X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=6586a68f3c3f07bd03428c21ce2188812d8a6bd5;hb=f84a68869b1864eea585ade8ac36939fd88c8a93;hp=496a8bb94247e43897b4858469f8742ad11044c9;hpb=59183747dbffe3ab6b141c5440d2f70799ae360b;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 496a8bb..6586a68 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 +58,13 @@ public class AlignFrame extends Frame implements ActionListener,
       ex.printStackTrace();
     }
 
-    this.applet = applet;
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
+    seqLimits.setState(viewport.showJVSuffix);
+
     if(applet!=null)
     {
       String param = applet.getParameter("sortBy");
@@ -83,13 +92,13 @@ 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)
@@ -102,6 +111,8 @@ public class AlignFrame extends Frame implements ActionListener,
    this.addKeyListener(this);
    alignPanel.seqPanel.seqCanvas.addKeyListener(this);
    alignPanel.idPanel.idCanvas.addKeyListener(this);
+   alignPanel.scalePanel.addKeyListener(this);
+   alignPanel.annotationPanel.addKeyListener(this);
 
     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
@@ -115,9 +126,16 @@ public class AlignFrame extends Frame implements ActionListener,
    });
 
 
-   add(alignPanel, BorderLayout.CENTER);
-   jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-
+   if(embedded)
+   {
+     setEmbedded();
+   }
+   else
+   {
+     add(alignPanel, BorderLayout.CENTER);
+     jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+                                      DEFAULT_HEIGHT);
+   }
    alignPanel.validate();
    alignPanel.repaint();
   }
@@ -138,83 +156,44 @@ 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;
-
+      sequenceFeatures.setState(true);
       alignPanel.repaint();
-
-    }
-    catch (Exception ex)
-    {
-      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
@@ -227,6 +206,10 @@ 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();
@@ -245,22 +228,164 @@ 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;
+       }
+       alignPanel.seqPanel.seqCanvas.repaint();
+       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();
+        }
+
+        alignPanel.repaint();
         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;
+      }
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -289,125 +414,160 @@ public void itemStateChanged(ItemEvent evt)
             renderGapsMenuItem_actionPerformed();
     else if(evt.getSource()==annotationPanelMenuItem)
             annotationPanelMenuItem_actionPerformed();
+      else if(evt.getSource()==sequenceFeatures)
+      {
+           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)
+    else if(source==invertColSel)
+    { viewport.invertColumnSelection(); alignPanel.repaint(); }
+    else if(source==remove2LeftMenuItem)
             remove2LeftMenuItem_actionPerformed();
-    else if(evt.getSource()==remove2RightMenuItem)
+    else if(source==remove2RightMenuItem)
             remove2RightMenuItem_actionPerformed();
-    else if(evt.getSource()==removeGappedColumnMenuItem)
+    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()==overviewMenuItem)
+    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(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);
@@ -415,7 +575,7 @@ 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,
@@ -426,110 +586,104 @@ public void itemStateChanged(ItemEvent evt)
                                                       viewport.showJVSuffix));
   }
 
-  public void closeMenuItem_actionPerformed()
+  void launchFullApplication()
   {
-    PaintRefresher.components.remove(viewport.alignment);
-    if(PaintRefresher.components.size()==0 && applet==null)
-      System.exit(0);
+    StringBuffer url = new StringBuffer(jalviewServletURL);
 
-    this.dispose();
-  }
+    url.append("?open="+
+               appendProtocol( viewport.applet.getParameter("file") ) );
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
+    if(viewport.applet.getParameter("features")!=null)
+    {
+      url.append( "&features=" );
+      url.append( appendProtocol( viewport.applet.getParameter("features") ) );
+    }
 
-  void updateEditMenuBar()
-  {
-    if (historyList.size() > 0)
+    if(viewport.applet.getParameter("annotations")!=null)
     {
-      undoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) historyList.peek();
-      undoMenuItem.setLabel("Undo " + hi.getDescription());
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
     }
-    else
+
+    if(viewport.applet.getParameter("jnetfile")!=null)
     {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setLabel("Undo");
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
     }
 
-    if (redoList.size() > 0)
+    if(viewport.applet.getParameter("defaultColour")!=null)
     {
-      redoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) redoList.peek();
-      redoMenuItem.setLabel("Redo " + hi.getDescription());
+      url.append("&colour=" +
+                 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
+          );
     }
-    else
+
+    if(viewport.applet.getParameter("userDefinedColour")!=null)
     {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setLabel("Redo");
+      url.append( "&colour=" +
+                 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
+         );
     }
+
+    showURL(url.toString(), "FULL_APP");
   }
 
