diff --git a/tools/cooja/java/se/sics/cooja/CoreComm.java b/tools/cooja/java/se/sics/cooja/CoreComm.java
index 0370277c9..153a007b7 100644
--- a/tools/cooja/java/se/sics/cooja/CoreComm.java
+++ b/tools/cooja/java/se/sics/cooja/CoreComm.java
@@ -1,7 +1,7 @@
 /*
  * Copyright (c) 2006, Swedish Institute of Computer Science. All rights
  * reserved.
- * 
+ *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  * 1. Redistributions of source code must retain the above copyright notice,
@@ -12,7 +12,7 @@
  * Institute nor the names of its contributors may be used to endorse or promote
  * products derived from this software without specific prior written
  * permission.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND ANY
  * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -23,8 +23,8 @@
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * $Id: CoreComm.java,v 1.10 2007/05/11 10:15:42 fros4943 Exp $
+ *
+ * $Id: CoreComm.java,v 1.11 2008/02/12 15:03:02 fros4943 Exp $
  */
 
 package se.sics.cooja;
@@ -52,7 +52,7 @@ import se.sics.cooja.dialogs.MessageList;
  * that even if a mote type is deleted, a new one cannot be created using the
  * same corecomm class without restarting the JVM and thus the entire
  * simulation.
- * 
+ *
  * Each implemented CoreComm class needs read access to the following core
  * variables:
  * <ul>
@@ -65,7 +65,7 @@ import se.sics.cooja.dialogs.MessageList;
  * <li>getReferenceAbsAddr()
  * <li>getMemory(int start, int length, byte[] mem)
  * <li>setMemory(int start, int length, byte[] mem)
- * 
+ *
  * @author Fredrik Osterlind
  */
 public abstract class CoreComm {
@@ -80,7 +80,7 @@ public abstract class CoreComm {
   /**
    * Has any library been loaded? Since libraries can't be unloaded the entire
    * simulator may have to be restarted.
-   * 
+   *
    * @return True if any library has been loaded this session
    */
   public static boolean hasLibraryBeenLoaded() {
@@ -92,24 +92,26 @@ public abstract class CoreComm {
    * library can be removed, but not unloaded during one session. And a new
    * library file, named the same as an earlier loaded and removed file, can't
    * be loaded either.
-   * 
+   *
    * @param libraryFile
    *          Library file
    * @return True if a library has already been loaded from the given file's
    *         filename
    */
   public static boolean hasLibraryFileBeenLoaded(File libraryFile) {
-    for (File loadedFile : coreCommFiles)
+    for (File loadedFile : coreCommFiles) {
       if (loadedFile != null
-          && loadedFile.getName().equals(libraryFile.getName()))
+          && loadedFile.getName().equals(libraryFile.getName())) {
         return true;
+      }
+    }
     return false;
   }
 
   /**
    * Get the class name of next free core communicator class. If null is
    * returned, no classes are available.
-   * 
+   *
    * @return Class name
    */
   public static String getAvailableClassName() {
@@ -119,7 +121,7 @@ public abstract class CoreComm {
   /**
    * Generates new source file by reading default source template and replacing
    * the class name field.
-   * 
+   *
    * @param className
    *          Java class name (without extension)
    * @throws MoteTypeCreationException
@@ -151,8 +153,9 @@ public abstract class CoreComm {
       destFilename = className + ".java";
 
       File dir = new File("se/sics/cooja/corecomm");
-      if (!dir.exists())
+      if (!dir.exists()) {
         dir.mkdirs();
+      }
 
       sourceFileWriter = new BufferedWriter(new OutputStreamWriter(
           new FileOutputStream("se/sics/cooja/corecomm/" + destFilename)));
@@ -168,10 +171,12 @@ public abstract class CoreComm {
       templateFileReader.close();
     } catch (Exception e) {
       try {
-        if (sourceFileWriter != null)
+        if (sourceFileWriter != null) {
           sourceFileWriter.close();
-        if (templateFileReader != null)
+        }
+        if (templateFileReader != null) {
           templateFileReader.close();
+        }
       } catch (Exception e2) {
       }
 
@@ -181,16 +186,17 @@ public abstract class CoreComm {
     }
 
     File genFile = new File("se/sics/cooja/corecomm/" + destFilename);
-    if (genFile.exists())
+    if (genFile.exists()) {
       return;
+    }
 
-    throw (MoteTypeCreationException) new MoteTypeCreationException(
+    throw new MoteTypeCreationException(
         "Could not generate corecomm source file: " + className + ".java");
   }
 
   /**
    * Compiles Java class.
-   * 
+   *
    * @param className
    *          Java class name (without extension)
    * @throws MoteTypeCreationException
@@ -222,8 +228,9 @@ public abstract class CoreComm {
       }
       p.waitFor();
 
-      if (classFile.exists())
+      if (classFile.exists()) {
         return;
+      }
 
       // Try including cooja.jar
       cmd = new String[] {
@@ -246,8 +253,9 @@ public abstract class CoreComm {
       }
       p.waitFor();
 
-      if (classFile.exists())
+      if (classFile.exists()) {
         return;
+      }
 
     } catch (IOException e) {
       MoteTypeCreationException exception = (MoteTypeCreationException) new MoteTypeCreationException(
@@ -271,7 +279,7 @@ public abstract class CoreComm {
 
   /**
    * Loads given Java class file from disk.
-   * 
+   *
    * @param classFile
    *          Java class (without extension)
    * @return Loaded class
@@ -282,8 +290,9 @@ public abstract class CoreComm {
       throws MoteTypeCreationException {
     Class loadedClass = null;
     try {
-      ClassLoader urlClassLoader = new URLClassLoader(new URL[] { new File(".")
-          .toURL() }, CoreComm.class.getClassLoader());
+      ClassLoader urlClassLoader = new URLClassLoader(
+          new URL[] { new File(".").toURI().toURL() },
+          CoreComm.class.getClassLoader());
       loadedClass = urlClassLoader.loadClass("se.sics.cooja.corecomm."
           + className);
 
@@ -296,9 +305,10 @@ public abstract class CoreComm {
           "Could not load corecomm class file: " + className + ".class")
           .initCause(e);
     }
-    if (loadedClass == null)
-      throw (MoteTypeCreationException) new MoteTypeCreationException(
+    if (loadedClass == null) {
+      throw new MoteTypeCreationException(
           "Could not load corecomm class file: " + className + ".class");
+    }
 
     return loadedClass;
   }
@@ -306,7 +316,7 @@ public abstract class CoreComm {
   /**
    * Create and return an instance of the core communicator identified by
    * className. This core communicator will load the native library libFile.
-   * 
+   *
    * @param className
    *          Class name of core communicator
    * @param libFile
@@ -353,14 +363,14 @@ public abstract class CoreComm {
   /**
    * Returns absolute memory location of the core variable referenceVar. Used to
    * get offset between relative and absolute memory addresses.
-   * 
+   *
    * @return Absolute memory address
    */
   public abstract int getReferenceAbsAddr();
 
   /**
    * Fills an byte array with memory segment identified by start and length.
-   * 
+   *
    * @param start
    *          Start address of segment
    * @param length
@@ -372,7 +382,7 @@ public abstract class CoreComm {
 
   /**
    * Overwrites a memory segment identified by start and length.
-   * 
+   *
    * @param start
    *          Start address of segment
    * @param length
diff --git a/tools/cooja/java/se/sics/cooja/Simulation.java b/tools/cooja/java/se/sics/cooja/Simulation.java
index 239026f81..aff6f3c04 100644
--- a/tools/cooja/java/se/sics/cooja/Simulation.java
+++ b/tools/cooja/java/se/sics/cooja/Simulation.java
@@ -24,7 +24,7 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
- * $Id: Simulation.java,v 1.18 2007/10/03 14:20:57 fros4943 Exp $
+ * $Id: Simulation.java,v 1.19 2008/02/12 15:03:43 fros4943 Exp $
  */
 
 package se.sics.cooja;
@@ -470,7 +470,7 @@ public class Simulation extends Observable implements Runnable {
         // Show configure simulation dialog
         boolean createdOK = false;
         if (visAvailable) {
-          createdOK = CreateSimDialog.showDialog(GUI.frame, this);
+          createdOK = CreateSimDialog.showDialog(GUI.getTopParentContainer(), this);
         } else {
           createdOK = true;
         }
diff --git a/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java b/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java
index 4f060e8d2..cfe0dfbc4 100644
--- a/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java
+++ b/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteType.java
@@ -26,12 +26,13 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: ContikiMoteType.java,v 1.24 2008/02/11 14:00:19 fros4943 Exp $
+ * $Id: ContikiMoteType.java,v 1.25 2008/02/12 15:04:43 fros4943 Exp $
  */
 
 package se.sics.cooja.contikimote;
 
 import java.awt.BorderLayout;
+import java.awt.Container;
 import java.awt.Dimension;
 import java.io.*;
 import java.security.*;
@@ -202,10 +203,10 @@ public class ContikiMoteType implements MoteType {
     return new ContikiMote(this, simulation);
   }
 
