X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=6586a68f3c3f07bd03428c21ce2188812d8a6bd5;hb=f84a68869b1864eea585ade8ac36939fd88c8a93;hp=e1d8ce81296987e7fe6af6b838d4e3045116dbf2;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e1d8ce8..6586a68 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -23,6 +23,7 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
+import jalview.commands.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
@@ -36,8 +37,8 @@ public class AlignFrame extends Frame implements ActionListener,
 {
   public AlignmentPanel alignPanel;
   public AlignViewport viewport;
-  int NEW_WINDOW_WIDTH = 700;
-  int NEW_WINDOW_HEIGHT = 500;
+  int DEFAULT_WIDTH = 700;
+  int DEFAULT_HEIGHT = 500;
 
   String jalviewServletURL;
 
@@ -91,13 +92,13 @@ public class AlignFrame extends Frame implements ActionListener,
         if (param != null)
         {
           int width = Integer.parseInt(param);
-          NEW_WINDOW_WIDTH = width;
+          DEFAULT_WIDTH = width;
         }
         param = applet.getParameter("windowHeight");
         if (param != null)
         {
           int height = Integer.parseInt(param);
-          NEW_WINDOW_HEIGHT = height;
+          DEFAULT_HEIGHT = height;
         }
       }
       catch (Exception ex)
@@ -110,6 +111,8 @@ public class AlignFrame extends Frame implements ActionListener,
    this.addKeyListener(this);
    alignPanel.seqPanel.seqCanvas.addKeyListener(this);
    alignPanel.idPanel.idCanvas.addKeyListener(this);
+   alignPanel.scalePanel.addKeyListener(this);
+   alignPanel.annotationPanel.addKeyListener(this);
 
     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
@@ -130,8 +133,8 @@ public class AlignFrame extends Frame implements ActionListener,
    else
    {
      add(alignPanel, BorderLayout.CENTER);
-     jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
-                                      NEW_WINDOW_HEIGHT);
+     jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+                                      DEFAULT_HEIGHT);
    }
    alignPanel.validate();
    alignPanel.repaint();
@@ -258,7 +261,10 @@ 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;
 
@@ -266,7 +272,10 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_BACK_SPACE:
         if(viewport.cursorMode)
         {
-          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                                || evt.isShiftDown()
+                                                || evt.isAltDown()
+              );
         }
        else
         {
@@ -327,7 +336,56 @@ 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;
+      }
+      case KeyEvent.VK_PAGE_UP:
+        if (viewport.wrapAlignment)
+          alignPanel.scrollUp(true);
+        else
+          alignPanel.setScrollValues(viewport.startRes,
+                                     viewport.startSeq
+                                     - viewport.endSeq + viewport.startSeq);
+        break;
+      case KeyEvent.VK_PAGE_DOWN:
+        if (viewport.wrapAlignment)
+          alignPanel.scrollUp(false);
+        else
+          alignPanel.setScrollValues(viewport.startRes,
+                                     viewport.startSeq
+                                     + viewport.endSeq - viewport.startSeq);
+        break;
+      }
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -372,117 +430,137 @@ 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()==loadApplication)
+    else if(source==loadApplication)
       launchFullApplication();
-    else if(evt.getSource()==closeMenuItem)
+    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();
 
  }
@@ -497,7 +575,7 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
@@ -521,6 +599,18 @@ public void itemStateChanged(ItemEvent evt)
       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=" +
@@ -579,62 +669,21 @@ public void itemStateChanged(ItemEvent evt)
 
   void updateEditMenuBar()
   {
-    if (historyList.size() > 0)
-    {
-      undoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) historyList.peek();
-      undoMenuItem.setLabel("Undo " + hi.getDescription());
-    }
-    else
-    {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setLabel("Undo");
-    }
-
-    if (redoList.size() > 0)
-    {
-      redoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) redoList.peek();
-      redoMenuItem.setLabel("Redo " + hi.getDescription());
-    }
-    else
-    {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setLabel("Redo");
-    }
   }
 
