X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=604da7b405a585062b0fcd0e0d8621d96d102202;hb=22b7f97726482cb0ee32389811126e62aaead61d;hp=01bea4d2ca495a78d649b46ceea508837daecc2b;hpb=d355ad106f73e0de0abc3fb3f375af4eaf352591;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 01bea4d..604da7b 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -23,6 +23,7 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
+import jalview.commands.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
@@ -36,13 +37,20 @@ public class AlignFrame extends Frame implements ActionListener,
 {
   public AlignmentPanel alignPanel;
   public AlignViewport viewport;
-  int NEW_WINDOW_WIDTH = 700;
-  int NEW_WINDOW_HEIGHT = 500;
-  jalview.bin.JalviewLite applet;
+  int DEFAULT_WIDTH = 700;
+  int DEFAULT_HEIGHT = 500;
 
+  String jalviewServletURL;
 
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
+
+   public AlignFrame(AlignmentI al,
+                     jalview.bin.JalviewLite applet,
+                     String title,
+                     boolean embedded)
   {
+
+    jalviewServletURL = applet.getParameter("APPLICATION_URL");
+
     try{
       jbInit();
     }catch(Exception ex)
@@ -50,12 +58,16 @@ public class AlignFrame extends Frame implements ActionListener,
       ex.printStackTrace();
     }
 
-    this.applet = applet;
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
 
+    viewport.updateConservation(alignPanel);
+    viewport.updateConsensus(alignPanel);
+
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
+    seqLimits.setState(viewport.showJVSuffix);
+
     if(applet!=null)
     {
       String param = applet.getParameter("sortBy");
@@ -83,13 +95,13 @@ public class AlignFrame extends Frame implements ActionListener,
         if (param != null)
         {
           int width = Integer.parseInt(param);
-          NEW_WINDOW_WIDTH = width;
+          DEFAULT_WIDTH = width;
         }
         param = applet.getParameter("windowHeight");
         if (param != null)
         {
           int height = Integer.parseInt(param);
-          NEW_WINDOW_HEIGHT = height;
+          DEFAULT_HEIGHT = height;
         }
       }
       catch (Exception ex)
@@ -102,22 +114,20 @@ public class AlignFrame extends Frame implements ActionListener,
    this.addKeyListener(this);
    alignPanel.seqPanel.seqCanvas.addKeyListener(this);
    alignPanel.idPanel.idCanvas.addKeyListener(this);
-
-    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-     public void propertyChange(java.beans.PropertyChangeEvent evt)
-     {
-       if (evt.getPropertyName().equals("alignment"))
-       {
-         alignmentChanged();
-       }
-     }
-   });
-
-
-   add(alignPanel, BorderLayout.CENTER);
-   jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-
+   alignPanel.scalePanel.addKeyListener(this);
+   alignPanel.annotationPanel.addKeyListener(this);
+
+
+   if(embedded)
+   {
+     setEmbedded();
+   }
+   else
+   {
+     add(alignPanel, BorderLayout.CENTER);
+     jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+                                      DEFAULT_HEIGHT);
+   }
    alignPanel.validate();
    alignPanel.repaint();
   }
@@ -138,88 +148,44 @@ public class AlignFrame extends Frame implements ActionListener,
    * @param String DOCUMENT ME!
    */
 
-  public void parseFeaturesFile(String file)
+  public void parseFeaturesFile(String file, String type)
   {
-    try
+    Hashtable featureLinks = new Hashtable();
+    boolean featuresFile = false;
+    try{
+      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours,
+                                         featureLinks,
+                                         true);
+    }
+    catch(Exception ex)
     {
-      URL url = new URL(file);
-
-      BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));
-      SequenceI seq = null;
-      String line, type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-      int lineNo = 0;
-      while ( (line = in.readLine()) != null)
-      {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
-        {
-          type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = st.nextToken();
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = viewport.alignment.findIndex(viewport.alignment.findName(
-                token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
-
-          type = st.nextToken();
-
-          if(fr.getColour(type)==null)
-          {
-            // Probably the old style groups file
-            UserColourScheme ucs = new UserColourScheme(type);
-            fr.setColour(type, ucs.findColour("A"));
-          }
-
-          sf = new SequenceFeature(type, desc, "", start, end);
-
-          seq.addSequenceFeature(sf);
-        }
-      }
+      ex.printStackTrace();
+    }
 
+    if(featuresFile)
+    {
+      if(featureLinks.size()>0)
+        alignPanel.seqPanel.seqCanvas
+            .getFeatureRenderer().featureLinks = featureLinks;
       viewport.showSequenceFeatures = true;
-      viewMenu.addSeparator();
-      viewMenu.add(sequenceFeatures);
-      viewMenu.add(featureSettings);
-
-
+      sequenceFeatures.setState(true);
       alignPanel.repaint();
-
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex);
     }
+
   }
 
