diff --git a/src/GF/Shell/Commands.hs b/src/GF/Shell/Commands.hs
index aac758ae7..42a4f013c 100644
--- a/src/GF/Shell/Commands.hs
+++ b/src/GF/Shell/Commands.hs
@@ -431,7 +431,7 @@ displaySStateJavaX env state = unlines $ tagXML "gfedit" $ concat [
   zipper = stateSState state
   linAll = map lin lgrs
   gr     = firstStateGrammar env
-  mark   = markOptJava -- to be: markOptXML
+  mark   = markOptJava  --to be: markOptXML 
 
 langAbstract = language "Abstract"
 langXML      = language "XML"
diff --git a/src/JavaGUI/GFEditor.java b/src/JavaGUI/GFEditor.java
index 2625f2e3a..4fb7699ef 100644
--- a/src/JavaGUI/GFEditor.java
+++ b/src/JavaGUI/GFEditor.java
@@ -1,4 +1,4 @@
-//package javaGUI;                                 
+//package javaGUI;                                
 
 import java.awt.*;
 import java.awt.event.*;
@@ -10,9 +10,15 @@ import java.io.*;
 import java.util.*;
 //import gfWindow.GrammarFilter;
 
-public class GFEditor extends JFrame implements ActionListener, KeyListener {
+public class GFEditor extends JFrame implements ActionListener, CaretListener,
+    KeyListener {                        
 
     public static boolean debug = false;
+    public static String focusPosition="";
+    public static int selStart = -1;
+    public static int selEnd = -1;
+    public static String restString = "";
+
     public static boolean newObject = false;
     public static boolean finished = false;
     private String parseInput = "";
@@ -25,6 +31,7 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
     private static String treeString = "";
     private static String fileString = "";
     public static Vector commands = new Vector();
+    public static Vector outputVector = new Vector();
     public static Hashtable nodeTable = new Hashtable();
     JFileChooser fc1 = new  JFileChooser("./");
     JFileChooser fc = new  JFileChooser("./");
@@ -41,8 +48,6 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
     private static boolean waiting = false;
     public static boolean treeChanged = true;
     private static String result;
-    private static int selectionStart;
-    private static int selectionEnd;
     private static BufferedReader fromProc;   
     private static BufferedWriter toProc;
     private static String commandPath = new String("GF");
@@ -229,6 +234,7 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
         cp = getContentPane();
         cp.setLayout(new BorderLayout());
         output.setToolTipText("Linearizations' display area");   
+        output.addCaretListener(this);
         output.setEditable(false);
         output.setLineWrap(true);
         output.setWrapStyleWord(true);
@@ -433,7 +439,7 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
                 result = fromProc.readLine();
                 if (debug) System.out.println("1 "+result);
               }
-              output.append(outputString);
+              appendMarked(outputString, -1,-1);
               while ((result.indexOf("newcat")==-1)&&(result.indexOf("<lin ")==-1)){
                 result = fromProc.readLine();
                 if (debug) System.out.println("1 "+result);
@@ -467,7 +473,7 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
                 }                                   
               }
             }           
-            output.append("*** NOTHING MORE TO READ FROM " + commandPath + "\n");
+            appendMarked("*** NOTHING MORE TO READ FROM " + commandPath + "\n", -1,-1);
           } catch (IOException e) {
           System.out.println("Could not read from external process");
         }
@@ -478,6 +484,7 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
              output.setText("");
              outputString = ""; 
              if (debug) System.out.println("output cleared");     
+             outputVector = new Vector();             
              toProc.write(text, 0, text.length());
              toProc.newLine();
              toProc.flush();
@@ -612,7 +619,7 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
           if (debug) System.out.println("7 "+result);                     
         }
         if (s.length()>1)
-          output.append("-------------"+'\n'+s);  
+          appendMarked("-------------"+'\n'+s,-1,-1);  
         result = fromProc.readLine();             
         if (debug) System.out.println("7 "+result);          
      } catch(IOException e){ }
@@ -712,65 +719,60 @@ public class GFEditor extends JFrame implements ActionListener, KeyListener {
   }
 
   public void outputAppend(){
-    int i, j, k, l, l2, m;
-    i=result.indexOf("type=");
-    j=result.indexOf('>',i);
+    int i, j, k, l, l2, m=0, n=0;
     l = result.indexOf("<focus");
+    i=result.indexOf("type=",l);
+    j=result.indexOf('>',i);
     l2 = result.indexOf("focus");    
     if (l2!=-1){
 