-  public boolean configureAndInit(JFrame parentFrame, Simulation simulation,
+  public boolean configureAndInit(Container parentContainer, Simulation simulation,
       boolean visAvailable) throws MoteTypeCreationException {
     if (visAvailable) {
-      return ContikiMoteTypeDialog.showDialog(parentFrame, simulation, this);
+      return ContikiMoteTypeDialog.showDialog(parentContainer, simulation, this);
     } else {
 
       // Create temp output directory if not already exists
@@ -1401,7 +1402,7 @@ public class ContikiMoteType implements MoteType {
     }
 
     mySimulation = simulation;
-    boolean createdOK = configureAndInit(GUI.frame, simulation, visAvailable);
+    boolean createdOK = configureAndInit(GUI.getTopParentContainer(), simulation, visAvailable);
     return createdOK;
   }
 
diff --git a/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteTypeDialog.java b/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteTypeDialog.java
index 1e6ec2a44..9fccaa401 100644
--- a/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteTypeDialog.java
+++ b/tools/cooja/java/se/sics/cooja/contikimote/ContikiMoteTypeDialog.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: ContikiMoteTypeDialog.java,v 1.39 2008/01/08 12:33:25 fros4943 Exp $
+ * $Id: ContikiMoteTypeDialog.java,v 1.40 2008/02/12 15:04:20 fros4943 Exp $
  */
 
 package se.sics.cooja.contikimote;
@@ -116,19 +116,29 @@ public class ContikiMoteTypeDialog extends JDialog {
    * Shows a dialog for configuring a Contiki mote type and compiling the shared
    * library it uses.
    *
-   * @param parentFrame
-   *          Parent frame for dialog
+   * @param parentContainer
+   *          Parent container for dialog
    * @param simulation
    *          Simulation holding (or that will hold) mote type
    * @param moteTypeToConfigure
    *          Mote type to configure
-   * @return True if compilation succeded and library is ready to be loaded
+   * @return True if compilation succeeded and library is ready to be loaded
    */
-  public static boolean showDialog(Frame parentFrame, Simulation simulation,
+  public static boolean showDialog(Container parentContainer, Simulation simulation,
       ContikiMoteType moteTypeToConfigure) {
 
-    final ContikiMoteTypeDialog myDialog = new ContikiMoteTypeDialog(
-        parentFrame);
+    ContikiMoteTypeDialog myDialog = null;
+    if (parentContainer instanceof Window) {
+      myDialog = new ContikiMoteTypeDialog((Window) parentContainer);
+    } else if (parentContainer instanceof Dialog) {
+      myDialog = new ContikiMoteTypeDialog((Dialog) parentContainer);
+    } else if (parentContainer instanceof Frame) {
+      myDialog = new ContikiMoteTypeDialog((Frame) parentContainer);
+    } else {
+      logger.fatal("Unknown parent container type: " + parentContainer);
+      return false;
+    }
+
     myDialog.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
 
     myDialog.myMoteType = moteTypeToConfigure;
@@ -403,7 +413,7 @@ public class ContikiMoteTypeDialog extends JDialog {
 
     // Set position and focus of dialog
     myDialog.pack();
-    myDialog.setLocationRelativeTo(parentFrame);
+    myDialog.setLocationRelativeTo(parentContainer);
     myDialog.textDescription.requestFocus();
     myDialog.textDescription.select(0, myDialog.textDescription.getText()
         .length());
@@ -428,9 +438,20 @@ public class ContikiMoteTypeDialog extends JDialog {
     return false;
   }
 
+  private ContikiMoteTypeDialog(Dialog dialog) {
+    super(dialog, "Add Mote Type", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
+  private ContikiMoteTypeDialog(Window window) {
+    super(window, "Add Mote Type", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
   private ContikiMoteTypeDialog(Frame frame) {
-    super(frame, "Add Mote Type", true);
+    super(frame, "Add Mote Type", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
 
+  private void setupDialog() {
     myDialog = this;
 
     JLabel label;
@@ -2513,8 +2534,8 @@ public class ContikiMoteTypeDialog extends JDialog {
         // Find and load the mote interface classes
         for (String moteInterface : moteInterfaces) {
           try {
-            Class<? extends MoteInterface> newMoteInterfaceClass = classLoader
-                .loadClass(moteInterface).asSubclass(MoteInterface.class);
+            Class<? extends MoteInterface> newMoteInterfaceClass =
+              myGUI.tryLoadClass(this, MoteInterface.class, moteInterface);
             moteIntfClasses.add(newMoteInterfaceClass);
             // logger.info("Loaded mote interface: " + newMoteInterfaceClass);
           } catch (Exception ce) {
diff --git a/tools/cooja/java/se/sics/cooja/dialogs/AddMoteDialog.java b/tools/cooja/java/se/sics/cooja/dialogs/AddMoteDialog.java
index 9121d2f9d..0cad5a35f 100644
--- a/tools/cooja/java/se/sics/cooja/dialogs/AddMoteDialog.java
+++ b/tools/cooja/java/se/sics/cooja/dialogs/AddMoteDialog.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: AddMoteDialog.java,v 1.4 2007/11/29 05:37:35 fros4943 Exp $
+ * $Id: AddMoteDialog.java,v 1.5 2008/02/12 15:05:14 fros4943 Exp $
  */
 
 package se.sics.cooja.dialogs;
@@ -74,19 +74,30 @@ public class AddMoteDialog extends JDialog {
    * Shows a dialog which enables a user to create and add motes of the given
    * type.
    *
-   * @param parentFrame
-   *          Parent frame for dialog
+   * @param parentContainer
+   *          Parent container for dialog
    * @param simulation
    *          Simulation
    * @param moteType
    *          Mote type
    * @return New motes or null if aborted
    */
-  public static Vector<Mote> showDialog(Frame parentFrame,
+  public static Vector<Mote> showDialog(Container parentContainer,
       Simulation simulation, MoteType moteType) {
 
-    AddMoteDialog myDialog = new AddMoteDialog(parentFrame, simulation, moteType);
-    myDialog.setLocationRelativeTo(parentFrame);
+    AddMoteDialog myDialog = null;
+    if (parentContainer instanceof Window) {
+      myDialog = new AddMoteDialog((Window)parentContainer, simulation, moteType);
+    } else if (parentContainer instanceof Dialog) {
+      myDialog = new AddMoteDialog((Dialog)parentContainer, simulation, moteType);
+    } else if (parentContainer instanceof Frame) {
+      myDialog = new AddMoteDialog((Frame)parentContainer, simulation, moteType);
+    } else {
+      logger.fatal("Unknown parent container type: " + parentContainer);
+      return null;
+    }
+
+    myDialog.setLocationRelativeTo(parentContainer);
     myDialog.checkSettings();
 
     if (myDialog != null) {
@@ -96,7 +107,19 @@ public class AddMoteDialog extends JDialog {
   }
 
   private AddMoteDialog(Frame frame, Simulation simulation, MoteType moteType) {
-    super(frame, "Add motes (" + moteType.getDescription() + ")", true);
+    super(frame, "Add motes (" + moteType.getDescription() + ")", ModalityType.APPLICATION_MODAL);
+    setupDialog(simulation, moteType);
+  }
+  private AddMoteDialog(Window window, Simulation simulation, MoteType moteType) {
+    super(window, "Add motes (" + moteType.getDescription() + ")", ModalityType.APPLICATION_MODAL);
+    setupDialog(simulation, moteType);
+  }
+  private AddMoteDialog(Dialog dialog, Simulation simulation, MoteType moteType) {
+    super(dialog, "Add motes (" + moteType.getDescription() + ")", ModalityType.APPLICATION_MODAL);
+    setupDialog(simulation, moteType);
+  }
+
+  private void setupDialog(Simulation simulation, MoteType moteType) {
     this.moteType = moteType;
     this.simulation = simulation;
 
