X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=86c079c115b07702f843488f0006a9f3ea8d825c;hb=8240aa86ee94d4c372af7deb1452a8294ff8800b;hp=7a0052fcf945b4bebc0708315ffc15c5fdcf5fb6;hpb=f7d45a21db810c5f8f7ca668d1a28f1403defe32;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7a0052f..86c079c 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
@@ -38,7 +38,8 @@ 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,
@@ -46,6 +47,9 @@ public class AlignFrame extends Frame implements ActionListener,
                      String title,
                      boolean embedded)
   {
+
+    jalviewServletURL = applet.getParameter("APPLICATION_URL");
+
     try{
       jbInit();
     }catch(Exception ex)
@@ -53,12 +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");
@@ -105,6 +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()
     {
@@ -148,106 +155,35 @@ public class AlignFrame extends Frame implements ActionListener,
    * @param String DOCUMENT ME!
    */
 
-  public void parseFeaturesFile(String file)
+  public void parseFeaturesFile(String file, String type)
   {
-    String line = null;
-    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)
     {
-      BufferedReader in = null;
-      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-      if (is != null)
-      {
-        in = new BufferedReader(new java.io.InputStreamReader(is));
-      }
-      else
-      {
-        URL url = new URL(file);
-        in = new BufferedReader(new InputStreamReader(url.openStream()));
-      }
-
-      SequenceI seq = null;
-      String type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-      int lineNo = 0;
-      String featureGroup = null;
-      while ( (line = in.readLine()) != null)
-      {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
-        {
-          type = st.nextToken();
-          if(type.equalsIgnoreCase("startgroup"))
-          {
-            featureGroup = st.nextToken();
-          }
-          else if(type.equalsIgnoreCase("endgroup"))
-          {
-            //We should check whether this is the current group,
-            //but at present theres no way of showing more than 1 group
-            st.nextToken();
-            featureGroup = null;
-          }
-          else
-          {
-            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);
-
-          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, featureGroup);
-
-          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)
-    {
-      ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex +"\n"+line);
     }
+
   }
 
+
   public void keyPressed(KeyEvent evt)
   {
     if (viewport.cursorMode
@@ -269,7 +205,7 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_C:
-        if (viewport.cursorMode)
+        if (viewport.cursorMode && !evt.isControlDown())
         {
           alignPanel.seqPanel.setCursorColumn();
         }
@@ -324,19 +260,23 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_SPACE:
         if(viewport.cursorMode)
         {
-          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
+          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());
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                                || evt.isShiftDown()
+                                                || evt.isAltDown()
+              );
         }
-        break;
-
-      case KeyEvent.VK_BACK_SPACE:
-        if(!viewport.cursorMode)
+       else
         {
           cut_actionPerformed();
           alignPanel.seqPanel.seqCanvas.repaint();
@@ -395,6 +335,40 @@ public class AlignFrame extends Frame implements ActionListener,
           findMenuItem_actionPerformed();
         }
         break;
+      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;
+      }
+
     }
   }
   public void keyReleased(KeyEvent evt)
@@ -440,115 +414,137 @@ public void itemStateChanged(ItemEvent evt)
   }
  public void actionPerformed(ActionEvent evt)
  {
-    if(evt.getSource()==inputText)
+    Object source = evt.getSource();
+
+    if(source==inputText)
       inputText_actionPerformed();
-    else if(evt.getSource()==loadTree)
+    else if(source==loadTree)
       loadTree_actionPerformed();
-    else if(evt.getSource()==closeMenuItem)
+    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()==featureSettings)
+    else if(source==showColumns)
+    {
+      viewport.showAllHiddenColumns(); alignPanel.repaint();
+    }
+    else if(source==showSeqs)
+    {
+      viewport.showAllHiddenSeqs();
+    }
+    else if(source == hideColumns)
+    {
+      viewport.hideSelectedColumns(); alignPanel.repaint();
+    }
+    else if(source == hideSequences && viewport.getSelectionGroup()!=null)
+    {
+      viewport.hideAllSelectedSeqs();
+    }
+    else if(source==featureSettings)
             featureSettings_actionPerformed();
-    else if(evt.getSource()==overviewMenuItem)
+    else if(source==overviewMenuItem)
             overviewMenuItem_actionPerformed();
-    else if(evt.getSource()==noColourmenuItem)
+    else if(source==noColourmenuItem)
             noColourmenuItem_actionPerformed();
-    else if(evt.getSource()==clustalColour)
+    else if(source==clustalColour)
             clustalColour_actionPerformed();
-    else if(evt.getSource()==zappoColour)
+    else if(source==zappoColour)
             zappoColour_actionPerformed();
-    else if(evt.getSource()==taylorColour)
+    else if(source==taylorColour)
             taylorColour_actionPerformed();
-    else if(evt.getSource()==hydrophobicityColour)
+    else if(source==hydrophobicityColour)
             hydrophobicityColour_actionPerformed();
-    else if(evt.getSource()==helixColour)
+    else if(source==helixColour)
             helixColour_actionPerformed();
-    else if(evt.getSource()==strandColour)
+    else if(source==strandColour)
             strandColour_actionPerformed();
-    else if(evt.getSource()==turnColour)
+    else if(source==turnColour)
             turnColour_actionPerformed();
-    else if(evt.getSource()==buriedColour)
+    else if(source==buriedColour)
             buriedColour_actionPerformed();
-    else if(evt.getSource()==nucleotideColour)
+    else if(source==nucleotideColour)
             nucleotideColour_actionPerformed();
-    else if(evt.getSource()==modifyPID)
+    else if(source==modifyPID)
             modifyPID_actionPerformed();
-    else if(evt.getSource()==modifyConservation)
+    else if(source==modifyConservation)
             modifyConservation_actionPerformed();
-    else if(evt.getSource()==userDefinedColour)
+    else if(source==userDefinedColour)
             userDefinedColour_actionPerformed();
-    else if(evt.getSource()==PIDColour)
+    else if(source==PIDColour)
             PIDColour_actionPerformed();
-    else if(evt.getSource()==BLOSUM62Colour)
+    else if(source==BLOSUM62Colour)
             BLOSUM62Colour_actionPerformed();
-    else if(evt.getSource()==annotationColour)
+    else if(source==annotationColour)
            new AnnotationColourChooser(viewport, alignPanel);
-    else if(evt.getSource()==sortPairwiseMenuItem)
+    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();
 