       // in case focus tag is cut into two lines:
       if (l==-1) l=l2-7;         
-
+      m=result.indexOf("position",l);
+      System.out.println("POSITION START: "+m); 
+      n=result.indexOf("]",m);
+      System.out.println("POSITION END: "+n); 
+      focusPosition = result.substring(m+9,n);
       if (debug) System.out.println("form Lin1: "+result);
       statusLabel.setText(" "+result.substring(i+5,j));
       //cutting <focus>
-      result= result.substring(0,l)+result.substring(j+1);
-      i=result.indexOf("/f",l);
-System.out.println("/ is at the position"+i);
+      result= result.substring(0,l)+result.substring(j+2);
+      i=result.indexOf("/focus",l);
+      if (debug) System.out.println("/ is at the position"+i);
       j=result.indexOf('>',i);
-      k=result.length()-j;
+      k=result.length()-j-1;
       if (debug) System.out.println("form Lin2: "+result);
-      m = output.getText().length();
       
-      //cutting </focus>    
-      // in case focus tag is cut into two lines:
       if (debug)
         System.out.println("char at the previous position"+result.charAt(i-1));
+      //cutting </focus>    
+      // in case focus tag is cut into two lines:
       if (result.charAt(i-1)!='<') 
-        result= result.substring(0,i-8)+result.substring(j+1);
+        result= result.substring(0,i-8)+result.substring(j+2);
       else
-        result= result.substring(0,i-1)+result.substring(j+1);
+        result= result.substring(0,i-1)+result.substring(j+2);
       j= result.indexOf("<focus");
       l2 = result.indexOf("focus");    
-      // in case focus tag is cut into to lines:
+      // in case focus tag is cut into two lines:
       if ((l2!=-1)&&(j==-1)) j=l2-7;
+
+      // appending the resulting string
       // only one focus 
       if (j==-1){
-        output.append(result+'\n'); 
-        selectionStart=m+l;
-        selectionEnd=output.getText().length()-k; 
-        try {  
-          output.getHighlighter().addHighlight(selectionStart, selectionEnd, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
-//          output.getHighlighter().addHighlight(selectionStart, selectionEnd, new DefaultHighlighter.DefaultHighlightPainter(Color.white) );
-        } catch (Exception e) {}
+        System.out.println("ONE FOCUS");
+        appendMarked(result+'\n',l,result.length()-k); 
       } 
       //several focuses
       else {
-        output.append(result.substring(0,j));           
+        System.out.println("MANY FOCUSes");
+        appendMarked(result.substring(0,j),l,i);           
         result = result.substring(j); 
-        selectionStart=m+l;
-        selectionEnd=m+i-1; 
-        try {  
-//          output.getHighlighter().addHighlight(selectionStart, selectionEnd, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
-          output.getHighlighter().addHighlight(selectionStart, selectionEnd, new DefaultHighlighter.DefaultHighlightPainter(Color.white) );
-        } catch (Exception e) {}
         outputAppend();
       }
       if (debug) System.out.println("form Lin3: "+result);
     }   
-    else 
-      output.append(result+'\n');          
+    else //no focus at all (message?):
+      appendMarked(result+'\n', -1,-1);          
     firstLin=false;
   }
 