diff --git a/tools/cooja/java/se/sics/cooja/dialogs/CreateSimDialog.java b/tools/cooja/java/se/sics/cooja/dialogs/CreateSimDialog.java
index 3a320bdd4..d84f9f052 100644
--- a/tools/cooja/java/se/sics/cooja/dialogs/CreateSimDialog.java
+++ b/tools/cooja/java/se/sics/cooja/dialogs/CreateSimDialog.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: CreateSimDialog.java,v 1.7 2007/09/30 12:03:49 fros4943 Exp $
+ * $Id: CreateSimDialog.java,v 1.8 2008/02/12 15:06:09 fros4943 Exp $
  */
 
 package se.sics.cooja.dialogs;
@@ -70,12 +70,22 @@ public class CreateSimDialog extends JDialog {
   /**
    * Shows a dialog for configuring a simulation.
    *
-   * @param parentFrame Parent frame for dialog
+   * @param parentContainer Parent container for dialog
    * @param simulationToConfigure Simulation to configure
    * @return True if simulation configured correctly
    */
-  public static boolean showDialog(Frame parentFrame, Simulation simulationToConfigure) {
-    final CreateSimDialog myDialog = new CreateSimDialog(parentFrame, simulationToConfigure.getGUI());
+  public static boolean showDialog(Container parentContainer, Simulation simulationToConfigure) {
+    final CreateSimDialog myDialog;
+    if (parentContainer instanceof Window) {
+      myDialog = new CreateSimDialog((Window) parentContainer, simulationToConfigure.getGUI());
+    } else if (parentContainer instanceof Dialog) {
+      myDialog = new CreateSimDialog((Dialog) parentContainer, simulationToConfigure.getGUI());
+    } else if (parentContainer instanceof Frame) {
+      myDialog = new CreateSimDialog((Frame) parentContainer, simulationToConfigure.getGUI());
+    } else {
+      logger.fatal("Unknown parent container type: " + parentContainer);
+      return false;
+    }
 
     myDialog.setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE);
     myDialog.addWindowListener(new WindowListener() {
@@ -149,7 +159,7 @@ public class CreateSimDialog extends JDialog {
 
 
     // Set position and focus of dialog
-    myDialog.setLocationRelativeTo(parentFrame);
+    myDialog.setLocationRelativeTo(parentContainer);
     myDialog.title.requestFocus();
     myDialog.title.select(0, myDialog.title.getText().length());
 
@@ -172,9 +182,20 @@ public class CreateSimDialog extends JDialog {
     return false;
   }
 
+  private CreateSimDialog(Dialog dialog, GUI gui) {
+    super(dialog, "Create new simulation", ModalityType.TOOLKIT_MODAL);
+    setupDialog(gui);
+  }
+  private CreateSimDialog(Window window, GUI gui) {
+    super(window, "Create new simulation", ModalityType.TOOLKIT_MODAL);
+    setupDialog(gui);
+  }
   private CreateSimDialog(Frame frame, GUI gui) {
-    super(frame, "Create new simulation", true);
+    super(frame, "Create new simulation", ModalityType.TOOLKIT_MODAL);
+    setupDialog(gui);
+  }
 
+  private void setupDialog(GUI gui) {
     myDialog = this;
     myGUI = gui;
 
diff --git a/tools/cooja/java/se/sics/cooja/dialogs/ExternalToolsDialog.java b/tools/cooja/java/se/sics/cooja/dialogs/ExternalToolsDialog.java
index 9a076210d..160c8e585 100644
--- a/tools/cooja/java/se/sics/cooja/dialogs/ExternalToolsDialog.java
+++ b/tools/cooja/java/se/sics/cooja/dialogs/ExternalToolsDialog.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: ExternalToolsDialog.java,v 1.7 2007/09/28 07:21:21 fros4943 Exp $
+ * $Id: ExternalToolsDialog.java,v 1.8 2008/02/12 15:06:09 fros4943 Exp $
  */
 
 package se.sics.cooja.dialogs;
@@ -61,21 +61,43 @@ public class ExternalToolsDialog extends JDialog {
   /**
    * Creates a dialog for viewing/editing external tools settings.
    *
-   * @param parentFrame
-   *          Parent frame for dialog
+   * @param parentContainer
+   *          Parent container for dialog
    */
-  public static void showDialog(Frame parentFrame) {
-    ExternalToolsDialog myDialog = new ExternalToolsDialog(parentFrame);
-    myDialog.setLocationRelativeTo(parentFrame);
+  public static void showDialog(Container parentContainer) {
+
+    ExternalToolsDialog myDialog = null;
+    if (parentContainer instanceof Window) {
+      myDialog = new ExternalToolsDialog((Window) parentContainer);
+    } else if (parentContainer instanceof Dialog) {
+      myDialog = new ExternalToolsDialog((Dialog) parentContainer);
+    } else if (parentContainer instanceof Frame) {
+      myDialog = new ExternalToolsDialog((Frame) parentContainer);
+    } else {
+      logger.fatal("Unknown parent container type: " + parentContainer);
+      return;
+    }
+    myDialog.setLocationRelativeTo(parentContainer);
 
     if (myDialog != null) {
       myDialog.setVisible(true);
     }
   }
 
+  private ExternalToolsDialog(Dialog dialog) {
+    super(dialog, "Edit Settings", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
+  private ExternalToolsDialog(Window window) {
+    super(window, "Edit Settings", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
   private ExternalToolsDialog(Frame frame) {
-    super(frame, "Edit Settings", true);
+    super(frame, "Edit Settings", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
 
+  private void setupDialog() {
     myDialog = this;
 
     JLabel label;
diff --git a/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoriesDialog.java b/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoriesDialog.java
index 08b4590b9..1225b9a49 100644
--- a/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoriesDialog.java
+++ b/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoriesDialog.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: ProjectDirectoriesDialog.java,v 1.4 2007/08/21 14:18:04 fros4943 Exp $
+ * $Id: ProjectDirectoriesDialog.java,v 1.5 2008/02/12 15:06:09 fros4943 Exp $
  */
 
 package se.sics.cooja.dialogs;
@@ -63,30 +63,37 @@ public class ProjectDirectoriesDialog extends JDialog {
   private List changableProjectsList = new List();
   private List fixedProjectsList = null;
   private Vector<File> changableProjects = null;
-  private Vector<File> fixedProjects = null;
 
   private ProjectDirectoriesDialog myDialog;
-  private Frame myParentFrame = null;
-  private Dialog myParentDialog = null;
 
   /**
    * Allows user to alter the given project directories list by adding new,
    * reordering or removing project directories. Only the changable project directories
    * can be altered.
    *
-   * @param parentFrame
-   *          Parent frame
+   * @param parentContainer
+   *          Parent container
    * @param changableProjects
    *          Changeable project directories
    * @param fixedProjects
    *          Fixed project directory
    * @return Null if dialog aborted, else the new CHANGEABLE project directory list.
    */
-  public static Vector<File> showDialog(Frame parentFrame,
+  public static Vector<File> showDialog(Container parentContainer,
       Vector<File> changableProjects, Vector<File> fixedProjects) {
-    ProjectDirectoriesDialog myDialog = new ProjectDirectoriesDialog(parentFrame,
-        changableProjects, fixedProjects);
-    myDialog.setLocationRelativeTo(parentFrame);
+
+    ProjectDirectoriesDialog myDialog = null;
+    if (parentContainer instanceof Window) {
+      myDialog = new ProjectDirectoriesDialog((Window) parentContainer, changableProjects, fixedProjects);
+    } else if (parentContainer instanceof Dialog) {
+      myDialog = new ProjectDirectoriesDialog((Dialog) parentContainer, changableProjects, fixedProjects);
+    } else if (parentContainer instanceof Frame) {
+      myDialog = new ProjectDirectoriesDialog((Frame) parentContainer, changableProjects, fixedProjects);
+    } else {
+      logger.fatal("Unknown parent container type: " + parentContainer);
+      return null;
+    }
+    myDialog.setLocationRelativeTo(parentContainer);
 
     if (myDialog != null) {
       myDialog.setVisible(true);
@@ -123,19 +130,23 @@ public class ProjectDirectoriesDialog extends JDialog {
 
   private ProjectDirectoriesDialog(Frame frame, Vector<File> changableProjects,
       Vector<File> fixedProjects) {
-    super(frame, "Manage Project Directories", true);
-    myParentFrame = frame;
-    init(changableProjects, fixedProjects);
+    super(frame, "Manage Project Directories", ModalityType.APPLICATION_MODAL);
+    setupDialog(changableProjects, fixedProjects);
   }
 
   private ProjectDirectoriesDialog(Dialog dialog, Vector<File> changableProjects,
       Vector<File> fixedProjects) {
-    super(dialog, "Manage Project Directories", true);
-    myParentDialog = dialog;
-    init(changableProjects, fixedProjects);
+    super(dialog, "Manage Project Directories", ModalityType.APPLICATION_MODAL);
+    setupDialog(changableProjects, fixedProjects);
   }
 
