Index: trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDgenerateJacaretoReplay.java
===================================================================
--- trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDgenerateJacaretoReplay.java	(revision 1856)
+++ trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDgenerateJacaretoReplay.java	(revision 1857)
@@ -342,5 +342,9 @@
         StructureNode.nextRef = 0;
 
-        writeJacaretoXML(sequences, filename, classpath, basepath, classpathext);
+        int index = 1;
+        for( List<Event> sequence : sequences ) {
+            writeJacaretoXML(sequence, filename+"_"+index, classpath, basepath, classpathext);
+            index++;
+        }
     }
 
@@ -450,5 +454,5 @@
      * 
      */
-    private void writeJacaretoEvents(BufferedWriter writer, Collection<List<Event>> sequences)
+    private void writeJacaretoEvents(BufferedWriter writer, List<Event> sequence)
         throws IOException
     {
@@ -461,59 +465,57 @@
         structure.addRecordable(); // ApplicationStarter
 
-        for (List<Event> sequence : sequences) {
-            for (Iterator<Event> eventIter = sequence.iterator(); eventIter.hasNext();) {
-                Event event = eventIter.next();
-
-                if (event.getType() instanceof MouseButtonDown) {
-                    handleMouseButtonDown(writer, event);
+        for (Iterator<Event> eventIter = sequence.iterator(); eventIter.hasNext();) {
+            Event event = eventIter.next();
+
+            if (event.getType() instanceof MouseButtonDown) {
+                handleMouseButtonDown(writer, event);
+            }
+            else if (event.getType() instanceof MouseButtonUp) {
+                handleMouseButtonUp(writer, event);
+            }
+            else if (event.getType() instanceof MouseDoubleClick) {
+                handleMouseDoubleClick(writer, event);
+            }
+            else if (event.getType() instanceof MouseClick) {
+                if (event.getTarget() instanceof JFCMenuButton) {
+                    // if a menu file was provided, use the improved event
+                    // generation
+                    if (menuList != null) {
+                        if (menuElements.isEmpty()) {
+                            // parse the menu structure
+                            GUIModel model = ((IGUIElement) event.getTarget()).getGUIModel();
+                            getMenuElements(model.getRootElements(), model);
+                        }
+
+                        Stack<JFCGUIElement> hierarchy =
+                            findMenuItemHierarchy((JFCGUIElement) event.getTarget());
+
+                        while (!hierarchy.empty()) {
+                            generateFullClick(writer, event, hierarchy.pop());
+                        }
+                        continue;
+                    }
                 }
-                else if (event.getType() instanceof MouseButtonUp) {
-                    handleMouseButtonUp(writer, event);
-                }
-                else if (event.getType() instanceof MouseDoubleClick) {
-                    handleMouseDoubleClick(writer, event);
-                }
-                else if (event.getType() instanceof MouseClick) {
-                    if (event.getTarget() instanceof JFCMenuButton) {
-                        // if a menu file was provided, use the improved event
-                        // generation
-                        if (menuList != null) {
-                            if (menuElements.isEmpty()) {
-                                // parse the menu structure
-                                GUIModel model = ((IGUIElement) event.getTarget()).getGUIModel();
-                                getMenuElements(model.getRootElements(), model);
-                            }
-
-                            Stack<JFCGUIElement> hierarchy =
-                                findMenuItemHierarchy((JFCGUIElement) event.getTarget());
-
-                            while (!hierarchy.empty()) {
-                                generateFullClick(writer, event, hierarchy.pop());
-                            }
-                            continue;
-                        }
-                    }
-
-                    handleMouseClick(writer, event);
-                }
-                else if (event.getType() instanceof KeyboardFocusChange) {
-                    handleKeyboardFocusChange(writer, event);
-                }
-                else if (event.getType() instanceof MouseDragAndDrop) {
-                    handleMouseDragAndDrop(writer, event);
-                }
-                else if (event.getType() instanceof KeyPressed) {
-                    handleKeyPressed(writer, event);
-                }
-                else if (event.getType() instanceof KeyReleased) {
-                    handleKeyReleased(writer, event);
-                }
-                else if (event.getType() instanceof TextInput) {
-                    handleTextInput(writer, event);
-                }
-                else {