+
   public void keyPressed(KeyEvent evt)
   {
+    if (viewport.cursorMode
+        && evt.getKeyCode() >= KeyEvent.VK_0
+        && evt.getKeyCode() <= KeyEvent.VK_9)
+    {
+      alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+    }
+
     switch (evt.getKeyCode())
     {
       case 27: // escape key
@@ -232,15 +198,19 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_C:
+        if (viewport.cursorMode && !evt.isControlDown())
+        {
+          alignPanel.seqPanel.setCursorColumn();
+        }
         if (evt.isControlDown() || evt.isMetaDown())
         {
           copy_actionPerformed();
         }
         break;
       case KeyEvent.VK_V:
-        if (evt.isControlDown() || evt.isMetaDown())
+        if (evt.isControlDown())
         {
-          paste(true);
+          paste(evt.isShiftDown());
         }
         break;
       case KeyEvent.VK_A:
@@ -250,22 +220,220 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_DOWN:
-        moveSelectedSequences(false);
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.moveCursor(0,1);
+        }
+        else
+          moveSelectedSequences(false);
         break;
+
       case KeyEvent.VK_UP:
-        moveSelectedSequences(true);
+        if (viewport.cursorMode)
+        {
+          alignPanel.seqPanel.moveCursor(0,-1);
+        }
+        else
+          moveSelectedSequences(true);
+        break;
+
+      case KeyEvent.VK_LEFT:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.moveCursor(-1,0);
+        }
         break;
+
+      case KeyEvent.VK_RIGHT:
+        if (viewport.cursorMode)
+        {
+          alignPanel.seqPanel.moveCursor(1,0);
+        }
+        break;
+      case KeyEvent.VK_SPACE:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                                                || evt.isShiftDown()
+                                                || evt.isAltDown()
+              );
+        }
+        break;
+
+      case KeyEvent.VK_DELETE:
+      case KeyEvent.VK_BACK_SPACE:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                                || evt.isShiftDown()
+                                                || evt.isAltDown());
+        }
+       else
+        {
+          cut_actionPerformed();
+          alignPanel.seqPanel.seqCanvas.repaint();
+        }
+        break;
+
+      case KeyEvent.VK_S:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.setCursorRow();
+        }
+        break;
+      case KeyEvent.VK_P:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.setCursorPosition();
+        }
+        break;
+
+      case KeyEvent.VK_ENTER:
+      case KeyEvent.VK_COMMA:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.setCursorRowAndColumn();
+        }
+        break;
+
+      case KeyEvent.VK_Q:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+        }
+        break;
+      case KeyEvent.VK_M:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+        }
+        break;
+
+     case KeyEvent.VK_F2:
+       viewport.cursorMode = ! viewport.cursorMode;
+       statusBar.setText("Keyboard editing mode is "+
+           (viewport.cursorMode ? "on" : "off"));
+       if(viewport.cursorMode)
+       {
+         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+       }
+       break;
+
       case KeyEvent.VK_F:
         if (evt.isControlDown())
         {
           findMenuItem_actionPerformed();
         }
         break;
-      case KeyEvent.VK_BACK_SPACE:
-      case KeyEvent.VK_DELETE:
-        cut_actionPerformed();
+
+      case KeyEvent.VK_H:
+      {
+        boolean toggleSeqs = !evt.isControlDown();
+        boolean toggleCols = !evt.isShiftDown();
+        boolean hide = false;
+        SequenceGroup sg = viewport.getSelectionGroup();
+
+        if(toggleSeqs)
+        {
+          if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+          {
+            hide = true;
+            viewport.hideAllSelectedSeqs();
+          }
+          else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+            viewport.showAllHiddenSeqs();
+        }
+
+        if(toggleCols)
+        {
+          if (viewport.colSel.getSelected().size() > 0)
+          {
+            viewport.hideSelectedColumns();
+            if(!toggleSeqs)
+                   viewport.selectionGroup = sg;
+          }
+          else if (!hide)
+            viewport.showAllHiddenColumns();
+        }
         break;
-    }
+      }
+
+      case KeyEvent.VK_PAGE_UP:
+        if (viewport.wrapAlignment)
+          alignPanel.scrollUp(true);
+        else
+          alignPanel.setScrollValues(viewport.startRes,
+                                     viewport.startSeq
+                                     - viewport.endSeq + viewport.startSeq);
+        break;
+
+      case KeyEvent.VK_PAGE_DOWN:
+        if (viewport.wrapAlignment)
+          alignPanel.scrollUp(false);
+        else
+          alignPanel.setScrollValues(viewport.startRes,
+                                     viewport.startSeq
+                                     + viewport.endSeq - viewport.startSeq);
+        break;
+
+      case KeyEvent.VK_Z:
+        if (evt.isControlDown())
+        {
+          undoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_Y:
+        if (evt.isControlDown())
+        {
+          redoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_L:
+        if (evt.isControlDown())
+        {
+          trimAlignment(true);
+        }
+        break;
+
+      case KeyEvent.VK_R:
+        if (evt.isControlDown())
+        {
+          trimAlignment(false);
+        }
+        break;
+
+      case KeyEvent.VK_E:
+        if (evt.isControlDown())
+        {
+          if (evt.isShiftDown())
+            this.removeAllGapsMenuItem_actionPerformed();
+          else
+            removeGappedColumnMenuItem_actionPerformed();
+        }
+        break;
+      case KeyEvent.VK_I:
+        if (evt.isControlDown())
+        {
+          if (evt.isAltDown())
+            viewport.invertColumnSelection();
+          else
+            this.invertSequenceMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_U:
+      if (evt.isControlDown())
+      {
+       this.deleteGroups_actionPerformed();
+      }
+      break;
+
+
+      }
+      alignPanel.repaint();
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -295,130 +463,159 @@ public void itemStateChanged(ItemEvent evt)
     else if(evt.getSource()==annotationPanelMenuItem)
             annotationPanelMenuItem_actionPerformed();
       else if(evt.getSource()==sequenceFeatures)
-       {     viewport.showSequenceFeatures(sequenceFeatures.getState());
+      {
+           viewport.showSequenceFeatures(sequenceFeatures.getState());
             alignPanel.seqPanel.seqCanvas.repaint();
-        }
+      }
       else if(evt.getSource()==conservationMenuItem)
             conservationMenuItem_actionPerformed();
       else if(evt.getSource()==abovePIDThreshold)
             abovePIDThreshold_actionPerformed();
           else if(evt.getSource()==applyToAllGroups)
             applyToAllGroups_actionPerformed();
+      else if(evt.getSource()==autoCalculate)
+          viewport.autocalculateConsensus = autoCalculate.getState();
   }
  public void actionPerformed(ActionEvent evt)
  {
-    if(evt.getSource()==inputText)
+    Object source = evt.getSource();
+
+    if(source==inputText)
       inputText_actionPerformed();
-    else if(evt.getSource()==closeMenuItem)
+    else if(source==loadTree)
+      loadTree_actionPerformed();
+    else if(source==loadApplication)
+      launchFullApplication();
+    else if(source==closeMenuItem)
       closeMenuItem_actionPerformed();
-    else if(evt.getSource()==copy)
+    else if(source==copy)
       copy_actionPerformed();
-    else if(evt.getSource()==undoMenuItem)
+    else if(source==undoMenuItem)
       undoMenuItem_actionPerformed();
-    else if(evt.getSource()==redoMenuItem)
+    else if(source==redoMenuItem)
       redoMenuItem_actionPerformed();
-    else if(evt.getSource()==inputText)
+    else if(source==inputText)
             inputText_actionPerformed();
-    else if(evt.getSource()==closeMenuItem)
+    else if(source==closeMenuItem)
             closeMenuItem_actionPerformed();
-    else if(evt.getSource()==undoMenuItem)
+    else if(source==undoMenuItem)
             undoMenuItem_actionPerformed();
-    else if(evt.getSource()==redoMenuItem)
+    else if(source==redoMenuItem)
             redoMenuItem_actionPerformed();
-    else if(evt.getSource()==copy)
+    else if(source==copy)
             copy_actionPerformed();
-    else if(evt.getSource()==pasteNew)
+    else if(source==pasteNew)
             pasteNew_actionPerformed();
-    else if(evt.getSource()==pasteThis)
+    else if(source==pasteThis)
             pasteThis_actionPerformed();
-    else if(evt.getSource()==cut)
+    else if(source==cut)
             cut_actionPerformed();
-    else if(evt.getSource()==delete)
+    else if(source==delete)
             delete_actionPerformed();
-    else if(evt.getSource()==deleteGroups)
+    else if(source==deleteGroups)
             deleteGroups_actionPerformed();
-    else if(evt.getSource()==selectAllSequenceMenuItem)
+    else if(source==selectAllSequenceMenuItem)
             selectAllSequenceMenuItem_actionPerformed();
-    else if(evt.getSource()==deselectAllSequenceMenuItem)
+    else if(source==deselectAllSequenceMenuItem)
             deselectAllSequenceMenuItem_actionPerformed();
-    else if(evt.getSource()==invertSequenceMenuItem)
+    else if(source==invertSequenceMenuItem)
             invertSequenceMenuItem_actionPerformed();
-    else if(evt.getSource()==remove2LeftMenuItem)
-            remove2LeftMenuItem_actionPerformed();
-    else if(evt.getSource()==remove2RightMenuItem)
-            remove2RightMenuItem_actionPerformed();
-    else if(evt.getSource()==removeGappedColumnMenuItem)
+    else if(source==invertColSel)
+    { viewport.invertColumnSelection(); alignPanel.repaint(); }
+    else if(source==remove2LeftMenuItem)
+            trimAlignment(true);
+    else if(source==remove2RightMenuItem)
+            trimAlignment(false);
+    else if(source==removeGappedColumnMenuItem)
             removeGappedColumnMenuItem_actionPerformed();
-    else if(evt.getSource()==removeAllGapsMenuItem)
+    else if(source==removeAllGapsMenuItem)
             removeAllGapsMenuItem_actionPerformed();
-    else if(evt.getSource()==findMenuItem)
+    else if(source==findMenuItem)
             findMenuItem_actionPerformed();
-    else if(evt.getSource()==font)
+    else if(source==font)
             font_actionPerformed();
-    else if(evt.getSource()==featureSettings)
+    else if(source==showColumns)
+    {
+      viewport.showAllHiddenColumns(); alignPanel.repaint();
+    }
+    else if(source==showSeqs)
+    {
+      viewport.showAllHiddenSeqs();
+    }
+    else if(source == hideColumns)
+    {
+      viewport.hideSelectedColumns(); alignPanel.repaint();
+    }
+    else if(source == hideSequences && viewport.getSelectionGroup()!=null)
+    {
+      viewport.hideAllSelectedSeqs();
+    }
+    else if(source==featureSettings)
             featureSettings_actionPerformed();
-    else if(evt.getSource()==overviewMenuItem)
+    else if(source==overviewMenuItem)
             overviewMenuItem_actionPerformed();
-    else if(evt.getSource()==noColourmenuItem)
+    else if(source==noColourmenuItem)
             noColourmenuItem_actionPerformed();
-    else if(evt.getSource()==clustalColour)
+    else if(source==clustalColour)
             clustalColour_actionPerformed();
-    else if(evt.getSource()==zappoColour)
+    else if(source==zappoColour)
             zappoColour_actionPerformed();
-    else if(evt.getSource()==taylorColour)
+    else if(source==taylorColour)
             taylorColour_actionPerformed();
-    else if(evt.getSource()==hydrophobicityColour)
+    else if(source==hydrophobicityColour)
             hydrophobicityColour_actionPerformed();
-    else if(evt.getSource()==helixColour)
+    else if(source==helixColour)
             helixColour_actionPerformed();
-    else if(evt.getSource()==strandColour)
+    else if(source==strandColour)
             strandColour_actionPerformed();
-    else if(evt.getSource()==turnColour)
+    else if(source==turnColour)
             turnColour_actionPerformed();
-    else if(evt.getSource()==buriedColour)
+    else if(source==buriedColour)
             buriedColour_actionPerformed();
-    else if(evt.getSource()==nucleotideColour)
+    else if(source==nucleotideColour)
             nucleotideColour_actionPerformed();
-    else if(evt.getSource()==modifyPID)
+    else if(source==modifyPID)
             modifyPID_actionPerformed();
-    else if(evt.getSource()==modifyConservation)
+    else if(source==modifyConservation)
             modifyConservation_actionPerformed();
-    else if(evt.getSource()==userDefinedColour)
+    else if(source==userDefinedColour)
             userDefinedColour_actionPerformed();
-    else if(evt.getSource()==PIDColour)
+    else if(source==PIDColour)
             PIDColour_actionPerformed();
-    else if(evt.getSource()==BLOSUM62Colour)
+    else if(source==BLOSUM62Colour)
             BLOSUM62Colour_actionPerformed();
-    else if(evt.getSource()==sortPairwiseMenuItem)
+    else if(source==annotationColour)
+           new AnnotationColourChooser(viewport, alignPanel);
+    else if(source==sortPairwiseMenuItem)
             sortPairwiseMenuItem_actionPerformed();
-    else if(evt.getSource()==sortIDMenuItem)
+    else if(source==sortIDMenuItem)
             sortIDMenuItem_actionPerformed();
-    else if(evt.getSource()==sortGroupMenuItem)
+    else if(source==sortGroupMenuItem)
             sortGroupMenuItem_actionPerformed();
-    else if(evt.getSource()==removeRedundancyMenuItem)
+    else if(source==removeRedundancyMenuItem)
             removeRedundancyMenuItem_actionPerformed();
-    else if(evt.getSource()==pairwiseAlignmentMenuItem)
+    else if(source==pairwiseAlignmentMenuItem)
             pairwiseAlignmentMenuItem_actionPerformed();
-    else if(evt.getSource()==PCAMenuItem)
+    else if(source==PCAMenuItem)
             PCAMenuItem_actionPerformed();
-    else if(evt.getSource()==averageDistanceTreeMenuItem)
+    else if(source==averageDistanceTreeMenuItem)
             averageDistanceTreeMenuItem_actionPerformed();
-    else if(evt.getSource()==neighbourTreeMenuItem)
+    else if(source==neighbourTreeMenuItem)
             neighbourTreeMenuItem_actionPerformed();
-    else if(evt.getSource()==njTreeBlosumMenuItem)
+    else if(source==njTreeBlosumMenuItem)
             njTreeBlosumMenuItem_actionPerformed();
-    else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
+    else if(source==avDistanceTreeBlosumMenuItem)
             avTreeBlosumMenuItem_actionPerformed();
-    else if(evt.getSource()==documentation)
+    else if(source==documentation)
             documentation_actionPerformed();
-    else if(evt.getSource()==about)
+    else if(source==about)
             about_actionPerformed();
 