-  private void init(Vector<File> changablePlatforms, Vector<File> fixedProjects) {
+  private ProjectDirectoriesDialog(Window window, Vector<File> changableProjects,
+      Vector<File> fixedProjects) {
+    super(window, "Manage Project Directories", ModalityType.APPLICATION_MODAL);
+    setupDialog(changableProjects, fixedProjects);
+  }
+
+  private void setupDialog(Vector<File> changablePlatforms, Vector<File> fixedProjects) {
     myDialog = this;
 
     JPanel mainPane = new JPanel();
@@ -339,11 +350,7 @@ public class ProjectDirectoriesDialog extends JDialog {
         }
 
         // Show merged configuration
-        if (myParentFrame != null) {
-          ConfigViewer.showDialog(myParentFrame, config);
-        } else {
-          ConfigViewer.showDialog(myParentDialog, config);
-        }
+        ConfigViewer.showDialog(ProjectDirectoriesDialog.this, config);
       }
     });
     addRemovePane.add(button);
@@ -353,10 +360,10 @@ public class ProjectDirectoriesDialog extends JDialog {
     button = new JButton("Add manually");
     button.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
-        ProjectDirectoryInputDialog pathDialog = new ProjectDirectoryInputDialog(myParentFrame);
+        ProjectDirectoryInputDialog pathDialog = new ProjectDirectoryInputDialog(ProjectDirectoriesDialog.this);
         pathDialog.pack();
 
-        pathDialog.setLocationRelativeTo(myParentFrame);
+        pathDialog.setLocationRelativeTo(ProjectDirectoriesDialog.this);
         pathDialog.setVisible(true);
 
         File projectPath = pathDialog.getProjectDirectory();
diff --git a/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoryInputDialog.java b/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoryInputDialog.java
index dfab5a946..9a5468fa4 100644
--- a/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoryInputDialog.java
+++ b/tools/cooja/java/se/sics/cooja/dialogs/ProjectDirectoryInputDialog.java
@@ -21,9 +21,20 @@ class ProjectDirectoryInputDialog extends JDialog implements ActionListener, Pro
   private String buttonAdd = "Add";
   private String buttonCancel = "Cancel";
 
-  public ProjectDirectoryInputDialog(Frame parent) {
-    super(parent, true);
+  public ProjectDirectoryInputDialog(Window window) {
+    super(window, ModalityType.APPLICATION_MODAL);
+    setupDialog();
+  }
+  public ProjectDirectoryInputDialog(Dialog dialog) {
+    super(dialog, ModalityType.APPLICATION_MODAL);
+    setupDialog();
+  }
+  public ProjectDirectoryInputDialog(Frame frame) {
+    super(frame, ModalityType.APPLICATION_MODAL);
+    setupDialog();
+  }
 
+  public void setupDialog() {
     setTitle("Enter path");
 
     textField = new JTextField(10);
@@ -37,7 +48,7 @@ class ProjectDirectoryInputDialog extends JDialog implements ActionListener, Pro
       public void changedUpdate(DocumentEvent e) {
         pathChanged();
       }
-    });    
+    });
 
     Object[] objects = {"Enter path to project directory", textField};
     Object[] options = {buttonAdd, buttonCancel};
diff --git a/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteType.java b/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteType.java
index 3ff7fcf66..875cb500e 100644
--- a/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteType.java
+++ b/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteType.java
@@ -26,12 +26,13 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: MantisMoteType.java,v 1.5 2007/09/18 11:33:58 fros4943 Exp $
+ * $Id: MantisMoteType.java,v 1.6 2008/02/12 15:10:49 fros4943 Exp $
  */
 
 package se.sics.cooja.mantismote;
 
 import java.awt.BorderLayout;
+import java.awt.Container;
 import java.awt.Dimension;
 import java.io.File;
 import java.util.*;
@@ -40,7 +41,6 @@ import java.util.regex.Pattern;
 
 import javax.swing.Box;
 import javax.swing.BoxLayout;
-import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import org.apache.log4j.Logger;
@@ -61,7 +61,7 @@ import se.sics.cooja.contikimote.ContikiMoteType;
  * Mantis system in order to create the initial memory. When a new mote is
  * created the createInitialMemory() method should be called to get this initial
  * memory for the mote.
- * 
+ *
  * @author Fredrik Osterlind
  */
 @ClassDescription("Mantis Mote Type")
@@ -96,7 +96,7 @@ public class MantisMoteType implements MoteType {
    * loaded by the first available CoreComm. Each mote generated from this mote
    * type will have the interfaces specified in the given mote interface class
    * list.
-   * 
+   *
    * @param libFile
    *          Library file to load
    * @param objFile
@@ -106,21 +106,22 @@ public class MantisMoteType implements MoteType {
    */
   public MantisMoteType(File libFile, File objFile,
       Vector<Class<? extends MoteInterface>> moteInterfaceClasses) {
-    if (!doInit(libFile, objFile, moteInterfaceClasses))
+    if (!doInit(libFile, objFile, moteInterfaceClasses)) {
       logger.fatal("Mantis mote type creation failed!");
+    }
   }
- 
+
   /**
    * This is an mote type initialization method and should normally never be
    * called by any other part than the mote type constructor. It is called from
    * the constructor with an identifier argument, but not from the standard
    * constructor. This method may be called from the simulator when loading
    * configuration files, and the libraries must be recompiled.
-   * 
+   *
    * This method allocates a core communicator, loads the Mantis library file,
    * creates variable name to address mappings and finally creates the Mantis
    * mote initial memory.
-   * 
+   *
    * @param libFile Library file
    * @param objFile Object file
    * @param moteInterfaceClasses Mote interface classes
@@ -131,7 +132,7 @@ public class MantisMoteType implements MoteType {
     myObjectFilename = objFile.getAbsolutePath();
     myIdentifier = libFile.getName();
     myDescription = libFile.getAbsolutePath();
-    
+
     // Allocate core communicator class
     libraryClassName = CoreComm.getAvailableClassName();
     try {
@@ -195,7 +196,7 @@ public class MantisMoteType implements MoteType {
       logger.fatal("BSS section size parsing failed");
       return false;
     }
-    
+
     // Get offset between relative and absolute addresses
     offsetRelToAbs = myCoreComm.getReferenceAbsAddr() - (Integer) varAddresses.get("referenceVar");
 
@@ -209,17 +210,17 @@ public class MantisMoteType implements MoteType {
     myInitialMemory = new SectionMoteMemory(varAddresses);
     myInitialMemory.setMemorySegment(relDataSectionAddr, initialDataSection);
     myInitialMemory.setMemorySegment(relBssSectionAddr, initialBssSection);
-    
+
     this.moteInterfaceClasses = moteInterfaceClasses;
-    
+
     return true;
   }
-  
+
   /**
    * Creates and returns a copy of this mote type's initial memory (just after
    * the init function has been run). When a new mote is created it should get
    * it's memory from here.
-   * 
+   *
    * @return Initial memory of a mote type
    */
   public SectionMoteMemory createInitialMemory() {
@@ -237,7 +238,7 @@ public class MantisMoteType implements MoteType {
   /**
    * Copy core memory to given memory. This should not be used directly, but
    * instead via MantisMote.getMemory().
-   * 
+   *
    * @param mem
    *          Memory to set
    */
@@ -246,7 +247,7 @@ public class MantisMoteType implements MoteType {
       int startAddr = mem.getStartAddrOfSection(i);
       int size = mem.getSizeOfSection(i);
       byte[] data = mem.getDataOfSection(i);
-      
+
       getCoreMemory(startAddr + offsetRelToAbs,
           size, data);
     }
@@ -255,7 +256,7 @@ public class MantisMoteType implements MoteType {
   /**
    * Copy given memory to the Mantis system. This should not be used directly,
    * but instead via MantisMote.setMemory().
-   * 
+   *
    * @param mem
    *          New memory
    */
@@ -277,7 +278,7 @@ public class MantisMoteType implements MoteType {
 
