Methods for finding classes given a path and finding classes that implement a given interface. This stuff was mostly copied from private methods in WalkerManager, so there's some code redundancy. At some point, those calls could be replaced with these.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1053 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/PackageUtils.java

@@ -0,0 +1,56 @@
+package org.broadinstitute.sting.utils;
+
+import java.util.List;
+import java.util.ArrayList;
+import java.io.File;
+import java.io.IOException;
+
+/**
+ * PackageUtils contains some useful methods for package introspection.
+ */
+public class PackageUtils {
+    /**
+     * Private constructor.  No instantiating this class!
+     */
+    private PackageUtils() {}
+
+    /**
+     * Return the classes that implement the specified interface.
+     *
+     * @param iface  the interface which returned classes should implement.
+     * @return       the list of classes that implement the interface.  How is that not clear by now?!!!!111one!!
+     */
+    public static ArrayList<Class> getClassesImplementingInterface(Class iface) {
+        try {
+            final File location = JVMUtils.getLocationFor(iface);
+
+            List<Class> potentialClasses = getClassesFromLocation(location);
+            ArrayList<Class> implementingClasses = new ArrayList<Class>();
+
+            for (Class potentialClass : potentialClasses) {
+                if (JVMUtils.isConcreteImplementationOf(potentialClass, iface)) {
+                    implementingClasses.add(potentialClass);
+                }
+            }
+
+            return implementingClasses;
+        } catch (IOException e) {
+            throw new StingException(String.format("Unable to inspect package containing '%s'", iface.getName()));
+        }
+    }
+
+    /**
+     * Return a list of classes at the specified location
+     * @param location      the location  where we should start searching (as returned by JVMUtils.getLocationFor(Class))
+     * @return              a list of classes at this location
+     * @throws IOException  thrown if the jar or directory cannot be inspected
+     */
+    public static List<Class> getClassesFromLocation(File location) throws IOException {
+        if (location.getAbsolutePath().endsWith(".jar"))
+            return JVMUtils.loadInternalClassesFromJar(location);
+        else {
+            List<String> classFileNames = PathUtils.findFilesInPath(location, "", "class", true);
+            return JVMUtils.loadInternalClasses(classFileNames);
+        }
+    }
+}