-                    Console.traceln(Level.WARNING, "No handler for event \"" + event +
-                        "\". Skipped.");
-                }
+
+                handleMouseClick(writer, event);
+            }
+            else if (event.getType() instanceof KeyboardFocusChange) {
+                handleKeyboardFocusChange(writer, event);
+            }
+            else if (event.getType() instanceof MouseDragAndDrop) {
+                handleMouseDragAndDrop(writer, event);
+            }
+            else if (event.getType() instanceof KeyPressed) {
+                handleKeyPressed(writer, event);
+            }
+            else if (event.getType() instanceof KeyReleased) {
+                handleKeyReleased(writer, event);
+            }
+            else if (event.getType() instanceof TextInput) {
+                handleTextInput(writer, event);
+            }
+            else {
+                Console.traceln(Level.WARNING, "No handler for event \"" + event +
+                    "\". Skipped.");
             }
         }
@@ -737,5 +739,5 @@
     }
 
-    private void writeJacaretoXML(Collection<List<Event>> sequences,
+    private void writeJacaretoXML(List<Event> sequence,
                                   String filename,
                                   String classpath,
@@ -747,5 +749,5 @@
         try {
             writeJacaretoHead(writer, classpath, basepath, classpathext);
-            writeJacaretoEvents(writer, sequences);
+            writeJacaretoEvents(writer, sequence);
             writeJacaretoTail(writer);
             writeLine(writer, "</JacaretoStructure>");
Index: trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDparseJFCDirwithJacaretoIndices.java
===================================================================
--- trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDparseJFCDirwithJacaretoIndices.java	(revision 1857)
+++ trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDparseJFCDirwithJacaretoIndices.java	(revision 1857)
@@ -0,0 +1,242 @@
+//   Copyright 2012 Georg-August-Universität Göttingen, Germany
+//
+//   Licensed under the Apache License, Version 2.0 (the "License");
+//   you may not use this file except in compliance with the License.
+//   You may obtain a copy of the License at
+//
+//       http://www.apache.org/licenses/LICENSE-2.0
+//
+//   Unless required by applicable law or agreed to in writing, software
+//   distributed under the License is distributed on an "AS IS" BASIS,
+//   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//   See the License for the specific language governing permissions and
+//   limitations under the License.
+
+package de.ugoe.cs.autoquest.plugin.jfc.commands;
+
+import java.io.File;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.logging.Level;
+
+import de.ugoe.cs.autoquest.CommandHelpers;
+import de.ugoe.cs.autoquest.eventcore.Event;
+import de.ugoe.cs.autoquest.eventcore.guimodel.GUIModel;
+import de.ugoe.cs.autoquest.eventcore.guimodel.IGUIElement;
+import de.ugoe.cs.autoquest.plugin.jfc.JFCSimplifiedLogParser;
+import de.ugoe.cs.autoquest.plugin.jfc.guimodel.JFCGUIElement;
+import de.ugoe.cs.autoquest.plugin.jfc.guimodel.JFCGUIElementSpec;
+import de.ugoe.cs.autoquest.plugin.jfc.guimodel.JFCMenu;
+import de.ugoe.cs.autoquest.plugin.jfc.guimodel.JFCMenuButton;
+import de.ugoe.cs.util.console.Command;
+import de.ugoe.cs.util.console.Console;
+import de.ugoe.cs.util.console.GlobalDataContainer;
+
+/**
+ * <p>
+ * TODO comment
+ * </p>
+ * 
+ * @author Steffen Herbold
+ */
+public class CMDparseJFCDirwithJacaretoIndices implements Command {
+
+    private List<String> menuList;
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see de.ugoe.cs.util.console.Command#run(java.util.List)
+     */
+    @Override
+    public void run(List<Object> parameters) {
+        String path;
+        String sequencesName = "sequences";
+
+        try {
+            path = (String) parameters.get(0);
+            if (parameters.size() >= 2) {
+                sequencesName = (String) parameters.get(1);
+            }
+            if (parameters.size() >= 3) {
+                menuList =
+                    Files.readAllLines(Paths.get((String) parameters.get(2)),
+                                       Charset.defaultCharset());
+            }
+
+        }
+        catch (Exception e) {
+            throw new IllegalArgumentException();
+        }
+
+        File folder = new File(path);
+        if (!folder.isDirectory()) {
+            Console.printerrln(path + " is not a directory");
+            return;
+        }
+
+        JFCSimplifiedLogParser parser = new JFCSimplifiedLogParser();
+
+        String absolutPath = folder.getAbsolutePath();
+        for (String filename : folder.list()) {
+            String source = absolutPath + File.separator + filename;
+            Console.traceln(Level.INFO, "Processing file: " + source);
+
+            try {
+                parser.parseFile(source);
+            }
+            catch (Exception e) {
+                Console.printerrln("Could not parse " + source + ": " + e.getMessage());
+            }
+        }
+
