X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2b53d7672379948c423b3f0ca158c2fe8e183c4a;hb=7bc213bae5828287329a3490faba291706599b03;hp=01bea4d2ca495a78d649b46ceea508837daecc2b;hpb=d355ad106f73e0de0abc3fb3f375af4eaf352591;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 01bea4d..2b53d76 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -40,9 +40,17 @@ public class AlignFrame extends Frame implements ActionListener,
   int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
+  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)
@@ -56,6 +64,8 @@ public class AlignFrame extends Frame implements ActionListener,
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
+    seqLimits.setState(viewport.showJVSuffix);
+
     if(applet!=null)
     {
       String param = applet.getParameter("sortBy");
@@ -115,9 +125,16 @@ 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, NEW_WINDOW_WIDTH,
+                                      NEW_WINDOW_HEIGHT);
+   }
    alignPanel.validate();
    alignPanel.repaint();
   }
@@ -138,88 +155,44 @@ 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
@@ -232,6 +205,10 @@ 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();
@@ -250,21 +227,108 @@ 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());
+        }
+        break;
+
+      case KeyEvent.VK_DELETE:
+      case KeyEvent.VK_BACK_SPACE:
+        if(viewport.cursorMode)
+        {
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
+        }
+       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();
-        break;
     }
   }
   public void keyReleased(KeyEvent evt)
@@ -295,20 +359,27 @@ 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)
       inputText_actionPerformed();
+    else if(evt.getSource()==loadTree)
+      loadTree_actionPerformed();
+    else if(evt.getSource()==loadApplication)
+      launchFullApplication();
     else if(evt.getSource()==closeMenuItem)
       closeMenuItem_actionPerformed();
     else if(evt.getSource()==copy)
@@ -389,6 +460,8 @@ public void itemStateChanged(ItemEvent evt)
             PIDColour_actionPerformed();
     else if(evt.getSource()==BLOSUM62Colour)
             BLOSUM62Colour_actionPerformed();
+    else if(evt.getSource()==annotationColour)
+           new AnnotationColourChooser(viewport, alignPanel);
     else if(evt.getSource()==sortPairwiseMenuItem)
             sortPairwiseMenuItem_actionPerformed();
     else if(evt.getSource()==sortIDMenuItem)
@@ -418,7 +491,7 @@ public void itemStateChanged(ItemEvent evt)
 
   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 +499,7 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
@@ -437,6 +510,63 @@ public void itemStateChanged(ItemEvent evt)
                                                       viewport.showJVSuffix));
   }
 
+  void launchFullApplication()
+  {
+    StringBuffer url = new StringBuffer(jalviewServletURL);
+
+    url.append("?open="+
+               appendProtocol( applet.getParameter("file") ) );
+
+    if(applet.getParameter("features")!=null)
+    {
+      url.append( "&features=" );
+      url.append( appendProtocol( applet.getParameter("features") ) );
+    }
+
+    if(applet.getParameter("defaultColour")!=null)
+    {
+      url.append("&colour=" +
+                 removeWhiteSpace(applet.getParameter("defaultColour"))
+          );
+    }
+
+    if(applet.getParameter("userDefinedColour")!=null)
+    {
+      url.append( "&colour=" +
+                 removeWhiteSpace( 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 = applet.getCodeBase()+url;
+    }
+    return url;
+  }
+
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.components.remove(viewport.alignment);
@@ -502,41 +632,7 @@ public void itemStateChanged(ItemEvent evt)
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    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);
-        }
-      }
-    }
+    hi.restore();
 
     updateEditMenuBar();
 
@@ -556,13 +652,13 @@ 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 +672,13 @@ 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;
         }
@@ -606,7 +702,7 @@ 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 +712,7 @@ public void itemStateChanged(ItemEvent evt)
     int index = 0, startRes, endRes;
     char ch;
 
-    for (int i = 0; i < sg.getSize(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
         SequenceI seq = null;
 
@@ -723,7 +819,10 @@ 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),
+                                       applet,
+                                       newtitle,
+                                       false);
 
         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
                                          NEW_WINDOW_HEIGHT);
@@ -759,10 +858,10 @@ 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);
@@ -825,6 +924,11 @@ 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);
@@ -938,10 +1042,10 @@ public void itemStateChanged(ItemEvent evt)
     int start=0, end = viewport.alignment.getWidth();
 
     if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().sequences != null
-        && viewport.getSelectionGroup().sequences.size()>0)
+        && viewport.getSelectionGroup().getSequences(false) != null
+        && viewport.getSelectionGroup().getSize(false)>0)
     {
-      seqs = viewport.getSelectionGroup().sequences;
+      seqs = viewport.getSelectionGroup().getSequences(true);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes()+1;
     }
@@ -999,8 +1103,13 @@ public void itemStateChanged(ItemEvent evt)
 
   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();
@@ -1042,7 +1151,8 @@ 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();
     }
@@ -1278,7 +1388,7 @@ 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 +1408,7 @@ 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 +1417,7 @@ 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);
@@ -1420,17 +1530,12 @@ 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().getSize(false) > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
@@ -1460,8 +1565,8 @@ 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 +1624,36 @@ 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
-    {
-      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);
   }
 
-  public void addTreeMenuItem(final TreePanel treePanel, String 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);
+  }
+
+  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);
+  }
+
+  void addTreeMenuItem(final TreePanel treePanel, String title)
   {
     final MenuItem item = new MenuItem(title);
     sortByTreeMenu.add(item);
@@ -1598,7 +1713,7 @@ 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);
       }
     }
 
@@ -1642,6 +1757,7 @@ public void itemStateChanged(ItemEvent evt)
     {
       try
       {
+        System.out.println("Show url: "+url);
         applet.getAppletContext().showDocument(new java.net.URL(url),
                                                target);
       }
@@ -1657,15 +1773,17 @@ 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();
@@ -1723,6 +1841,8 @@ 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();
@@ -1764,19 +1884,12 @@ 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);
@@ -1908,6 +2021,7 @@ 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);
 
@@ -1924,7 +2038,9 @@ 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);
 
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
@@ -1935,7 +2051,10 @@ 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);
@@ -1970,6 +2089,9 @@ public void itemStateChanged(ItemEvent evt)
         viewMenu.add(renderGapsMenuItem);
         viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
+        viewMenu.add(sequenceFeatures);
+        viewMenu.add(featureSettings);
+    viewMenu.addSeparator();
         viewMenu.add(overviewMenuItem);
         colourMenu.add(applyToAllGroups);
         colourMenu.addSeparator();
@@ -1991,11 +2113,13 @@ 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);
@@ -2057,21 +2181,21 @@ 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();
-
+   // applet.validate();
 
     alignPanel.setSize(applet.size().width, applet.size().height
                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);
 
      applet.add(alignPanel, BorderLayout.CENTER);
      applet.validate();
+
   }
 
 
@@ -2080,6 +2204,7 @@ public void itemStateChanged(ItemEvent evt)
       viewPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+  MenuItem annotationColour = new MenuItem();
 
   public void mousePressed(MouseEvent evt)
   {