-  public void addHistoryItem(HistoryItem hi)
+
+  String removeWhiteSpace(String colour)
   {
-    historyList.push(hi);
-    updateEditMenuBar();
+    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 && viewport.applet==null)
+      System.exit(0);
+
+    this.dispose();
+  }
+
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
+
+  void updateEditMenuBar()
+  {
+  }
+
+
   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());
   }
 
   protected void redoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) redoList.pop();
-    restoreHistoryItem(hi);
-    updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
   }
 
   // used by undo and redo
-  void restoreHistoryItem(HistoryItem hi)
+  void restoreHistoryItem(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
-    {
-      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)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > hi.getSequences().size() - 1; i--)
-        {
-          viewport.alignment.deleteSequence(i);
-        }
-      }
-    }
-
-    updateEditMenuBar();
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -545,13 +699,13 @@ 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;
         }
@@ -565,13 +719,13 @@ 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;
         }
@@ -584,7 +738,8 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-  StringBuffer copiedSequences;
+  static StringBuffer copiedSequences;
+  static Vector copiedHiddenColumns;
   protected void copy_actionPerformed()
   {
     if (viewport.getSelectionGroup() == null)
@@ -595,7 +750,7 @@ 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);
@@ -605,7 +760,26 @@ 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;
 
@@ -662,8 +836,8 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void pasteThis_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-                                   HistoryItem.PASTE));
+  //  addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+   //                                HistoryItem.PASTE));
     paste(false);
   }
 
@@ -712,10 +886,22 @@ 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
       {
@@ -738,8 +924,8 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void delete_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
+    //addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+    //                               HistoryItem.HIDE));
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -748,10 +934,10 @@ public void itemStateChanged(ItemEvent evt)
 
     SequenceGroup sg = viewport.getSelectionGroup();
     boolean allSequences = false;
-    if(sg.sequences.size()==viewport.alignment.getHeight())
+    if(sg.getSize(false)==viewport.alignment.getHeight())
           allSequences = true;
 
-    for (int i = 0; i < sg.sequences.size(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
@@ -814,9 +1000,15 @@ public void itemStateChanged(ItemEvent evt)
 
   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);
@@ -835,160 +1027,29 @@ public void itemStateChanged(ItemEvent evt)
 
   public void remove2LeftMenuItem_actionPerformed()
   {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    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 (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-      }
-
-      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)
-      {
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
-      }
-
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveRight(max))
-        {
-          viewport.alignment.deleteGroup(sg);
-        }
-      }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
-
   }
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gapped Columns",
-                                   viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    //This is to maintain viewport position on first residue
-    //of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
-
-    viewport.getAlignment().removeGaps();
-
-    viewport.setStartRes(seq.findIndex(startRes)-1);
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    //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 current;
-    int jSize;
-
-    Vector seqs=null;
-
-    int start=0, end = viewport.alignment.getWidth();
-
-    if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().sequences != null
-        && viewport.getSelectionGroup().sequences.size()>0)
-    {
-      seqs = viewport.getSelectionGroup().sequences;
-      start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes()+1;
-    }
-    else
-      seqs = viewport.alignment.getSequences();
-
-    for (int i = 0; i < seqs.size(); i++)
-    {
-      current = (SequenceI) seqs.elementAt(i);
-      jSize = current.getLength();
-
-      // Removing a range is much quicker than removing gaps
-      // one by one for long sequences
-      int j = start;
-      int rangeStart=-1, rangeEnd=-1;
-
-      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 ();
+    viewport.alignment.padGaps();
+    if(viewport.autocalculateConsensus)
+    {
+      viewport.updateConsensus();
+      viewport.updateConservation();
+    }
+
     resetAllColourSchemes();
     if(alignPanel.overviewPanel!=null)
       alignPanel.overviewPanel.updateOverviewImage();
@@ -1009,7 +1070,7 @@ public void itemStateChanged(ItemEvent evt)
                           viewport.alignment.getWidth());
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
       if (cs.conservationApplied())
       {
         Alignment al = (Alignment) viewport.alignment;
@@ -1030,7 +1091,8 @@ public void itemStateChanged(ItemEvent evt)
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+        ((ClustalxColourScheme)sg.cs).resetClustalX(
+            sg.getSequences(true), sg.getWidth());
       }
       sg.recalcConservation();
     }
@@ -1073,6 +1135,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
+
   protected void scaleAbove_actionPerformed()
   {
     viewport.setScaleAboveWrapped(scaleAbove.getState());
@@ -1115,6 +1178,11 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
 