  }
@@ -574,10 +570,79 @@ public void itemStateChanged(ItemEvent evt)
                                                       viewport.showJVSuffix));
   }
 
+  void launchFullApplication()
+  {
+    StringBuffer url = new StringBuffer(jalviewServletURL);
+
+    url.append("?open="+
+               appendProtocol( viewport.applet.getParameter("file") ) );
+
+    if(viewport.applet.getParameter("features")!=null)
+    {
+      url.append( "&features=" );
+      url.append( appendProtocol( viewport.applet.getParameter("features") ) );
+    }
+
+    if(viewport.applet.getParameter("annotations")!=null)
+    {
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
+    }
+
+    if(viewport.applet.getParameter("jnetfile")!=null)
+    {
+      url.append( "&annotations=" );
+      url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );
+    }
+
+    if(viewport.applet.getParameter("defaultColour")!=null)
+    {
+      url.append("&colour=" +
+                 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
+          );
+    }
+
+    if(viewport.applet.getParameter("userDefinedColour")!=null)
+    {
+      url.append( "&colour=" +
+                 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
+         );
+    }
+
+    showURL(url.toString(), "FULL_APP");
+  }
+
+
+  String removeWhiteSpace(String colour)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < colour.length(); i++)
+    {
+      if (Character.isWhitespace(colour.charAt(i)))
+        sb.append("%20");
+      else
+        sb.append(colour.charAt(i));
+    }
+
+    return sb.toString();
+  }
+
+
+  String appendProtocol(String url)
+  {
+    try{
+       new URL(url);
+    }catch(java.net.MalformedURLException ex)
+    {
+      url = viewport.applet.getCodeBase()+url;
+    }
+    return url;
+  }
+
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.components.remove(viewport.alignment);
-    if(PaintRefresher.components.size()==0 && applet==null)
+    if(PaintRefresher.components.size()==0 && viewport.applet==null)
       System.exit(0);
 
     this.dispose();
@@ -616,21 +681,28 @@ public void itemStateChanged(ItemEvent evt)
   public void addHistoryItem(HistoryItem hi)
   {
     historyList.push(hi);
+    redoList.removeAllElements();
     updateEditMenuBar();
   }
 
   protected void undoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
+    HistoryItem nh,hi = (HistoryItem) historyList.pop();
+    redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
+    if (hi.alColumnChanges!=null)
+      nh.alColumnChanges=hi.alColumnChanges.getInverse();
     restoreHistoryItem(hi);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) redoList.pop();
+    HistoryItem nh,hi = (HistoryItem) redoList.pop();
+    historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
+                                  HistoryItem.HIDE));
+    if (hi.alColumnChanges!=null)
+      nh.alColumnChanges=hi.alColumnChanges.getInverse();
     restoreHistoryItem(hi);
     updateEditMenuBar();
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -639,8 +711,7 @@ public void itemStateChanged(ItemEvent evt)
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    hi.restore();
-
+    hi.restore(viewport.getColumnSelection());
     updateEditMenuBar();
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -659,13 +730,13 @@ 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;
         }
@@ -679,13 +750,13 @@ 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;
         }
@@ -698,7 +769,8 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
-  StringBuffer copiedSequences;
+  static StringBuffer copiedSequences;
+  static Vector copiedHiddenColumns;
   protected void copy_actionPerformed()
   {
     if (viewport.getSelectionGroup() == null)
@@ -709,7 +781,7 @@ 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);
@@ -719,7 +791,26 @@ 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;
 