  }
 
   public void inputText_actionPerformed()
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
@@ -426,7 +623,7 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
@@ -437,25 +634,96 @@ public void itemStateChanged(ItemEvent evt)
                                                       viewport.showJVSuffix));
   }
 
+  void launchFullApplication()
+  {
+    StringBuffer url = new StringBuffer(jalviewServletURL);
+
+    url.append("?open="+
+               appendProtocol( viewport.applet.getParameter("file") ) );
+
+    if(viewport.applet.getParameter("features")!=null)
+    {
+      url.append( "&features=" );
+      url.append( appendProtocol( viewport.applet.getParameter("features") ) );
+    }
+
+    if(viewport.applet.getParameter("annotations")!=null)
+    {
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
+    }
+
+    if(viewport.applet.getParameter("jnetfile")!=null)
+    {
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
+    }
+
+    if(viewport.applet.getParameter("defaultColour")!=null)
+    {
+      url.append("&colour=" +
+                 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
+          );
+    }
+
+    if(viewport.applet.getParameter("userDefinedColour")!=null)
+    {
+      url.append( "&colour=" +
+                 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
+         );
+    }
+
+    showURL(url.toString(), "FULL_APP");
+  }
+
+
+  String removeWhiteSpace(String colour)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < colour.length(); i++)
+    {
+      if (Character.isWhitespace(colour.charAt(i)))
+        sb.append("%20");
+      else
+        sb.append(colour.charAt(i));
+    }
+
+    return sb.toString();
+  }
+
+
+  String appendProtocol(String url)
+  {
+    try{
+       new URL(url);
+    }catch(java.net.MalformedURLException ex)
+    {
+      url = viewport.applet.getCodeBase()+url;
+    }
+    return url;
+  }
+
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.components.remove(viewport.alignment);
-    if(PaintRefresher.components.size()==0 && applet==null)
+    if(PaintRefresher.components.size()==0 && viewport.applet==null)
       System.exit(0);
 