   /**
    * Returns all mote interfaces of this mote type
-   * 
+   *
    * @return All mote interfaces
    */
   public Vector<Class<? extends MoteInterface>> getMoteInterfaces() {
@@ -296,7 +297,7 @@ public class MantisMoteType implements MoteType {
     return myIdentifier;
   }
 
-  public void setIdentifier(String identifier) {    
+  public void setIdentifier(String identifier) {
     myIdentifier = identifier;
   }
 
@@ -360,9 +361,11 @@ public class MantisMoteType implements MoteType {
     return new MantisMote(this, mySimulation);
   }
 
-  public boolean configureAndInit(JFrame parentFrame, Simulation simulation, boolean visAvailable) {
-    if (!visAvailable) logger.fatal(">>>>>>> NOT IMPLEMENTED");
-    return MantisMoteTypeDialog.showDialog(parentFrame, simulation, this);
+  public boolean configureAndInit(Container parentContainer, Simulation simulation, boolean visAvailable) {
+    if (!visAvailable) {
+      logger.fatal(">>>>>>> NOT IMPLEMENTED");
+    }
+    return MantisMoteTypeDialog.showDialog(parentContainer, simulation, this);
   }
 
   public Collection<Element> getConfigXML() {
@@ -406,7 +409,7 @@ public class MantisMoteType implements MoteType {
       }
     }
 
-    boolean createdOK = configureAndInit(GUI.frame, simulation, visAvailable);
+    boolean createdOK = configureAndInit(GUI.getTopParentContainer(), simulation, visAvailable);
     return createdOK;
   }
 
diff --git a/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteTypeDialog.java b/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteTypeDialog.java
index 32eb3da90..1dc56bf09 100644
--- a/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteTypeDialog.java
+++ b/tools/cooja/java/se/sics/cooja/mantismote/MantisMoteTypeDialog.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: MantisMoteTypeDialog.java,v 1.5 2007/03/24 00:44:55 fros4943 Exp $
+ * $Id: MantisMoteTypeDialog.java,v 1.6 2008/02/12 15:10:49 fros4943 Exp $
  */
 
 package se.sics.cooja.mantismote;
@@ -44,15 +44,15 @@ import se.sics.cooja.dialogs.MessageList;
 
 /**
  * A dialog for configuring Mantis mote types and compiling KMantis mote type
- * libraries. 
- * 
+ * libraries.
+ *
  * The dialog takes a Mantis mote type as argument and pre-selects the values
  * already set in that mote type before showing the dialog. Any changes made to
  * the settings are written to the mote type if the compilation is successful
  * and the user presses OK.
- * 
+ *
  * This dialog uses external tools to scan for sources and compile libraries.
- * 
+ *
  * @author Fredrik Osterlind
  */
 public class MantisMoteTypeDialog extends JDialog {
@@ -74,12 +74,12 @@ public class MantisMoteTypeDialog extends JDialog {
 
   private JTextField textID, textOutputFiles, textDescription, textMantisBinary;
   private JButton createButton, compileButton;
-  
+
   private File objFile = null;
   private File workingDir = null;
   private File libFile = null;
   private File srcFile = null;
-  
+
   private Vector<Class<? extends MoteInterface>> moteInterfaceClasses = null;
 
   private boolean settingsOK = false; // Do all settings seem correct?
@@ -92,20 +92,29 @@ public class MantisMoteTypeDialog extends JDialog {
 
   /**
    * Shows a dialog for configuring a Mantis mote type.
-   * 
-   * @param parentFrame
-   *          Parent frame for dialog
+   *
+   * @param parentContainer
+   *          Parent container for dialog
    * @param simulation
    *          Simulation holding (or that will hold) mote type
    * @param moteTypeToConfigure
    *          Mote type to configure
    * @return True if mote type configuration succeded and library is ready to be loaded
    */
-  public static boolean showDialog(Frame parentFrame, Simulation simulation,
+  public static boolean showDialog(Container parentContainer, Simulation simulation,
       MantisMoteType moteTypeToConfigure) {
 
-    final MantisMoteTypeDialog myDialog = new MantisMoteTypeDialog(
-        parentFrame);
+    MantisMoteTypeDialog myDialog = null;
+    if (parentContainer instanceof Window) {
+      myDialog = new MantisMoteTypeDialog((Window) parentContainer);
+    } else if (parentContainer instanceof Dialog) {
+      myDialog = new MantisMoteTypeDialog((Dialog) parentContainer);
+    } else if (parentContainer instanceof Frame) {
+      myDialog = new MantisMoteTypeDialog((Frame) parentContainer);
+    } else {
+      logger.fatal("Unknown parent container type: " + parentContainer);
+      return false;
+    }
 
     myDialog.myMoteType = moteTypeToConfigure;
     myDialog.allOtherTypes = simulation.getMoteTypes();
@@ -160,7 +169,7 @@ public class MantisMoteTypeDialog extends JDialog {
     myDialog.moteInterfaceClasses = new Vector<Class<? extends MoteInterface>>();
     for (String moteInterface : moteInterfaces) {
       try {
-        Class<? extends MoteInterface> newMoteInterfaceClass = 
+        Class<? extends MoteInterface> newMoteInterfaceClass =
           simulation.getGUI().tryLoadClass(simulation.getGUI(), MoteInterface.class, moteInterface);
         myDialog.moteInterfaceClasses.add(newMoteInterfaceClass);
         /*logger.info("Loaded Mantis mote interface: " + newMoteInterfaceClass);*/
@@ -172,7 +181,7 @@ public class MantisMoteTypeDialog extends JDialog {
 
     // Set position and focus of dialog
     myDialog.pack();
-    myDialog.setLocationRelativeTo(parentFrame);
+    myDialog.setLocationRelativeTo(parentContainer);
     myDialog.textDescription.requestFocus();
     myDialog.textDescription.select(0, myDialog.textDescription.getText().length());
     myDialog.pathsWereUpdated();
@@ -185,9 +194,20 @@ public class MantisMoteTypeDialog extends JDialog {
     return false;
   }
 
+  private MantisMoteTypeDialog(Dialog dialog) {
+    super(dialog, "Configure Mantis Mote Type", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
+  private MantisMoteTypeDialog(Window window) {
+    super(window, "Configure Mantis Mote Type", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
   private MantisMoteTypeDialog(Frame frame) {
-    super(frame, "Configure Mantis Mote Type", true);
+    super(frame, "Configure Mantis Mote Type", ModalityType.TOOLKIT_MODAL);
+    setupDialog();
+  }
 
+  private void setupDialog() {
     myDialog = this;
 
     JLabel label;
@@ -361,8 +381,9 @@ public class MantisMoteTypeDialog extends JDialog {
         if (compilationThread != null && compilationThread.isAlive()) {
           compilationThread.interrupt();
         }
-        if (progressDialog != null && progressDialog.isDisplayable())
+        if (progressDialog != null && progressDialog.isDisplayable()) {
           progressDialog.dispose();
+        }
       }
     });
 
@@ -385,30 +406,31 @@ public class MantisMoteTypeDialog extends JDialog {
       if (srcFile.exists()) {
         srcFile.delete();
       }
-      
+
       if (srcFile.exists()) {
         throw new Exception("could not remove old source file");
       }
-      
+
       generateSourceFile(srcFile);
-      
+
       if (!srcFile.exists()) {
         throw new Exception("source file not created");
       }
     } catch (Exception e) {
       libraryCreatedOK = false;
       progressBar.setBackground(Color.ORANGE);
-      if (e.getMessage() != null)
+      if (e.getMessage() != null) {
         progressBar.setString("source file generation failed: " + e.getMessage());
-      else
+      } else {
         progressBar.setString("source file generation failed");
-         
+      }
+
       progressBar.setIndeterminate(false);
       progressBar.setValue(0);
       createButton.setEnabled(libraryCreatedOK);
       return;
     }
-    
+
     // Test compile shared library
     progressBar.setString("..compiling..");
 
@@ -418,7 +440,7 @@ public class MantisMoteTypeDialog extends JDialog {
 
     compilationThread = new Thread(new Runnable() {
       public void run() {
-        compilationSucceded = 
+        compilationSucceded =
           MantisMoteTypeDialog.compileLibrary(
               libFile,
               objFile,
@@ -445,8 +467,9 @@ public class MantisMoteTypeDialog extends JDialog {
       libraryCreatedOK = false;
     } else {
       libraryCreatedOK = true;
-      if (!libFile.exists())
+      if (!libFile.exists()) {
         libraryCreatedOK = false;
+      }
     }
 
     if (libraryCreatedOK) {
@@ -467,7 +490,7 @@ public class MantisMoteTypeDialog extends JDialog {
   /**
    * Generates new source file by reading default source template and replacing
    * certain field in order to be loadable from given Java class.
-   * 
+   *
    * @param outputFile Source file to create
    * @throws Exception
    */
@@ -500,7 +523,7 @@ public class MantisMoteTypeDialog extends JDialog {
       }
 
       sourceFile = new BufferedReader(reader);
-      
+
       destFile = new BufferedWriter(new OutputStreamWriter(
           new FileOutputStream(outputFile)));
 