+        Collection<List<Event>> sequences = parser.getSequences();
+
+        GUIModel targets = parser.getGuiModel();
+
+        generateJacaretoIndices(targets.getRootElements(), targets);
+
+        if (GlobalDataContainer.getInstance().addData(sequencesName, sequences)) {
+            CommandHelpers.dataOverwritten(sequencesName);
+        }
+
+        if (GlobalDataContainer.getInstance().addData(sequencesName + "_targets", targets)) {
+            CommandHelpers.dataOverwritten(sequencesName + "_targets");
+        }
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see de.ugoe.cs.util.console.Command#help()
+     */
+    @Override
+    public String help() {
+        // TODO Auto-generated method stub
+        System.out.println("parseJFCDirwithJacaretoIndices <path> {<sequencesName>} {<menuFile>}");
+        return null;
+    }
+
+    // duplicates to parseJFCwithJacaretoIndices
+    private int findPopupMenuIndex(IGUIElement item, GUIModel model) {
+        // TODO: refactor
+        int index = -1;
+        List<IGUIElement> children = model.getChildren(item);
+        IGUIElement menuChild = null;
+
+        // try to identify this popup menu by looking at its children
+        // find the first menu item child of this item
+        for (IGUIElement child : children) {
+            if (child instanceof JFCMenuButton || child instanceof JFCMenu) {
+                menuChild = child;
+                break;
+            }
+        }
+
+        if (menuChild == null) {
+            // this popup menu cannot be identified
+            // TODO: exception, logging etc
+            return -1;
+        }
+
+        // find line that contains this menu item name
+        String itemName = ((JFCGUIElement) menuChild).getName().trim().toLowerCase();
+        int lineOfItem = -1;
+
+        for (int i = 0; i < menuList.size(); i++) {
+            String name = "\"" + menuList.get(i).trim().toLowerCase() + "\"";
+            if (name.equals(itemName)) {
+                lineOfItem = i;
+                break;
+            }
+        }
+
+        if (lineOfItem == -1) {
+            // failed to find this item in the menu file
+            // TODO: exception, logging etc
+            return -1;
+        }
+
+        // find menu item's parent line
+        String stripped = menuList.get(lineOfItem).replaceFirst("^ *", "");
+        int indent = menuList.get(lineOfItem).length() - stripped.length();
+
+        if (indent != 0) {
+            for (int i = lineOfItem; i >= 0; i--) {
+                stripped = menuList.get(i).replaceFirst("^ *", "");
+                int oldIndent = menuList.get(i).length() - stripped.length();
+
+                if (oldIndent < indent) {
+                    lineOfItem = i;
+                    break;
+                }
+            }
+        }
+
+        // get the item's indentation
+        stripped = menuList.get(lineOfItem).replaceFirst("^ *", "");
+        indent = menuList.get(lineOfItem).length() - stripped.length();
+
+        if (indent == 0) {
+            // top level menu item, just count in which position it is
+            for (int i = 0; i <= lineOfItem; i++) {
+                if (!menuList.get(i).startsWith(" ")) {
+                    index++;
+                }
+            }
+        }
+        else {
+            // find the topmenu index in the menu file by going backwards
+            for (int i = lineOfItem; i >= 0; i--) {
+                stripped = menuList.get(i).replaceFirst("^ *", "");
+                int oldIndent = menuList.get(i).length() - stripped.length();
+
+                if (oldIndent < indent) {
+                    index = lineOfItem - i;
+                    break;
+                }
+            }
+        }
+
+        return index;
+    }
+
+    private void generateJacaretoIndices(List<IGUIElement> elements, GUIModel targets) {
+        HashMap<String, Integer> typeCount = new HashMap<>();
+
+        for (IGUIElement child : elements) {
+            String type = child.getSpecification().getType();
+            Integer count = typeCount.get(type);
+
+            if (count == null) {
+                count = 0;
+                typeCount.put(type, count);
+            }
+            else {
+                typeCount.put(type, ++count);
+            }
+
+            if (menuList != null && type.equals("javax.swing.JPopupMenu")) {
+                // try to use a workaround for popup menu index problems
+                int index = findPopupMenuIndex((IGUIElement) child, targets);
+                if (index != -1) {
+                    ((JFCGUIElementSpec) child.getSpecification()).setAltIndex(index);
+                }
+                else {
+                    // workaround failed, use normal method as fallback
+                    ((JFCGUIElementSpec) child.getSpecification()).setAltIndex(count);
+                }
+            }
+            else {
+                ((JFCGUIElementSpec) child.getSpecification()).setAltIndex(count);
+            }
+
+            generateJacaretoIndices(targets.getChildren(child), targets);
+        }
+    }
+
+}