     this.dispose();
   }
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
 
+  /**
+   * DOCUMENT ME!
+   */
   void updateEditMenuBar()
   {
-    if (historyList.size() > 0)
+
+    if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) historyList.peek();
-      undoMenuItem.setLabel("Undo " + hi.getDescription());
+      CommandI command = (CommandI) viewport.historyList.peek();
+      undoMenuItem.setLabel("Undo " + command.getDescription());
     }
     else
     {
@@ -463,11 +731,12 @@ public void itemStateChanged(ItemEvent evt)
       undoMenuItem.setLabel("Undo");
     }
 
-    if (redoList.size() > 0)
+    if (viewport.redoList.size() > 0)
     {
       redoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) redoList.peek();
-      redoMenuItem.setLabel("Redo " + hi.getDescription());
+
+      CommandI command = (CommandI) viewport.redoList.peek();
+      redoMenuItem.setLabel("Redo " + command.getDescription());
     }
     else
     {
@@ -476,71 +745,81 @@ public void itemStateChanged(ItemEvent evt)
     }
   }
 
-  public void addHistoryItem(HistoryItem hi)
+  public void addHistoryItem(CommandI command)
   {
-    historyList.push(hi);
-    updateEditMenuBar();
+    if(command.getSize()>0)
+    {
+      viewport.historyList.push(command);
+      viewport.redoList.removeAllElements();
+      updateEditMenuBar();
+      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void undoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
-                                  HistoryItem.HIDE));
-    restoreHistoryItem(hi);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    if(viewport.historyList.size()<1)
+      return;
+
+    CommandI command = (CommandI)viewport.historyList.pop();
+    viewport.redoList.push(command);
+    command.undoCommand();
+
+    AlignViewport originalSource = getOriginatingSource(command);
+
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    updateEditMenuBar();
+    originalSource.firePropertyChange("alignment", null,null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void redoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) redoList.pop();
-    restoreHistoryItem(hi);
+    CommandI command = (CommandI) viewport.redoList.pop();
+    viewport.historyList.push(command);
+    command.doCommand();
+
+    AlignViewport originalSource = getOriginatingSource(command);
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    originalSource.firePropertyChange("alignment", null, null);
   }
 
-  // used by undo and redo
-  void restoreHistoryItem(HistoryItem hi)
+  AlignViewport getOriginatingSource(CommandI command)
   {
-    if (hi.getType() == HistoryItem.SORT)
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences().
-            elementAt(i), i);
-      }
-    }
-    else
+    AlignViewport originalSource = viewport;
+    //For sequence removal and addition, we need to fire
+   //the property change event FROM the viewport where the
+   //original alignment was altered
+    if (command instanceof EditCommand)
     {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
-        if (restore.getLength() == 0)
-        {
-          // log.System.out.println(hi.getHidden().elementAt(i));
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(
-              restore,
-              hi.getAlignIndex(i));
-        }
-        else
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-        }
-      }
-      if (hi.getType() == HistoryItem.PASTE)
+      EditCommand editCommand = (EditCommand) command;
+      AlignmentI al = editCommand.getAlignment();
+      Vector comps = (Vector) PaintRefresher.components
+          .get(viewport.getSequenceSetId());
+      for (int i = 0; i < comps.size(); i++)
       {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > hi.getSequences().size() - 1; i--)
+        if (comps.elementAt(i) instanceof AlignmentPanel)
         {
-          viewport.alignment.deleteSequence(i);
+          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          {
+            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            break;
+          }
         }
       }
     }
-
-    updateEditMenuBar();
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    return originalSource;
   }
 
   public void moveSelectedSequences(boolean up)
@@ -556,13 +835,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = 1; i < viewport.alignment.getHeight(); i++)
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
+        if (!sg.getSequences(false).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-        if (sg.sequences.contains(temp))
+        if (sg.getSequences(false).contains(temp))
         {
           continue;
         }
@@ -576,13 +855,13 @@ public void itemStateChanged(ItemEvent evt)
       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.sequences.contains(seq))
+        if (!sg.getSequences(true).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.sequences.contains(temp))
+        if (sg.getSequences(true).contains(temp))
         {
           continue;
         }
@@ -595,7 +874,8 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-  StringBuffer copiedSequences;
+  static StringBuffer copiedSequences;
+  static Vector copiedHiddenColumns;
   protected void copy_actionPerformed()
   {
     if (viewport.getSelectionGroup() == null)
@@ -606,7 +886,7 @@ public void itemStateChanged(ItemEvent evt)
     SequenceGroup sg = viewport.getSelectionGroup();
     copiedSequences = new StringBuffer();
     Hashtable orderedSeqs = new Hashtable();
-    for (int i = 0; i < sg.getSize(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.alignment.findIndex(seq);
@@ -616,7 +896,26 @@ public void itemStateChanged(ItemEvent evt)
     int index = 0, startRes, endRes;
     char ch;
 
-    for (int i = 0; i < sg.getSize(); i++)
+    if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
+    {
+      copiedHiddenColumns = new Vector();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
+           i++)
+      {
+        int[] region = (int[])
+            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+
+        copiedHiddenColumns.addElement(new int[]
+                                 {region[0] - hiddenOffset,
+                                 region[1] - hiddenOffset});
+      }
+    }
+    else
+      copiedHiddenColumns = null;
+
+
+    for (int i = 0; i < sg.getSize(false); i++)
     {
         SequenceI seq = null;
 
@@ -673,8 +972,6 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void pasteThis_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-                                   HistoryItem.PASTE));
     paste(false);
   }
 