@@ -515,10 +538,12 @@ public class MantisMoteTypeDialog extends JDialog {
       sourceFile.close();
     } catch (Exception e) {
       try {
-        if (destFile != null)
+        if (destFile != null) {
           destFile.close();
-        if (sourceFile != null)
+        }
+        if (sourceFile != null) {
           sourceFile.close();
+        }
       } catch (Exception e2) {
       }
 
@@ -526,10 +551,10 @@ public class MantisMoteTypeDialog extends JDialog {
       throw e;
     }
   }
-  
+
   /**
    * Compiles a mote type shared library using the standard Mantis makefile.
-   * 
+   *
    * @param libFile Library file to create
    * @param binFile Binary file to link against
    * @param sourceFile Source file to compile
@@ -545,42 +570,48 @@ public class MantisMoteTypeDialog extends JDialog {
 
     // Check needed files
     if (!workingDir.exists()) {
-      if (errorStream != null)
+      if (errorStream != null) {
         errorStream.println("Bad paths");
+      }
       logger.fatal("Working directory does not exist");
       return false;
     }
     if (!workingDir.isDirectory()) {
-      if (errorStream != null)
+      if (errorStream != null) {
         errorStream.println("Bad paths");
+      }
       logger.fatal("Working directory is not a directory");
       return false;
     }
 
     if (libFile.exists()) {
-      if (errorStream != null)
+      if (errorStream != null) {
         errorStream.println("Bad output filenames");
+      }
       logger.fatal("Library already exists");
       return false;
     }
 
     if (!sourceFile.exists()) {
-      if (errorStream != null)
+      if (errorStream != null) {
         errorStream.println("Bad dependency files");
+      }
       logger.fatal("Source file not found");
       return false;
     }
 
     if (!binFile.exists()) {
-      if (errorStream != null)
+      if (errorStream != null) {
         errorStream.println("Bad dependency files");
+      }
       logger.fatal("Link object file not found");
       return false;
     }
 
     if (CoreComm.hasLibraryFileBeenLoaded(libFile)) {
-      if (errorStream != null)
+      if (errorStream != null) {
         errorStream.println("Bad output filenames");
+      }
       logger.fatal("A library has already been loaded with the same name before");
       return false;
     }
@@ -606,8 +637,9 @@ public class MantisMoteTypeDialog extends JDialog {
           String readLine;
           try {
             while ((readLine = input.readLine()) != null) {
-              if (outputStream != null && readLine != null)
+              if (outputStream != null && readLine != null) {
                 outputStream.println(readLine);
+              }
             }
           } catch (IOException e) {
             logger.warn("Error while reading from process");
@@ -620,8 +652,9 @@ public class MantisMoteTypeDialog extends JDialog {
           String readLine;
           try {
             while ((readLine = err.readLine()) != null) {
-              if (errorStream != null && readLine != null)
+              if (errorStream != null && readLine != null) {
                 errorStream.println(readLine);
+              }
             }
           } catch (IOException e) {
             logger.warn("Error while reading from process");
@@ -711,39 +744,42 @@ public class MantisMoteTypeDialog extends JDialog {
     } else {
       textOutputFiles.setText("");
     }
-    
+
     createButton.setEnabled(libraryCreatedOK = false);
     compileButton.setEnabled(settingsOK);
   }
-  
+
 
   private class MoteTypeEventHandler
       implements
         ActionListener,
         DocumentListener {
     public void insertUpdate(DocumentEvent e) {
-      if (myDialog.isVisible())
+      if (myDialog.isVisible()) {
         javax.swing.SwingUtilities.invokeLater(new Runnable() {
           public void run() {
             pathsWereUpdated();
           }
         });
+      }
     }
     public void removeUpdate(DocumentEvent e) {
-      if (myDialog.isVisible())
+      if (myDialog.isVisible()) {
         javax.swing.SwingUtilities.invokeLater(new Runnable() {
           public void run() {
             pathsWereUpdated();
           }
         });
+      }
     }
     public void changedUpdate(DocumentEvent e) {
-      if (myDialog.isVisible())
+      if (myDialog.isVisible()) {
         javax.swing.SwingUtilities.invokeLater(new Runnable() {
           public void run() {
             pathsWereUpdated();
           }
         });
+      }
     }
     public void actionPerformed(ActionEvent e) {
       if (e.getActionCommand().equals("cancel")) {
@@ -783,8 +819,9 @@ public class MantisMoteTypeDialog extends JDialog {
         }
         createButton.setEnabled(libraryCreatedOK = false);
         pathsWereUpdated();
-      } else
+      } else {
         logger.warn("Unhandled action: " + e.getActionCommand());
+      }
 
       createButton.setEnabled(libraryCreatedOK = false);
 
diff --git a/tools/cooja/java/se/sics/cooja/motes/AbstractApplicationMoteType.java b/tools/cooja/java/se/sics/cooja/motes/AbstractApplicationMoteType.java
index cde545e03..3ed37cc1d 100644
--- a/tools/cooja/java/se/sics/cooja/motes/AbstractApplicationMoteType.java
+++ b/tools/cooja/java/se/sics/cooja/motes/AbstractApplicationMoteType.java
@@ -1,7 +1,7 @@
 /*
  * Copyright (c) 2007, Swedish Institute of Computer Science. All rights
  * reserved.
- * 
+ *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  * 1. Redistributions of source code must retain the above copyright notice,
@@ -12,7 +12,7 @@
  * Institute nor the names of its contributors may be used to endorse or promote
  * products derived from this software without specific prior written
  * permission.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND ANY
  * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -23,13 +23,14 @@
  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- * 
- * $Id: AbstractApplicationMoteType.java,v 1.1 2007/05/31 07:21:29 fros4943 Exp $
+ *
+ * $Id: AbstractApplicationMoteType.java,v 1.2 2008/02/12 15:10:49 fros4943 Exp $
  */
 
 package se.sics.cooja.motes;
 
 import java.awt.BorderLayout;
+import java.awt.Container;
 import java.awt.Dimension;
 import java.util.*;
 import javax.swing.*;
@@ -62,7 +63,7 @@ public abstract class AbstractApplicationMoteType implements MoteType {
     description = "Application Mote Type #" + identifier;
   }
 
-  public boolean configureAndInit(JFrame parentFrame, Simulation simulation, boolean visAvailable) {
+  public boolean configureAndInit(Container parentContainer, Simulation simulation, boolean visAvailable) {
 
     if (identifier == null) {
       // Create unique identifier
@@ -104,7 +105,7 @@ public abstract class AbstractApplicationMoteType implements MoteType {
 
   /**
    * Returns all mote interfaces of this mote type
-   * 
+   *
    * @return All mote interfaces
    */
   public Vector<Class<? extends MoteInterface>> getMoteInterfaces() {
@@ -113,7 +114,7 @@ public abstract class AbstractApplicationMoteType implements MoteType {
 
   /**
    * Set mote interfaces of this mote type
-   * 
+   *
    * @param moteInterfaces
    *          New mote interfaces
    */
@@ -233,7 +234,7 @@ public abstract class AbstractApplicationMoteType implements MoteType {
       }
     }
 
-    boolean createdOK = configureAndInit(GUI.frame, simulation, visAvailable);
+    boolean createdOK = configureAndInit(GUI.getTopParentContainer(), simulation, visAvailable);
     return createdOK;
   }
 
diff --git a/tools/cooja/java/se/sics/cooja/motes/DisturberMoteType.java b/tools/cooja/java/se/sics/cooja/motes/DisturberMoteType.java
index 5110532a4..3c84cabad 100644
--- a/tools/cooja/java/se/sics/cooja/motes/DisturberMoteType.java
+++ b/tools/cooja/java/se/sics/cooja/motes/DisturberMoteType.java
@@ -32,6 +32,7 @@
 package se.sics.cooja.motes;
 
 import java.awt.BorderLayout;
+import java.awt.Container;
 import java.awt.Dimension;
 import java.util.*;
 import javax.swing.*;
@@ -76,7 +77,7 @@ public class DisturberMoteType implements MoteType {
     return new DisturberMote(this, simulation);
   }
 