+  public void featureSettings_actionPerformed()
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
   public void overviewMenuItem_actionPerformed()
   {
     if (alignPanel.overviewPanel != null)
@@ -1242,7 +1310,7 @@ public void itemStateChanged(ItemEvent evt)
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
 
     }
     viewport.setGlobalColourScheme(cs);
@@ -1261,7 +1329,7 @@ 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
         {
@@ -1281,7 +1349,7 @@ 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());
@@ -1290,7 +1358,7 @@ 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);
@@ -1377,8 +1445,8 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+   //                                HistoryItem.SORT));
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
@@ -1386,16 +1454,16 @@ public void itemStateChanged(ItemEvent evt)
 
   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();
 
@@ -1403,17 +1471,13 @@ 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));
@@ -1443,8 +1507,8 @@ 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;
@@ -1502,26 +1566,42 @@ 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);
@@ -1529,8 +1609,8 @@ 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();
       }
@@ -1581,7 +1661,7 @@ 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);
       }
     }
 
@@ -1617,7 +1697,7 @@ 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.");
     }
@@ -1625,7 +1705,8 @@ 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)
@@ -1640,15 +1721,17 @@ 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();
@@ -1706,6 +1789,8 @@ 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();
@@ -1731,12 +1816,11 @@ 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)
@@ -1747,19 +1831,12 @@ 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);
@@ -1891,6 +1968,7 @@ 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);
 
@@ -1903,6 +1981,27 @@ public void itemStateChanged(ItemEvent evt)
           seqLimits.setState(true);
     seqLimits.setLabel("Show Sequence Limits");
     seqLimits.addItemListener(this);
+    featureSettings.setLabel("Feature Settings...");
+    featureSettings.addActionListener(this);
+    sequenceFeatures.setLabel("Sequence Features");
+    sequenceFeatures.addItemListener(this);
+    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);
+
 
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
@@ -1913,7 +2012,10 @@ public void itemStateChanged(ItemEvent evt)
         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);
@@ -1925,7 +2027,8 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(selectAllSequenceMenuItem);
         editMenu.add(deselectAllSequenceMenuItem);
         editMenu.add(invertSequenceMenuItem);
-        editMenu.add(deleteGroups);
+    editMenu.add(invertColSel);
+    editMenu.add(deleteGroups);
         editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
@@ -1935,19 +2038,24 @@ public void itemStateChanged(ItemEvent evt)
         searchMenu.add(findMenuItem);
         viewMenu.add(font);
         viewMenu.addSeparator();
-        viewMenu.add(seqLimits);
-        viewMenu.addSeparator();
+    viewMenu.add(menu1);
+    viewMenu.add(menu2);
+    viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
         viewMenu.add(scaleAbove);
         viewMenu.add(scaleLeft);
         viewMenu.add(scaleRight);
         viewMenu.addSeparator();
+    viewMenu.add(seqLimits);
     viewMenu.add(viewBoxesMenuItem);
         viewMenu.add(viewTextMenuItem);
         viewMenu.add(colourTextMenuItem);
         viewMenu.add(renderGapsMenuItem);
         viewMenu.add(annotationPanelMenuItem);
-        viewMenu.addSeparator();
+    viewMenu.addSeparator();
+        viewMenu.add(sequenceFeatures);
+        viewMenu.add(featureSettings);
+    viewMenu.addSeparator();
         viewMenu.add(overviewMenuItem);
         colourMenu.add(applyToAllGroups);
         colourMenu.addSeparator();
@@ -1969,11 +2077,13 @@ 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);
@@ -1987,6 +2097,10 @@ 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);
   }
 
   public void setEmbedded()
@@ -2035,27 +2149,37 @@ public void itemStateChanged(ItemEvent evt)
     embeddedCalculate.addMouseListener(this);
     embeddedHelp.addMouseListener(this);
 
-    setVisible(false);
+   // setVisible(false);
     fileMenu.remove(closeMenuItem);
-    fileMenu.remove(2); // Seperator
+    fileMenu.remove(3); // Seperator
 
-    applet.setLayout(new BorderLayout());
-    applet.add(embeddedMenu, BorderLayout.NORTH);
-    applet.add(statusBar, BorderLayout.SOUTH);
-    applet.validate();
+    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;
+  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();
 
   public void mousePressed(MouseEvent evt)
   {