@@ -682,6 +979,7 @@ public void itemStateChanged(ItemEvent evt)
   {
     try
     {
+
       if (copiedSequences == null)
       {
         return;
@@ -694,26 +992,16 @@ public void itemStateChanged(ItemEvent evt)
         String name = st.nextToken();
         int start = Integer.parseInt(st.nextToken());
         int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
-
-        if (!newAlignment)
-        {
-          viewport.alignment.addSequence(sequence);
-        }
-        else
-        {
-          seqs.addElement(sequence);
-        }
+        seqs.addElement(new Sequence(name, st.nextToken(), start, end));
+      }
+      SequenceI[] newSeqs = new SequenceI[seqs.size()];
+      for (int i = 0; i < seqs.size(); i++)
+      {
+        newSeqs[i] = (SequenceI) seqs.elementAt(i);
       }
 
       if (newAlignment)
       {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        for (int i = 0; i < seqs.size(); i++)
-        {
-          newSeqs[i] = (SequenceI) seqs.elementAt(i);
-        }
-
         String newtitle = new String("Copied sequences");
         if (getTitle().startsWith("Copied sequences"))
         {
@@ -723,16 +1011,43 @@ public void itemStateChanged(ItemEvent evt)
         {
           newtitle = newtitle.concat("- from " + getTitle());
         }
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs),
+                                       viewport.applet,
+                                       newtitle,
+                                       false);
+        if (copiedHiddenColumns != null)
+        {
+          for (int i = 0; i < copiedHiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+            af.viewport.hideColumns(region[0], region[1]);
+          }
+        }
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                         NEW_WINDOW_HEIGHT);
+
+        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
+                                         DEFAULT_HEIGHT);
       }
       else
       {
+        for (int i = 0; i < newSeqs.length; i++)
+        {
+          viewport.alignment.addSequence(newSeqs[i]);
+        }
+
+        //!newAlignment
+        addHistoryItem(new EditCommand(
+            "Add sequences",
+            EditCommand.PASTE,
+            newSeqs,
+            0,
+            viewport.alignment.getWidth(),
+            viewport.alignment)
+            );
+
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+        viewport.firePropertyChange("alignment", null, null);
       }
 
     }
@@ -749,62 +1064,62 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void delete_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
-    if (viewport.getSelectionGroup() == null)
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg == null)
     {
       return;
     }
 
+    Vector seqs = new Vector();
+    SequenceI seq;
+    for (int i = 0; i < sg.getSize(false); i++)
+    {
+      seq = sg.getSequenceAt(i);
+      seqs.addElement(seq);
+    }
 
-    SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if(sg.sequences.size()==viewport.alignment.getHeight())
-          allSequences = true;
 
-    for (int i = 0; i < sg.sequences.size(); i++)
-    {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+   // If the cut affects all sequences, remove highlighted columns
+   if (sg.getSize(false) == viewport.alignment.getHeight())
+   {
+     viewport.getColumnSelection().removeElements(sg.getStartRes(),
+         sg.getEndRes() + 1);
+   }
 
-      // If the cut affects all sequences, remove highlighted columns
-      if (allSequences)
-      {
-        viewport.getColumnSelection().removeElements(sg.getStartRes(),
-                                                     sg.getEndRes() + 1);
-      }
 
+    SequenceI [] cut = new SequenceI[seqs.size()];
+    for(int i=0; i<seqs.size(); i++)
+      cut[i] = (SequenceI)seqs.elementAt(i);
+
+
+    /*
+    //ADD HISTORY ITEM
+    */
+    addHistoryItem(new EditCommand("Cut Sequences",
+                                      EditCommand.CUT,
+                                      cut,
+                                      sg.getStartRes(),
+                                      sg.getEndRes()-sg.getStartRes()+1,
+                                      viewport.alignment));
 
-      if (seq.getSequence().length() < 1)
-      {
-        viewport.getAlignment().deleteSequence(seq);
-      }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
-      }
-    }
 
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
+
+    viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+
     if (viewport.getAlignment().getHeight() < 1)
     {
-      try
-      {
         this.setVisible(false);
-      }
-      catch (Exception ex)
-      {}
     }
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-
   }
 
   protected void deleteGroups_actionPerformed()
   {
     viewport.alignment.deleteAllGroups();
+    viewport.sequenceColours=null;
     viewport.setSelectionGroup(null);
 
     alignPanel.repaint();
@@ -820,18 +1135,23 @@ public void itemStateChanged(ItemEvent evt)
     sg.setEndRes(viewport.alignment.getWidth()-1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed()
   {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1=null;
+      alignPanel.seqPanel.keyboardNo2=null;
+    }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void invertSequenceMenuItem_actionPerformed()
@@ -842,214 +1162,144 @@ public void itemStateChanged(ItemEvent evt)
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
-  public void remove2LeftMenuItem_actionPerformed()
+  void trimAlignment(boolean trimLeft)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
+    int column;
+
     if (colSel.size() > 0)
     {
-      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
-                                     HistoryItem.HIDE));
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0, min);
+      if(trimLeft)
+        column = colSel.getMin();
+      else
+        column = colSel.getMax();
 
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-      }
+      SequenceI [] seqs;
+      if(viewport.getSelectionGroup()!=null)
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      else
+        seqs = viewport.alignment.getSequencesArray();
 
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveLeft(min))
-        {
-          viewport.alignment.deleteGroup(sg);
-        }
-      }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
-  }
 
-  public void remove2RightMenuItem_actionPerformed()
-  {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
-                                     HistoryItem.HIDE));
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
-      if (viewport.getSelectionGroup() != null)
+      TrimRegionCommand trimRegion;
+      if(trimLeft)
       {
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
+        trimRegion = new TrimRegionCommand("Remove Left",
+                                    TrimRegionCommand.TRIM_LEFT,
+                                    seqs,
+                                    column,
+                                    viewport.alignment,
+                                    viewport.colSel,
+                                    viewport.selectionGroup);
+        viewport.setStartRes(0);
       }
+     else
+     {
+       trimRegion = new TrimRegionCommand("Remove Right",
+                                   TrimRegionCommand.TRIM_RIGHT,
+                                   seqs,
+                                   column,
+                                   viewport.alignment,
+                                   viewport.colSel,
+                                   viewport.selectionGroup);
+     }
+
+     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+      addHistoryItem(trimRegion);
 
       Vector groups = viewport.alignment.getGroups();
+
       for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveRight(max))
+
+        if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+            || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
           viewport.alignment.deleteGroup(sg);
         }
       }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
 
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
   }
 
+
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gapped Columns",
-                                   viewport.alignment,
-                                   HistoryItem.HIDE));
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
-    //This is to maintain viewport position on first residue
-    //of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
+    {
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequencesArray();
 
-    viewport.getAlignment().removeGaps();
 
-    viewport.setStartRes(seq.findIndex(startRes)-1);
+    RemoveGapColCommand removeGapCols =
+        new RemoveGapColCommand("Remove Gapped Columns",
+                                seqs,
+                                start, end,
+                                viewport.getGapCharacter());
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-  }
+    addHistoryItem(removeGapCols);
 
-  public void removeAllGapsMenuItem_actionPerformed()
-  {
-    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
-                                   HistoryItem.HIDE));
+    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
 
     //This is to maintain viewport position on first residue
     //of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
+   // ShiftList shifts;
+   // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+   // edit.alColumnChanges=shifts.getInverse();
+   // if (viewport.hasHiddenColumns)
+   //   viewport.getColumnSelection().compensateForEdits(shifts);
+   viewport.setStartRes(seq.findIndex(startRes)-1);
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
-    SequenceI current;
-    int jSize;
-
-    Vector seqs=null;
+  }
 
-    int start=0, end = viewport.alignment.getWidth();
+  public void removeAllGapsMenuItem_actionPerformed()
+  {
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
-    if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().sequences != null
-        && viewport.getSelectionGroup().sequences.size()>0)
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().sequences;
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes()+1;
+      end = viewport.getSelectionGroup().getEndRes();
     }
     else
-      seqs = viewport.alignment.getSequences();
+      seqs = viewport.alignment.getSequencesArray();
 