-  public boolean configureAndInit(JFrame parentFrame, Simulation simulation, boolean visAvailable) {
+  public boolean configureAndInit(Container parentContainer, Simulation simulation, boolean visAvailable) {
 
     if (identifier == null) {
       // Create unique identifier
@@ -251,7 +252,7 @@ public class DisturberMoteType implements MoteType {
       }
     }
 
-    boolean createdOK = configureAndInit(GUI.frame, simulation, visAvailable);
+    boolean createdOK = configureAndInit(GUI.getTopParentContainer(), simulation, visAvailable);
     return createdOK;
   }
 
diff --git a/tools/cooja/java/se/sics/cooja/motes/DummyMoteType.java b/tools/cooja/java/se/sics/cooja/motes/DummyMoteType.java
index 80f6deb19..f32c1885c 100644
--- a/tools/cooja/java/se/sics/cooja/motes/DummyMoteType.java
+++ b/tools/cooja/java/se/sics/cooja/motes/DummyMoteType.java
@@ -26,11 +26,12 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: DummyMoteType.java,v 1.4 2008/02/07 10:34:45 fros4943 Exp $
+ * $Id: DummyMoteType.java,v 1.5 2008/02/12 15:10:49 fros4943 Exp $
  */
 
 package se.sics.cooja.motes;
 
+import java.awt.Container;
 import java.util.*;
 
 import javax.swing.*;
@@ -61,7 +62,7 @@ public class DummyMoteType implements MoteType {
     return new DummyMote(this, simulation);
   }
 
-  public boolean configureAndInit(JFrame parentFrame, Simulation simulation, boolean visAvailable) {
+  public boolean configureAndInit(Container parentContainer, Simulation simulation, boolean visAvailable) {
 
     if (identifier == null) {
       // Create unique identifier
@@ -152,7 +153,7 @@ public class DummyMoteType implements MoteType {
       }
     }
 
-    boolean createdOK = configureAndInit(GUI.frame, simulation, visAvailable);
+    boolean createdOK = configureAndInit(GUI.getTopParentContainer(), simulation, visAvailable);
     return createdOK;
   }
 
diff --git a/tools/cooja/java/se/sics/cooja/plugins/LogListener.java b/tools/cooja/java/se/sics/cooja/plugins/LogListener.java
index 7495efaeb..6a131ea8f 100644
--- a/tools/cooja/java/se/sics/cooja/plugins/LogListener.java
+++ b/tools/cooja/java/se/sics/cooja/plugins/LogListener.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: LogListener.java,v 1.7 2008/02/08 14:42:33 fros4943 Exp $
+ * $Id: LogListener.java,v 1.8 2008/02/12 15:11:40 fros4943 Exp $
  */
 
 package se.sics.cooja.plugins;
@@ -155,7 +155,7 @@ public class LogListener extends VisPlugin {
       public void actionPerformed(ActionEvent ev) {
         JFileChooser fc = new JFileChooser();
 
-        int returnVal = fc.showSaveDialog(GUI.frame);
+        int returnVal = fc.showSaveDialog(GUI.getTopParentContainer());
         if (returnVal == JFileChooser.APPROVE_OPTION) {
           File saveFile = fc.getSelectedFile();
 
@@ -163,9 +163,8 @@ public class LogListener extends VisPlugin {
             String s1 = "Overwrite";
             String s2 = "Cancel";
             Object[] options = { s1, s2 };
-            int n = JOptionPane
-            .showOptionDialog(
-                GUI.frame,
+            int n = JOptionPane.showOptionDialog(
+                GUI.getTopParentContainer(),
                 "A file with the same name already exists.\nDo you want to remove it?",
                 "Overwrite existing file?", JOptionPane.YES_NO_OPTION,
                 JOptionPane.QUESTION_MESSAGE, null, options, s1);
diff --git a/tools/cooja/java/se/sics/cooja/plugins/Visualizer2D.java b/tools/cooja/java/se/sics/cooja/plugins/Visualizer2D.java
index d0ad4566b..604155138 100644
--- a/tools/cooja/java/se/sics/cooja/plugins/Visualizer2D.java
+++ b/tools/cooja/java/se/sics/cooja/plugins/Visualizer2D.java
@@ -26,7 +26,7 @@
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  *
- * $Id: Visualizer2D.java,v 1.11 2007/05/30 20:57:58 fros4943 Exp $
+ * $Id: Visualizer2D.java,v 1.12 2008/02/12 15:11:40 fros4943 Exp $
  */
 
 package se.sics.cooja.plugins;
@@ -45,17 +45,17 @@ import se.sics.cooja.interfaces.*;
 /**
  * Visualizer2D is an abstract mote visualizer for simulations. All motes are
  * painted in the XY-plane, as seen from positive Z axis.
- * 
+ *
  * An implementation of this class must colorize the different motes, each mote
  * has two different colors; inner and outer.
- * 
+ *
  * By right-clicking the mouse on a mote a popup menu will be displayed. From
  * this menu mote plugins can be started. or the mote can be moved. Each
  * implementation may also register its own actions to be accessed from this
  * menu.
- * 
+ *
  * A Visualizer2D observers both the simulation and all mote positions.
- * 
+ *
  * @author Fredrik Osterlind
  */
 @ClassDescription("2D Mote Visualizer")
@@ -89,7 +89,7 @@ public abstract class Visualizer2D extends VisPlugin {
   private Mote highlightedMote = null;
   private Color highlightColor = Color.GRAY;
   private Timer highlightTimer = null;
-  
+
   public interface MoteMenuAction {
     public boolean isEnabled(Mote mote);
     public String getDescription(Mote mote);
@@ -126,7 +126,7 @@ public abstract class Visualizer2D extends VisPlugin {
 
   /**
    * Registers as an simulation observer and initializes the canvas.
-   * 
+   *
    * @param simulationToVisualize
    *          Simulation to visualize
    */
@@ -188,12 +188,14 @@ public abstract class Visualizer2D extends VisPlugin {
     // Detect mote highligts
     myGUI.addMoteHighligtObserver(moteHighligtObserver = new Observer() {
       public void update(Observable obs, Object obj) {
-        if (!(obj instanceof Mote))
+        if (!(obj instanceof Mote)) {
           return;
-        
-        if (highlightTimer != null && highlightTimer.isRunning())
+        }
+
+        if (highlightTimer != null && highlightTimer.isRunning()) {
           highlightTimer.stop();
-        
+        }
+
         highlightTimer = new Timer(100, null);
         highlightedMote = (Mote) obj;
         highlightTimer.addActionListener(new ActionListener() {
@@ -207,15 +209,16 @@ public abstract class Visualizer2D extends VisPlugin {
             }
 
             // Toggle color
-            if (highlightColor == Color.GRAY)
+            if (highlightColor == Color.GRAY) {
               highlightColor = Color.CYAN;
-            else
-              highlightColor = Color.GRAY; 
+            } else {
+              highlightColor = Color.GRAY;
+            }
             highlightTimer.setDelay(highlightTimer.getDelay()-1);
             repaint();
           }
         });
-        highlightTimer.start();          
+        highlightTimer.start();
       }
     });
 
@@ -231,31 +234,34 @@ public abstract class Visualizer2D extends VisPlugin {
     // Detect mouse events
     canvas.addMouseListener(new MouseListener() {
       public void mousePressed(MouseEvent e) {
-        if (e.isPopupTrigger())
+        if (e.isPopupTrigger()) {
           myPlugin.handlePopupRequest(e.getPoint().x, e.getPoint().y);
-        else if (SwingUtilities.isLeftMouseButton(e)){
+        } else if (SwingUtilities.isLeftMouseButton(e)){
           //myPlugin.handleMoveRequest(e.getPoint().x, e.getPoint().y, false);
           beginMoveRequest(e.getPoint().x, e.getPoint().y);
         }
       }
       public void mouseReleased(MouseEvent e) {
-        if (e.isPopupTrigger())
+        if (e.isPopupTrigger()) {
           myPlugin.handlePopupRequest(e.getPoint().x, e.getPoint().y);
-        else {
+        } else {
           myPlugin.handleMoveRequest(e.getPoint().x, e.getPoint().y, true);
         }
       }
       public void mouseEntered(MouseEvent e) {
-        if (e.isPopupTrigger())
+        if (e.isPopupTrigger()) {
           myPlugin.handlePopupRequest(e.getPoint().x, e.getPoint().y);
+        }
       }
       public void mouseExited(MouseEvent e) {
-        if (e.isPopupTrigger())
+        if (e.isPopupTrigger()) {
           myPlugin.handlePopupRequest(e.getPoint().x, e.getPoint().y);
+        }
       }
       public void mouseClicked(MouseEvent e) {
-        if (e.isPopupTrigger())
+        if (e.isPopupTrigger()) {
           myPlugin.handlePopupRequest(e.getPoint().x, e.getPoint().y);
+        }
       }
     });
 
