Revbump Picard dependencies at Tim/Kathleen's request. Exclude anonymous

classes from PluginManager.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5699 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java

@@ -80,6 +80,16 @@ public class JVMUtils {
                !Modifier.isInterface(clazz.getModifiers());
     }
 
+    /**
+     * Is the specified class anonymous?  The plugin manager (for one) generally requires that
+     * plugin classes be named so that they can easily be specified from the command line.
+     * @param clazz The class on which to perform the anonymous check.
+     * @return True if the class is anonymous; false otherwise.
+     */
+    public static boolean isAnonymous(Class clazz) {
+        return clazz.isAnonymousClass();
+    }
+
     /**
      * Retrieve all fields available in this object, regardless of where they are declared or
      * whether they're accessible.

java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java

@@ -133,6 +133,10 @@ public class PluginManager<PluginType> {
         // Load all classes types filtering them by concrete.
         Set<Class<? extends PluginType>> allTypes = reflections.getSubTypesOf(pluginType);
         for( Class<? extends PluginType> type: allTypes ) {
+            // The plugin manager does not support anonymous classes; to be a plugin, a class must have a name.
+            if(JVMUtils.isAnonymous(type))
+                continue;
+
             if( JVMUtils.isConcrete(type) )
                 plugins.add(type);
             else

settings/repository/edu.mit.broad/picard-private-parts-1859.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1816" status="integration" publication="20110102175300" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1859" status="integration" publication="20110427114200" />
 </ivy-module>

settings/repository/net.sf/picard-1.42.773.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.42.773" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.44.794.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.44.794" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.42.773.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.42.773" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.44.794.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.44.794" status="release" />
+</ivy-module>