-    for (int i = 0; i < seqs.size(); i++)
-    {
-      current = (SequenceI) seqs.elementAt(i);
-      jSize = current.getLength();
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
 
-      // Removing a range is much quicker than removing gaps
-      // one by one for long sequences
-      int j = start;
-      int rangeStart=-1, rangeEnd=-1;
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+                                           seqs,
+                                           start, end,
+                     viewport.getGapCharacter()));
 
-      do
-      {
-        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          if(rangeStart==-1)
-           {
-             rangeStart = j;
-             rangeEnd = j+1;
-           }
-           else
-           {
-             rangeEnd++;
-           }
-           j++;
-        }
-        else
-        {
-          if(rangeStart>-1)
-          {
-            current.deleteChars(rangeStart, rangeEnd);
-            j-=rangeEnd-rangeStart;
-            jSize-=rangeEnd-rangeStart;
-            rangeStart = -1;
-            rangeEnd = -1;
-          }
-          else
-            j++;
-        }
-      }
-      while (j < end && j < jSize);
-      if(rangeStart>-1)
-      {
-       current.deleteChars(rangeStart, rangeEnd);
-      }
-    }
     viewport.setStartRes(seq.findIndex(startRes)-1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-  }
 
-  public void alignmentChanged()
-  {
-    viewport.updateConsensus();
-    viewport.updateConservation ();
-    resetAllColourSchemes();
-    if(alignPanel.overviewPanel!=null)
-      alignPanel.overviewPanel.updateOverviewImage();
-
-    viewport.alignment.adjustSequenceAnnotations();
-    alignPanel.repaint();
-  }
-
-  void resetAllColourSchemes()
-  {
-    ColourSchemeI cs = viewport.globalColourScheme;
-    if(cs!=null)
-    {
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
-            resetClustalX(viewport.alignment.getSequences(),
-                          viewport.alignment.getWidth());
-      }
-
-      cs.setConsensus(viewport.vconsensus);
-      if (cs.conservationApplied())
-      {
-        Alignment al = (Alignment) viewport.alignment;
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, viewport.ConsPercGaps);
-
-        cs.setConservation(c);
-      }
-    }
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
-    int s, sSize = viewport.alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
-    {
-      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
-      }
-      sg.recalcConservation();
-    }
   }
 
-
-
   public void findMenuItem_actionPerformed()
   {
     new Finder(alignPanel);
@@ -1085,6 +1335,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
+
   protected void scaleAbove_actionPerformed()
   {
     viewport.setScaleAboveWrapped(scaleAbove.getState());
@@ -1259,7 +1510,7 @@ public void itemStateChanged(ItemEvent evt)
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
 
     }
     viewport.setGlobalColourScheme(cs);
@@ -1278,7 +1529,7 @@ public void itemStateChanged(ItemEvent evt)
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+          sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
         }
         else
         {
@@ -1298,7 +1549,7 @@ public void itemStateChanged(ItemEvent evt)
             || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
         }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
@@ -1307,7 +1558,7 @@ public void itemStateChanged(ItemEvent evt)
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.sequences, 0,
+                                            sg.getSequences(true), 0,
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
@@ -1394,25 +1645,25 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
     alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+   //                                HistoryItem.SORT));
     AlignmentSorter.sortByID(viewport.getAlignment());
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+  //                                 HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     alignPanel.repaint();
 
@@ -1420,17 +1671,13 @@ public void itemStateChanged(ItemEvent evt)
 
   public void removeRedundancyMenuItem_actionPerformed()
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
-    Frame frame = new Frame();
-    frame.add(sp);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
-                                     400, 120);
-
+     new RedundancyPanel(alignPanel);
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed()
   {
-    if (viewport.getSelectionGroup().getSize() > 1)
+    if (viewport.getSelectionGroup()!=null
+        && viewport.getSelectionGroup().getSize(false) > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
@@ -1460,8 +1707,8 @@ public void itemStateChanged(ItemEvent evt)
     }
 
     if ( (viewport.getSelectionGroup() != null &&
-          viewport.getSelectionGroup().getSize() < 4 &&
-          viewport.getSelectionGroup().getSize() > 0)
+          viewport.getSelectionGroup().getSize(false) < 4 &&
+          viewport.getSelectionGroup().getSize(false) > 0)
         || viewport.getAlignment().getHeight() < 4)
     {
       return;
@@ -1519,26 +1766,42 @@ public void itemStateChanged(ItemEvent evt)
 
     }
 
-    final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize() > 3)
-    {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
-                         pwType,
-                         0, viewport.alignment.getWidth());
-    }
-    else
+    if ( (viewport.getSelectionGroup() != null &&
+          viewport.getSelectionGroup().getSize(false) > 1)
+      || (viewport.getSelectionGroup() == null
+          && viewport.alignment.getHeight() > 1))
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
+      final TreePanel tp = new TreePanel(viewport,
+                                         type,
+                                         pwType);
+
+      addTreeMenuItem(tp, title);
+
+      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
     }
+  }
 
-    addTreeMenuItem(tp, title);
+  void loadTree_actionPerformed()
+  {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+      cap.setText("Paste your Newick tree file here.");
+      cap.treeImport = true;
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
+  }
 
-    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+  public void loadTree(jalview.io.NewickFile tree, String treeFile)
+  {
+    TreePanel tp = new TreePanel(viewport,
+                                 treeFile,
+                                 "From File - ",
+                                 tree);
+    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+    addTreeMenuItem(tp, treeFile);
   }
 
-  public void addTreeMenuItem(final TreePanel treePanel, String title)
+  void addTreeMenuItem(final TreePanel treePanel, String title)
   {
     final MenuItem item = new MenuItem(title);
     sortByTreeMenu.add(item);
@@ -1546,8 +1809,8 @@ public void itemStateChanged(ItemEvent evt)
     {
       public void actionPerformed(ActionEvent evt)
       {
-        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-                                       HistoryItem.SORT));
+      //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+      //                                 HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }
@@ -1598,7 +1861,7 @@ public void itemStateChanged(ItemEvent evt)
         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);
         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
                      x, y += fh);
-        g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);
+        g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);
       }
     }
 