@@ -827,9 +918,18 @@ public void itemStateChanged(ItemEvent evt)
           newtitle = newtitle.concat("- from " + getTitle());
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
-                                       applet,
+                                       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);
@@ -865,10 +965,10 @@ 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);
@@ -931,6 +1031,11 @@ 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);
@@ -956,12 +1061,13 @@ public void itemStateChanged(ItemEvent evt)
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
-      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
+      HistoryItem edit;
+      addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
                                      HistoryItem.HIDE));
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0, min);
-
+      edit.addShift(0, min);
       if (viewport.getSelectionGroup() != null)
       {
         viewport.getSelectionGroup().adjustForRemoveLeft(min);
@@ -989,6 +1095,7 @@ public void itemStateChanged(ItemEvent evt)
                                      HistoryItem.HIDE));
       int max = colSel.getMax();
       viewport.getAlignment().trimRight(max);
+
       if (viewport.getSelectionGroup() != null)
       {
         viewport.getSelectionGroup().adjustForRemoveRight(max);
@@ -1010,7 +1117,8 @@ public void itemStateChanged(ItemEvent evt)
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gapped Columns",
+    HistoryItem edit;
+    addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment,
                                    HistoryItem.HIDE));
 
@@ -1028,7 +1136,10 @@ public void itemStateChanged(ItemEvent evt)
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+    // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
+    // TODO: columnSelection.compensateforedits should be called (and passed to history item)
+    HistoryItem editgaps;
+    addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
 
     //This is to maintain viewport position on first residue
@@ -1037,68 +1148,57 @@ public void itemStateChanged(ItemEvent evt)
     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)
+        && 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;
     }
     else
       seqs = viewport.alignment.getSequences();
 
+    /* Commented out regions below are partial implementation of todo above.
+     * divide start,end into visible chunks, and for each:
+     int diff=end-start+1;
+     int diffmax=0;
+     int dr[] = new int[seqs.size()];
+     */
     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);
-      }
+      //dr[i]=
+      current.removeGaps(start, end);
+      /*if (d<diff) // can only shift
+        diff=d;
+      if (diffmax<d)
+        diffmax=d;
+        */
     }
+    /* // after the end of each chunk -
+     * if (diff>0) {
+     // record shift for history.
+      editgaps.addShift(start, diff);
+      if (viewport.hasHiddenColumns && diffmax>diff) {
+      // pad sequence
+       StringBuffer gaps=new StringBuffer(diffmax);
+       for (int i=0,j=diffmax-diff; i<j; i++)
+       gaps.append(viewport.getGapCharacter());
+       for (int i=0, j=seqs.size(); i<j; i++) {
+       current = (SequenceI) seqs.elementAt(i);
+       if (dr[i]-diff>0) {
+       String sq = current.getSequence();
+       current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
+       }
+       }
+      }
+      }*/
+
     viewport.setStartRes(seq.findIndex(startRes)-1);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
@@ -1153,7 +1253,8 @@ 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();
     }
@@ -1196,6 +1297,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
+
   protected void scaleAbove_actionPerformed()
   {
     viewport.setScaleAboveWrapped(scaleAbove.getState());
@@ -1389,7 +1491,7 @@ 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
         {
@@ -1409,7 +1511,7 @@ 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());
@@ -1418,7 +1520,7 @@ 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);
@@ -1531,17 +1633,13 @@ 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));
@@ -1571,8 +1669,8 @@ 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;
@@ -1630,29 +1728,23 @@ 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);
+      addTreeMenuItem(tp, title);
 
-    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+    }
   }
 
   void loadTree_actionPerformed()
   {
-    TreePanel tp = null;
-
       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
       cap.setText("Paste your Newick tree file here.");
       cap.treeImport = true;
@@ -1664,8 +1756,9 @@ public void itemStateChanged(ItemEvent evt)
   public void loadTree(jalview.io.NewickFile tree, String treeFile)
   {
     TreePanel tp = new TreePanel(viewport,
-                      viewport.getAlignment().getSequences(),
-                      tree, "From File - ", treeFile);
+                                 treeFile,
+                                 "From File - ",
+                                 tree);
     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
@@ -1730,7 +1823,7 @@ 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);
       }
     }
 
@@ -1766,7 +1859,7 @@ 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.");
     }
@@ -1774,7 +1867,8 @@ 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)
@@ -1790,6 +1884,7 @@ public void itemStateChanged(ItemEvent evt)
 
     protected MenuBar alignFrameMenuBar = new MenuBar();
     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");
@@ -1883,12 +1978,11 @@ 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)
@@ -1900,6 +1994,7 @@ public void itemStateChanged(ItemEvent evt)
         outputTextboxMenu.add(item);
       }
         closeMenuItem.addActionListener(this);
+        loadApplication.addActionListener(this);
 
         loadTree.addActionListener(this);
         selectAllSequenceMenuItem.addActionListener(this);
@@ -2055,6 +2150,20 @@ public void itemStateChanged(ItemEvent evt)
     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);
@@ -2065,6 +2174,8 @@ 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);
@@ -2078,7 +2189,8 @@ 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);
@@ -2088,13 +2200,15 @@ 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);
@@ -2145,6 +2259,10 @@ 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()
@@ -2195,18 +2313,18 @@ public void itemStateChanged(ItemEvent evt)
 
    // 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();
 
   }
 
@@ -2217,6 +2335,13 @@ public void itemStateChanged(ItemEvent evt)
   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)
   {