@@ -283,7 +289,7 @@ public abstract class Visualizer2D extends VisPlugin {
 
     // Add menu action for clicking mote button
     addMoteMenuAction(new ButtonClickMoteMenuAction());
-    
+
     try {
       setSelected(true);
     } catch (java.beans.PropertyVetoException e) {
@@ -293,7 +299,7 @@ public abstract class Visualizer2D extends VisPlugin {
 
   /**
    * Add new mote menu action.
-   * 
+   *
    * @see MoteMenuAction
    * @param menuAction Menu action
    */
@@ -303,8 +309,9 @@ public abstract class Visualizer2D extends VisPlugin {
 
   private void handlePopupRequest(final int x, final int y) {
     final Vector<Mote> foundMotes = findMotesAtPosition(x, y);
-    if (foundMotes == null || foundMotes.size() == 0)
+    if (foundMotes == null || foundMotes.size() == 0) {
       return;
+    }
 
     JPopupMenu pickMoteMenu = new JPopupMenu();
     pickMoteMenu.add(new JLabel("Select action:"));
@@ -312,10 +319,6 @@ public abstract class Visualizer2D extends VisPlugin {
 
     // Add 'show mote plugins'-actions
     for (final Mote mote : foundMotes) {
-      final Point pos = new Point(canvas.getLocationOnScreen().x + x, canvas
-          .getLocationOnScreen().y
-          + y);
-
       pickMoteMenu.add(simulation.getGUI().createMotePluginsSubmenu(mote));
     }
 
@@ -345,8 +348,9 @@ public abstract class Visualizer2D extends VisPlugin {
 
   private void beginMoveRequest(final int x, final int y) {
     final Vector<Mote> foundMotes = findMotesAtPosition(x, y);
-    if (foundMotes == null || foundMotes.size() == 0)
+    if (foundMotes == null || foundMotes.size() == 0) {
       return;
+    }
 
     moteMoveBeginTime = System.currentTimeMillis();
     beginMoveRequest(foundMotes.get(0));
@@ -360,7 +364,7 @@ public abstract class Visualizer2D extends VisPlugin {
 
   private void handleMoveRequest(final int x, final int y,
       boolean wasJustReleased) {
-    
+
     if (!moteIsBeingMoved) {
       return;
     }
@@ -374,7 +378,7 @@ public abstract class Visualizer2D extends VisPlugin {
     // Stopped moving mote
     canvas.setCursor(Cursor.getDefaultCursor());
     moteIsBeingMoved = false;
-    
+
     Position newXYValues = transformPixelToPositon(new Point(x, y));
 
     if (moteMoveBeginTime <= 0 || System.currentTimeMillis() - moteMoveBeginTime > 300) {
@@ -382,7 +386,7 @@ public abstract class Visualizer2D extends VisPlugin {
           + "\nX=" + newXYValues.getXCoordinate() + "\nY="
           + newXYValues.getYCoordinate() + "\nZ="
           + moteToMove.getInterfaces().getPosition().getZCoordinate());
-      
+
       if (returnValue == JOptionPane.OK_OPTION) {
         moteToMove.getInterfaces().getPosition().setCoordinates(
             newXYValues.getXCoordinate(), newXYValues.getYCoordinate(),
@@ -396,7 +400,7 @@ public abstract class Visualizer2D extends VisPlugin {
 
   /**
    * Returns all motes at given position.
-   * 
+   *
    * @param clickedX
    *          X coordinate
    * @param clickedY
@@ -428,8 +432,9 @@ public abstract class Visualizer2D extends VisPlugin {
         motesFound.add(simulation.getMote(i));
       }
     }
-    if (motesFound.size() == 0)
+    if (motesFound.size() == 0) {
       return null;
+    }
 
     return motesFound;
   }
@@ -437,13 +442,13 @@ public abstract class Visualizer2D extends VisPlugin {
   /**
    * Get colors a certain mote should be painted with. May be overridden to get
    * a different color scheme.
-   * 
+   *
    * Normally this method returns an array of two colors, one for the state
    * (outer circle), the other for the type (inner circle).
-   * 
+   *
    * If this method only returns one color, the entire mote will be painted
    * using that.
-   * 
+   *
    * @param mote
    *          Mote to paint
    * @return Color[] { Inner color, Outer color }
@@ -479,7 +484,7 @@ public abstract class Visualizer2D extends VisPlugin {
         g.setColor(moteColors[0]);
         g.fillOval(x - MOTE_RADIUS, y - MOTE_RADIUS, 2 * MOTE_RADIUS,
             2 * MOTE_RADIUS);
-      } 
+      }
 
       g.setColor(Color.BLACK);
       g.drawOval(x - MOTE_RADIUS, y - MOTE_RADIUS, 2 * MOTE_RADIUS,
@@ -511,37 +516,43 @@ public abstract class Visualizer2D extends VisPlugin {
     for (int i = 0; i < simulation.getMotesCount(); i++) {
       motePos = simulation.getMote(i).getInterfaces().getPosition();
 
-      if (motePos.getXCoordinate() < smallestXCoord)
+      if (motePos.getXCoordinate() < smallestXCoord) {
         smallestXCoord = motePos.getXCoordinate();
+      }
 
-      if (motePos.getXCoordinate() > biggestXCoord)
+      if (motePos.getXCoordinate() > biggestXCoord) {
         biggestXCoord = motePos.getXCoordinate();
+      }
 
-      if (motePos.getYCoordinate() < smallestYCoord)
+      if (motePos.getYCoordinate() < smallestYCoord) {
         smallestYCoord = motePos.getYCoordinate();
+      }
 
-      if (motePos.getYCoordinate() > biggestYCoord)
+      if (motePos.getYCoordinate() > biggestYCoord) {
         biggestYCoord = motePos.getYCoordinate();
+      }
 
     }
 
     if ((biggestXCoord - smallestXCoord) == 0) {
       factorXCoordToPixel = 1;
-    } else
+    } else {
       factorXCoordToPixel = ((double) canvas.getPreferredSize().width - 2 * CANVAS_BORDER_WIDTH)
           / (biggestXCoord - smallestXCoord);
+    }
 
     if ((biggestYCoord - smallestYCoord) == 0) {
       factorYCoordToPixel = 1;
-    } else
+    } else {
       factorYCoordToPixel = ((double) canvas.getPreferredSize().height - 2 * CANVAS_BORDER_WIDTH)
           / (biggestYCoord - smallestYCoord);
+    }
   }
 
   /**
    * Transforms a real-world position to a pixel which can be painted onto the
    * current sized canvas.
-   * 
+   *
    * @param pos
    *          Real-world position
    * @return Pixel coordinates
@@ -554,7 +565,7 @@ public abstract class Visualizer2D extends VisPlugin {
   /**
    * Transforms real-world coordinates to a pixel which can be painted onto the
    * current sized canvas.
-   * 
+   *
    * @param x Real world X
    * @param y Real world Y
    * @param z Real world Z (ignored)
@@ -566,7 +577,7 @@ public abstract class Visualizer2D extends VisPlugin {
 
   /**
    * Transforms a pixel coordinate to a real-world. Z-value will always be 0.
-   * 
+   *
    * @param pixelPos
    *          On-screen pixel coordinate
    * @return Real world coordinate (z=0).
@@ -593,11 +604,11 @@ public abstract class Visualizer2D extends VisPlugin {
         + CANVAS_BORDER_WIDTH;
   }
   private double factorXPixelToCoord(int xPixel) {
-    return ((double) (xPixel - CANVAS_BORDER_WIDTH) / factorXCoordToPixel)
+    return ((xPixel - CANVAS_BORDER_WIDTH) / factorXCoordToPixel)
         + smallestXCoord;
   }
   private double factorYPixelToCoord(int yPixel) {
-    return ((double) (yPixel - CANVAS_BORDER_WIDTH) / factorYCoordToPixel)
+    return ((yPixel - CANVAS_BORDER_WIDTH) / factorYCoordToPixel)
         + smallestYCoord;
   }