@@ -1634,7 +1897,7 @@ public void itemStateChanged(ItemEvent evt)
 
   public void showURL(String url, String target)
   {
-    if (applet == null)
+    if (viewport.applet == null)
     {
       System.out.println("Not running as applet - no browser available.");
     }
@@ -1642,7 +1905,8 @@ public void itemStateChanged(ItemEvent evt)
     {
       try
       {
-        applet.getAppletContext().showDocument(new java.net.URL(url),
+        System.out.println("Show url: "+url);
+        viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
                                                target);
       }
       catch (Exception ex)
@@ -1657,15 +1921,17 @@ public void itemStateChanged(ItemEvent evt)
   //JBuilder Graphics here
 
     protected MenuBar alignFrameMenuBar = new MenuBar();
-    protected Menu fileMenu = new Menu();
-    protected MenuItem closeMenuItem = new MenuItem();
-    protected Menu editMenu = new Menu();
-    protected Menu viewMenu = new Menu();
-    protected Menu colourMenu = new Menu();
-    protected Menu calculateMenu = new Menu();
-    protected MenuItem selectAllSequenceMenuItem = new MenuItem();
-    protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
-    protected MenuItem invertSequenceMenuItem = new MenuItem();
+    protected Menu fileMenu = new Menu("File");
+    protected MenuItem loadApplication = new MenuItem("View in Full Application");
+    protected MenuItem loadTree = new MenuItem("Load Associated Tree");
+    protected MenuItem closeMenuItem = new MenuItem("Close");
+    protected Menu editMenu = new Menu("Edit");
+    protected Menu viewMenu = new Menu("View");
+    protected Menu colourMenu = new Menu("Colour");
+    protected Menu calculateMenu = new Menu("Calculate");
+    protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+    protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+    protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
     protected MenuItem remove2LeftMenuItem = new MenuItem();
     protected MenuItem remove2RightMenuItem = new MenuItem();
     protected MenuItem removeGappedColumnMenuItem = new MenuItem();
@@ -1706,8 +1972,7 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
     MenuItem findMenuItem = new MenuItem();
-    Menu searchMenu = new Menu();
-    protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
     protected MenuItem nucleotideColour = new MenuItem();
     MenuItem deleteGroups = new MenuItem();
     MenuItem delete = new MenuItem();
@@ -1723,6 +1988,8 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
     MenuItem modifyPID = new MenuItem();
     MenuItem modifyConservation = new MenuItem();
+    protected CheckboxMenuItem autoCalculate
+        = new CheckboxMenuItem("Autocalculate Consensus", true);
     protected Menu sortByTreeMenu = new Menu();
     Menu sort = new Menu();
     Menu calculate = new Menu();
@@ -1733,8 +2000,9 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
   Panel embeddedMenu;
   Label embeddedEdit;
-  Label embeddedSearch;
+  Label embeddedSelect;
   Label embeddedView;
+  Label embeddedFormat;
   Label embeddedColour;
   Label embeddedFile;
   Label embeddedHelp;
@@ -1748,12 +2016,11 @@ public void itemStateChanged(ItemEvent evt)
       MenuItem item;
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
+      for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
 
-        item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
-                            elementAt(
-                                i));
+        item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -1764,19 +2031,12 @@ public void itemStateChanged(ItemEvent evt)
 
         outputTextboxMenu.add(item);
       }
-
-        fileMenu.setLabel("File");
-        closeMenuItem.setLabel("Close");
         closeMenuItem.addActionListener(this);
-        editMenu.setLabel("Edit");
-        viewMenu.setLabel("View");
-        colourMenu.setLabel("Colour");
-        calculateMenu.setLabel("Calculate");
-        selectAllSequenceMenuItem.setLabel("Select all");
+        loadApplication.addActionListener(this);
+
+        loadTree.addActionListener(this);
         selectAllSequenceMenuItem.addActionListener(this);
-        deselectAllSequenceMenuItem.setLabel("Deselect All");
         deselectAllSequenceMenuItem.addActionListener(this);
-        invertSequenceMenuItem.setLabel("Invert Selection");
         invertSequenceMenuItem.addActionListener(this);
         remove2LeftMenuItem.setLabel("Remove Left");
         remove2LeftMenuItem.addActionListener(this);
@@ -1865,9 +2125,7 @@ public void itemStateChanged(ItemEvent evt)
         renderGapsMenuItem.addItemListener(this);
         findMenuItem.setLabel("Find...");
         findMenuItem.addActionListener(this);
-        searchMenu.setLabel("Search");
-
-        abovePIDThreshold.setLabel("Above Identity Threshold");
+    abovePIDThreshold.setLabel("Above Identity Threshold");
         abovePIDThreshold.addItemListener(this);
         nucleotideColour.setLabel("Nucleotide");
         nucleotideColour.addActionListener(this);
@@ -1908,6 +2166,7 @@ public void itemStateChanged(ItemEvent evt)
         sortByTreeMenu.setLabel("By Tree Order");
         sort.setLabel("Sort");
         calculate.setLabel("Calculate Tree");
+        autoCalculate.addItemListener(this);
         inputText.setLabel("Input from textbox");
         inputText.addActionListener(this);
 
