X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=64423b0ddbdeb2f5faeadfbd1936df01960c79b3;hb=6bfaf3d3a82e4eece77dc1c2d83aede7c4dbb690;hp=dfd58b2c292743a8227a32937bfd3af93752615f;hpb=92c8f4e119ed0b5b362ee9538ef65781dbf50136;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dfd58b2..64423b0 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -38,11 +38,18 @@ public class AlignFrame extends Frame implements ActionListener,
   public AlignViewport viewport;
   int NEW_WINDOW_WIDTH = 700;
   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)
@@ -50,12 +57,13 @@ 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");
@@ -102,6 +110,8 @@ 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 +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();
   }
@@ -138,83 +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;
-
+      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 +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();
@@ -245,21 +227,129 @@ 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();
+      case KeyEvent.VK_H:
+      {
+        SequenceGroup sg = viewport.getSelectionGroup();
+        boolean hide = false;
+        if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+        {
+          hide = true;
+          viewport.hideAllSelectedSeqs();
+        }
+        else if (viewport.colSel.getSelected().size() < 1)
+          viewport.showAllHiddenSeqs();
+
+        if (viewport.colSel.getSelected().size() > 0)
+          viewport.hideSelectedColumns();
+        else if (!hide)
+          viewport.showAllHiddenColumns();
+
+        alignPanel.repaint();
         break;
+      }
+
     }
   }
   public void keyReleased(KeyEvent evt)
@@ -289,125 +379,160 @@ 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 +540,7 @@ 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,
@@ -426,10 +551,73 @@ 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("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();
@@ -491,41 +679,7 @@ 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();
 
@@ -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;
 
@@ -712,7 +886,19 @@ 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);
@@ -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);
@@ -926,10 +1118,10 @@ 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;
     }
@@ -987,11 +1179,18 @@ 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();
+
+    viewport.alignment.adjustSequenceAnnotations();
     alignPanel.repaint();
   }
 
@@ -1028,7 +1227,8 @@ 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();
     }
@@ -1071,6 +1271,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
+
   protected void scaleAbove_actionPerformed()
   {
     viewport.setScaleAboveWrapped(scaleAbove.getState());
@@ -1113,6 +1314,11 @@ 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)
@@ -1259,7 +1465,7 @@ 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
         {
@@ -1279,7 +1485,7 @@ 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());
@@ -1288,7 +1494,7 @@ 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);
@@ -1401,17 +1607,13 @@ 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));
@@ -1441,8 +1643,8 @@ 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;
@@ -1500,26 +1702,42 @@ 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);
@@ -1579,7 +1797,7 @@ 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);
       }
     }
 
@@ -1615,7 +1833,7 @@ 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.");
     }
@@ -1623,7 +1841,8 @@ 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)
@@ -1638,15 +1857,17 @@ 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();
@@ -1704,6 +1925,8 @@ 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();
@@ -1729,12 +1952,11 @@ 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)
@@ -1745,19 +1967,12 @@ 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);
@@ -1872,6 +2087,7 @@ public void itemStateChanged(ItemEvent evt)
         font.addActionListener(this);
         scaleAbove.setLabel("Scale Above");
         scaleAbove.setState(true);
+        scaleAbove.setEnabled(false);
         scaleAbove.addItemListener(this);
         scaleLeft.setEnabled(false);
         scaleLeft.setState(true);
@@ -1888,6 +2104,7 @@ 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);
 
@@ -1900,6 +2117,27 @@ 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);
@@ -1910,7 +2148,10 @@ 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);
@@ -1922,7 +2163,8 @@ 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);
@@ -1932,19 +2174,24 @@ 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();
@@ -1966,11 +2213,13 @@ 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);
@@ -1984,6 +2233,10 @@ 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()
@@ -2032,27 +2285,37 @@ public void itemStateChanged(ItemEvent evt)
     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;
+  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)
   {