Index: /trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDgenerateAltIndex.java
===================================================================
--- /trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDgenerateAltIndex.java	(revision 1956)
+++ /trunk/autoquest-plugin-jfc/src/main/java/de/ugoe/cs/autoquest/plugin/jfc/commands/CMDgenerateAltIndex.java	(revision 1956)
@@ -0,0 +1,253 @@
+//   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.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+
+import de.ugoe.cs.autoquest.CommandHelpers;
+import de.ugoe.cs.autoquest.SequenceInstanceOf;
+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.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.GlobalDataContainer;
+
+/**
+ * <p>
+ * TODO comment
+ * </p>
+ * 
+ * @author Daniel May
+ */
+public class CMDgenerateAltIndex implements Command {
+
+    private List<String> menuList;
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see de.ugoe.cs.util.console.Command#run(java.util.List)
+     */
+    @SuppressWarnings("unchecked")
+    @Override
+    public void run(List<Object> parameters) {
+        String sequencesName = "sequences";
+
+        try {
+            sequencesName = (String) parameters.get(0);
+            if (parameters.size() >= 2) {
+                menuList =
+                    Files.readAllLines(Paths.get((String) parameters.get(1)),
+                                       Charset.defaultCharset());
+            }
+        }
+        catch (Exception e) {
+            throw new IllegalArgumentException();
+        }
+
+        Collection<List<Event>> sequences = null;
+        Object dataObject = GlobalDataContainer.getInstance().getData(sequencesName);
+        if (dataObject == null) {
+            CommandHelpers.objectNotFoundMessage(sequencesName);
+            return;
+        }
+        if (!SequenceInstanceOf.isCollectionOfSequences(dataObject)) {
+            CommandHelpers.objectNotType(sequencesName, "Collection<List<Event<?>>>");
+            return;
+        }
+        sequences = (Collection<List<Event>>) dataObject;
+        GUIModel model = null;
+
+        for (List<Event> sequence : sequences) {
+            if (model == null) {
+                // generate jacareto indices for the GUI model of this sequence
+                JFCGUIElement element = (JFCGUIElement) sequence.get(0).getTarget();
+                model = element.getGUIModel();
+                generateJacaretoIndices(model.getRootElements(), model);
+            }
+            else {
+                for (Iterator<Event> eventIter = sequence.iterator(); eventIter.hasNext();) {
+                    // find and set the alt index for every target
+                    IGUIElement target = (IGUIElement) eventIter.next().getTarget();
+                    findAltIndex(target, model.getRootElements(), model);
+                }
+            }
+        }
+    }
+
+    private void findAltIndex(IGUIElement target, List<IGUIElement> elements, GUIModel model) {
+        int altIndex = ((JFCGUIElementSpec) target.getSpecification()).getAltIndex();
+
+        if (altIndex < 0) {
+            for (IGUIElement child : elements) {
+                if (target.equals(child)) {
+                    int childAltIndex =
+                        ((JFCGUIElementSpec) child.getSpecification()).getAltIndex();
+
+                    if (childAltIndex > -1) {
+                        ((JFCGUIElementSpec) target.getSpecification()).setAltIndex(childAltIndex);
+                    }
+                    else {
+                        findAltIndex(target, model.getChildren(child), model);
+                    }
+                }
+                else {
+                    findAltIndex(target, model.getChildren(child), model);
+                }
+            }
+        }
+    }
+
+    /*
+     * (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);
+        }
+    }
+
+}