@@ -1924,18 +2183,38 @@ public void itemStateChanged(ItemEvent evt)
     featureSettings.addActionListener(this);
     sequenceFeatures.setLabel("Sequence Features");
     sequenceFeatures.addItemListener(this);
-    sequenceFeatures.setState(true);
-
+    sequenceFeatures.setState(false);
+    annotationColour.setLabel("by Annotation...");
+    annotationColour.addActionListener(this);
+    invertSequenceMenuItem.setLabel("Invert Sequence Selection");
+    invertColSel.setLabel("Invert Column Selection");
+    menu1.setLabel("Show");
+    showColumns.setLabel("All Columns ");
+    showSeqs.setLabel("All Sequences");
+    menu2.setLabel("Hide");
+    hideColumns.setLabel("Selected Columns");
+    hideSequences.setLabel("Selected Sequences");
+    invertColSel.addActionListener(this);
+    showColumns.addActionListener(this);
+    showSeqs.addActionListener(this);
+    hideColumns.addActionListener(this);
+    hideSequences.addActionListener(this);
+    formatMenu.setLabel("Format");
+    selectMenu.setLabel("Select");
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
-        alignFrameMenuBar.add(searchMenu);
-        alignFrameMenuBar.add(viewMenu);
-        alignFrameMenuBar.add(colourMenu);
+    alignFrameMenuBar.add(selectMenu);
+    alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(formatMenu);
+    alignFrameMenuBar.add(colourMenu);
         alignFrameMenuBar.add(calculateMenu);
         alignFrameMenuBar.add(helpMenu);
         fileMenu.add(inputText);
         fileMenu.add(outputTextboxMenu);
+        if(jalviewServletURL!=null)
+          fileMenu.add(loadApplication);
         fileMenu.addSeparator();
+        fileMenu.add(loadTree);
         fileMenu.add(closeMenuItem);
         editMenu.add(undoMenuItem);
         editMenu.add(redoMenuItem);
@@ -1943,32 +2222,19 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(copy);
         editMenu.add(pasteMenu);
         editMenu.add(delete);
-        editMenu.addSeparator();
-        editMenu.add(selectAllSequenceMenuItem);
-        editMenu.add(deselectAllSequenceMenuItem);
-        editMenu.add(invertSequenceMenuItem);
-        editMenu.add(deleteGroups);
-        editMenu.addSeparator();
+    editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
         editMenu.add(removeGappedColumnMenuItem);
         editMenu.add(removeAllGapsMenuItem);
         editMenu.add(removeRedundancyMenuItem);
-        searchMenu.add(findMenuItem);
-        viewMenu.add(font);
-        viewMenu.addSeparator();
-    viewMenu.add(seqLimits);
-        viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-        viewMenu.add(scaleAbove);
-        viewMenu.add(scaleLeft);
-        viewMenu.add(scaleRight);
-        viewMenu.addSeparator();
-    viewMenu.add(viewBoxesMenuItem);
-        viewMenu.add(viewTextMenuItem);
-        viewMenu.add(colourTextMenuItem);
-        viewMenu.add(renderGapsMenuItem);
-        viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(menu1);
+    viewMenu.add(menu2);
+    viewMenu.addSeparator();
+    viewMenu.add(annotationPanelMenuItem);
+    viewMenu.addSeparator();
+        viewMenu.add(sequenceFeatures);
+        viewMenu.add(featureSettings);
     viewMenu.addSeparator();
         viewMenu.add(overviewMenuItem);
         colourMenu.add(applyToAllGroups);
@@ -1991,11 +2257,13 @@ public void itemStateChanged(ItemEvent evt)
         colourMenu.add(modifyConservation);
         colourMenu.add(abovePIDThreshold);
         colourMenu.add(modifyPID);
-        calculateMenu.add(sort);
+    colourMenu.add(annotationColour);
+    calculateMenu.add(sort);
         calculateMenu.add(calculate);
         calculateMenu.addSeparator();
         calculateMenu.add(pairwiseAlignmentMenuItem);
         calculateMenu.add(PCAMenuItem);
+        calculateMenu.add(autoCalculate);
         this.add(statusBar, BorderLayout.SOUTH);
         pasteMenu.add(pasteNew);
         pasteMenu.add(pasteThis);
@@ -2009,40 +2277,57 @@ public void itemStateChanged(ItemEvent evt)
         calculate.add(njTreeBlosumMenuItem);
         helpMenu.add(documentation);
         helpMenu.add(about);
+    menu1.add(showColumns);
+    menu1.add(showSeqs);
+    menu2.add(hideColumns);
+    menu2.add(hideSequences);
+    formatMenu.add(font);
+    formatMenu.add(seqLimits);
+    formatMenu.add(wrapMenuItem);
+    formatMenu.add(scaleAbove);
+    formatMenu.add(scaleLeft);
+    formatMenu.add(scaleRight);
+    formatMenu.add(viewBoxesMenuItem);
+    formatMenu.add(viewTextMenuItem);
+    formatMenu.add(colourTextMenuItem);
+    formatMenu.add(renderGapsMenuItem);
+    selectMenu.add(findMenuItem);
+    selectMenu.addSeparator();
+    selectMenu.add(selectAllSequenceMenuItem);
+    selectMenu.add(deselectAllSequenceMenuItem);
+    selectMenu.add(invertSequenceMenuItem);
+    selectMenu.add(invertColSel);
+    selectMenu.add(deleteGroups);
   }
 
   public void setEmbedded()
   {
 
     embeddedMenu = new Panel();
-    embeddedEdit = new Label();
-    embeddedSearch = new Label();
-    embeddedView = new Label();
-    embeddedColour = new Label();
-    embeddedFile = new Label();
-    embeddedHelp = new Label();
-    embeddedCalculate = new Label();
+    embeddedEdit = new Label("Edit");
+    embeddedSelect = new Label("Select");
+    embeddedView = new Label("View");
+    embeddedFormat = new Label("Format");
+    embeddedColour = new Label("Colour");
+    embeddedFile = new Label("File");
+    embeddedHelp = new Label("Help");
+    embeddedCalculate = new Label("Calculate");
     flowLayout1 = new FlowLayout();
     embeddedMenu.setBackground(Color.lightGray);
     embeddedMenu.setLayout(flowLayout1);
-    embeddedEdit.setText("Edit");
     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedSearch.setText("Search");
-    embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedView.setText("View");
+    embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedColour.setText("Colour");
+    embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedFile.setText("File");
     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedHelp.setText("Help");
     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedCalculate.setText("Calculate");
     embeddedMenu.add(embeddedFile);
     embeddedMenu.add(embeddedEdit);
-    embeddedMenu.add(embeddedSearch);
+    embeddedMenu.add(embeddedSelect);
     embeddedMenu.add(embeddedView);
+    embeddedMenu.add(embeddedFormat);
     embeddedMenu.add(embeddedColour);
     embeddedMenu.add(embeddedCalculate);
     embeddedMenu.add(embeddedHelp);
@@ -2051,35 +2336,46 @@ public void itemStateChanged(ItemEvent evt)
     flowLayout1.setVgap(0);
     embeddedFile.addMouseListener(this);
     embeddedEdit.addMouseListener(this);
-    embeddedSearch.addMouseListener(this);
+    embeddedSelect.addMouseListener(this);
     embeddedView.addMouseListener(this);
+    embeddedFormat.addMouseListener(this);
     embeddedColour.addMouseListener(this);
     embeddedCalculate.addMouseListener(this);
     embeddedHelp.addMouseListener(this);
 
-    setVisible(false);
+   // setVisible(false);
     fileMenu.remove(closeMenuItem);
-    fileMenu.remove(2); // Seperator
-
-    applet.setLayout(new BorderLayout());
-    applet.add(embeddedMenu, BorderLayout.NORTH);
-    applet.add(statusBar, BorderLayout.SOUTH);
-    applet.validate();
+    fileMenu.remove(3); // Seperator
 
+    viewport.applet.setLayout(new BorderLayout());
+    viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
+    viewport.applet.add(statusBar, BorderLayout.SOUTH);
+   // viewport.applet.validate();
 
-    alignPanel.setSize(applet.size().width, applet.size().height
+    alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);
 
-     applet.add(alignPanel, BorderLayout.CENTER);
-     applet.validate();
+     viewport.applet.add(alignPanel, BorderLayout.CENTER);
+     viewport.applet.validate();
+
   }
 
 
 
   PopupMenu filePopup, editPopup, searchPopup,
-      viewPopup, colourPopup, calculatePopup, helpPopup;
+      viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+  MenuItem annotationColour = new MenuItem();
+  MenuItem invertColSel = new MenuItem();
+  Menu menu1 = new Menu();
+  MenuItem showColumns = new MenuItem();
+  MenuItem showSeqs = new MenuItem();
+  Menu menu2 = new Menu();
+  MenuItem hideColumns = new MenuItem();
+  MenuItem hideSequences = new MenuItem();
+  Menu formatMenu = new Menu();
+  Menu selectMenu = new Menu();
 
   public void mousePressed(MouseEvent evt)
   {
@@ -2093,14 +2389,18 @@ public void itemStateChanged(ItemEvent evt)
     {
       popup = editPopup = genPopupMenu(editPopup, editMenu);
     }
-    else if(source==embeddedSearch)
+    else if(source==embeddedSelect)
     {
-      popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
+      popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
     }
     else if(source==embeddedView)
     {
       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
     }
+    else if (source ==embeddedFormat)
+    {
+      popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
+    }
     else if(source==embeddedColour)
     {
       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);