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

@@ -0,0 +1,52 @@
+package org.broadinstitute.sting.utils.help;
+
+import com.sun.javadoc.FieldDoc;
+import com.sun.javadoc.PackageDoc;
+import com.sun.javadoc.ProgramElementDoc;
+
+import java.lang.reflect.Field;
+
+public class HelpUtils {
+    protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
+        for (Class interfaceClass : interfaceClasses)
+            if (assignableToClass(classDoc, interfaceClass, false))
+                return true;
+        return false;
+    }
+
+    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());
+    }
+}