@@ -824,7 +826,7 @@ System.out.println("/ is at the position"+i);
         }
       if (visible) {   
         if (!firstLin)
-          output.append("************"+'\n');  
+          appendMarked("************"+'\n',-1,-1);  
         if (debug) System.out.println("linearization for the language: "+result);
         outputAppend();
       }
@@ -1081,8 +1083,8 @@ System.out.println("/ is at the position"+i);
            String s = JOptionPane.showInputDialog("Command:", parseInput);
            if (s!=null) {
               parseInput = s;
-              s = "gf "+s;
-              //treeChanged = true; 
+              //s = "gf "+s; This is for debugging, otherwise shift the comment to the next line.
+              treeChanged = true; 
               send(s);
            }
         }
@@ -1408,6 +1410,187 @@ System.out.println("/ is at the position"+i);
     /** Handle the key released event. */
     public void keyReleased(KeyEvent e) {
     }
+    public void caretUpdate(CaretEvent e)
+    {
+     int j = 0;
+     int start = output.getSelectionStart();
+     int end = output.getSelectionEnd();
+     System.out.println("SELECTION START POSITION: "+start);
+     System.out.println("SELECTION END POSITION: "+end);
+     if (end>0) System.out.println(output.getText().charAt(end));
+     if (start<output.getText().length()-1) 
+       {
+       while ((j< outputVector.size())&&(((MarkedArea)outputVector.elementAt(j)).end < end))
+         j++;
+       if (j<outputVector.size())
+       {  if (end>=((MarkedArea)outputVector.elementAt(j)).begin) 
+           System.out.println("SELECTEDTEXT: "+
+             ((MarkedArea)outputVector.elementAt(j)).position+"\n");
+       } else 
+           System.out.println("no position in vector of size: "+outputVector.size());
+     }
+    }
+
+    public static void appendMarked(String s, int selectionStart, int selectionEnd)
+    {
+      System.out.println("STRING: "+s);
+      int oldLength = output.getText().length();
+      int currentLength = 0;
+      int newLength=0;
+      int addedLength=0;
+      int resultCurrent=0;
+      int resultNew=0;
+      boolean selectionCheck ;
+      String position = "";
+      int j, l, l2, n;
+      restString = s;
+      if (selectionStart>-1)
+      {
+        selStart = selectionStart;
+        selEnd = selectionEnd;
+        selectionCheck = (s.substring(selectionStart, selectionEnd).indexOf("<")==-1);
+        l = restString.indexOf("<subtree");
+        l2 = restString.indexOf("</subtree");
+        while ((l2>-1)||(l>-1))
+        { 
+          if ((l<l2)&&(l>-1))
+          {
+            j = restString.indexOf(">",l);
+            n = restString.indexOf("<",j);
+            // the tag has some words to register:
+            if ((n-j)>3)
+            {
+              //getting position:
+              position = String.valueOf(outputVector.size());
+              newLength = n-j-3+l;
+              //focus has a separate position:
+              if (selectionCheck&&(selEnd<n))
+              { selectionCheck=false;
+                System.out.println("SELECTION HAS A SEPARATE POSITION"); 
+                if ((selEnd<l)&&(currentLength<l-1))
+                { 
+                   // register the selection first:
+                   newLength = l-1;
+                   outputVector.add(new MarkedArea(currentLength+oldLength, newLength+oldLength, position)); 
+                   addedLength = newLength-currentLength+1;
+                   resultCurrent = currentLength+oldLength;
+                   resultNew = newLength+oldLength;
+                   System.out.println("APPENDING SelectedZONE First Before Tag:"
+                     +restString.substring(currentLength+j-l+1,newLength+j-l+1)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+                   currentLength = newLength+1;
+                   position = String.valueOf(outputVector.size());
+      
+                   // register the rest:
+                   newLength = n-j-3+l;
+                   addedLength = newLength-currentLength+1;
+                   resultCurrent = currentLength+oldLength;
+                   resultNew = newLength+oldLength;
+                   outputVector.add(new MarkedArea(currentLength+oldLength, newLength+oldLength, position)); 
+                   System.out.println("APPENDING ZONE Second:"+restString.substring(currentLength+j-l+1,newLength+j-l+1)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+                }
+                else 
+                  if (n-selEnd<=3)
+                    if (selStart-j<=3)
+                    {   // only selection is to register:
+                      addedLength = newLength-currentLength+1;
+                      resultCurrent = currentLength+oldLength;
+                      resultNew = newLength+oldLength;
+                      outputVector.add(new MarkedArea(resultCurrent, resultNew, position)); 
+                      System.out.println("APPENDING SelectedZONE ONLy:"+restString.substring(selStart,selEnd+1)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+                      currentLength = newLength+1;
+                    } 
+                    else
+                    {
+                      // register the rest:
+                      newLength = newLength - selEnd + selStart-1;
+                      resultCurrent = currentLength+oldLength;
+                      resultNew = newLength+oldLength;
+                      addedLength = newLength-currentLength+1; 
+                      outputVector.add(new MarkedArea(resultCurrent, resultNew, position)); 
+                      System.out.println("APPENDING ZONE First:"+restString.substring(currentLength+j-l+2,newLength+j-l+3)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+                      currentLength = newLength+1;
+                      position = String.valueOf(outputVector.size());
+
+                      //selection second:
+                      newLength = currentLength + selEnd - selStart;
+                      outputVector.add(new MarkedArea(currentLength+oldLength, newLength+oldLength, position)); 
+                      addedLength = newLength-currentLength+1; 
+                      resultCurrent = currentLength+oldLength;
+                      resultNew = newLength+oldLength;
+                      System.out.println("APPENDING SelectedZONE Second:"+restString.substring(currentLength+j-l+2,newLength+j-l+3)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);            
+                    }
+                  else
+                  { // selection first?:
+                    newLength = selEnd-j+l-1;
+                    outputVector.add(new MarkedArea(currentLength+oldLength, newLength+oldLength, position)); 
+                    addedLength = newLength-currentLength+1; 
+                    resultCurrent = currentLength+oldLength;
+                    resultNew = newLength+oldLength;
+                    System.out.println("APPENDING SelectedZONE First:"+restString.substring(currentLength+j-l+1,newLength+j-l+1)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+                    currentLength = newLength+1;
+                    position = String.valueOf(outputVector.size());
+      
+                    // register the rest:
+                    newLength = n-j-3+l;
+                    outputVector.add(new MarkedArea(currentLength+oldLength, newLength+oldLength, position)); 
+                    addedLength = newLength-currentLength+1; 
+                    resultCurrent = currentLength+oldLength;
+                    resultNew = newLength+oldLength;
+                    System.out.println("APPENDING ZONE Second:"+restString.substring(currentLength+j-l+1,newLength+j-l+1)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+                  }
+              }// if selectionCheck
+              else 
+              {
+                addedLength = newLength-currentLength+1; 
+                resultCurrent = currentLength+oldLength;
+                resultNew = newLength+oldLength;
+                outputVector.add(new MarkedArea(resultCurrent, resultNew, position)); 
+                System.out.println("APPENDNG ZONE:"+restString.substring(currentLength+j-l+2,newLength+j-l+3)+
+                     "Length: "+addedLength+" POSITION: "+resultCurrent + " "+resultNew);
+              } 
+            } //some words to register                     
+            currentLength = newLength+1;
+            removeSubTreeTag(l,j+1);
+            l = restString.indexOf("<subtree");
+            l2 = restString.indexOf("</subtree");
+          } // l<l2
+          else
+          { // cutting the </subtree> tags:
+            removeSubTreeTag(l2,l2+10);
+            l2 = restString.indexOf("</subtree");
+            l = restString.indexOf("<subtree");
+          }
+        } //while
+      } //if selectionStart>-1    
+      // appending:
+      output.append(restString);
+      if (selectionStart>-1)
+      try {  
+        output.getHighlighter().addHighlight(selStart+oldLength, selEnd+oldLength, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
+//        output.getHighlighter().addHighlight(selStart+oldLength, selEnd+oldLength, new DefaultHighlighter.DefaultHighlightPainter(Color.white) );
+      } catch (Exception e) {System.out.println("highlighting problem!");}
+    }
+
+    //updating:
+    public static void removeSubTreeTag (int start, int end)
+    {
+         int difference =end-start+1;
+         restString = restString.substring(0,start)+restString.substring(end+1);
+         if (selStart > end)
+         {  selStart -=difference;
+            selEnd -=difference;            
+         } 
+         else 
+           if (selEnd < start) ;
+           else selEnd -=difference;            
+    }
 
     public void listAction(int index) {
       if (index == -1)