-  public void addHistoryItem(HistoryItem hi)
-  {
-    historyList.push(hi);
-    updateEditMenuBar();
-  }
 
   protected void undoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) historyList.pop();
-    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
-                                  HistoryItem.HIDE));
-    restoreHistoryItem(hi);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed()
   {
-    HistoryItem hi = (HistoryItem) redoList.pop();
-    restoreHistoryItem(hi);
-    updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
   }
 
   // used by undo and redo
-  void restoreHistoryItem(HistoryItem hi)
+  void restoreHistoryItem(CommandI command)
   {
-    hi.restore();
-
-    updateEditMenuBar();
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -689,7 +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)
@@ -710,6 +760,25 @@ public void itemStateChanged(ItemEvent evt)
     int index = 0, startRes, endRes;
     char ch;
 
+    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;
@@ -767,8 +836,8 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void pasteThis_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-                                   HistoryItem.PASTE));
+  //  addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+   //                                HistoryItem.PASTE));
     paste(false);
   }
 
@@ -821,9 +890,18 @@ public void itemStateChanged(ItemEvent evt)
                                        viewport.applet,
                                        newtitle,
                                        false);
+        if (copiedHiddenColumns != null)
+        {
+          for (int i = 0; i < copiedHiddenColumns.size(); i++)
+          {
+            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+            af.viewport.hideColumns(region[0], region[1]);
+          }
+        }
+
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                         NEW_WINDOW_HEIGHT);
+        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
+                                         DEFAULT_HEIGHT);
       }
       else
       {
@@ -846,8 +924,8 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void delete_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
+    //addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+    //                               HistoryItem.HIDE));
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -949,154 +1027,18 @@ public void itemStateChanged(ItemEvent evt)
 
   public void remove2LeftMenuItem_actionPerformed()
   {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
-                                     HistoryItem.HIDE));
-      int min = colSel.getMin();
-      viewport.getAlignment().trimLeft(min);
-      colSel.compensateForEdit(0, min);
-
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveLeft(min);
-      }
-
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveLeft(min))
-        {
-          viewport.alignment.deleteGroup(sg);
-        }
-      }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
   }
 
   public void remove2RightMenuItem_actionPerformed()
   {
-    ColumnSelection colSel = viewport.getColumnSelection();
-    if (colSel.size() > 0)
-    {
-      addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
-                                     HistoryItem.HIDE));
-      int max = colSel.getMax();
-      viewport.getAlignment().trimRight(max);
-      if (viewport.getSelectionGroup() != null)
-      {
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
-      }
-
-      Vector groups = viewport.alignment.getGroups();
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveRight(max))
-        {
-          viewport.alignment.deleteGroup(sg);
-        }
-      }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
-
   }
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gapped Columns",
-                                   viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    //This is to maintain viewport position on first residue
-    //of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
-
-    viewport.getAlignment().removeGaps();
-
-    viewport.setStartRes(seq.findIndex(startRes)-1);
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
-                                   HistoryItem.HIDE));
-
-    //This is to maintain viewport position on first residue
-    //of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
-
-    SequenceI current;
-    int jSize;
-
-    Vector seqs=null;
-
-    int start=0, end = viewport.alignment.getWidth();
-
-    if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().getSequences(false) != null
-        && viewport.getSelectionGroup().getSize(false)>0)
-    {
-      seqs = viewport.getSelectionGroup().getSequences(true);
-      start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes()+1;
-    }
-    else
-      seqs = viewport.alignment.getSequences();
-
-    for (int i = 0; i < seqs.size(); i++)
-    {
-      current = (SequenceI) seqs.elementAt(i);
-      jSize = current.getLength();
-
-      // Removing a range is much quicker than removing gaps
-      // one by one for long sequences
-      int j = start;
-      int rangeStart=-1, rangeEnd=-1;
-
-      do
-      {
-        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
-        {
-          if(rangeStart==-1)
-           {
-             rangeStart = j;
-             rangeEnd = j+1;
-           }
-           else
-           {
-             rangeEnd++;
-           }
-           j++;
-        }
-        else
-        {
-          if(rangeStart>-1)
-          {
-            current.deleteChars(rangeStart, rangeEnd);
-            j-=rangeEnd-rangeStart;
-            jSize-=rangeEnd-rangeStart;
-            rangeStart = -1;
-            rangeEnd = -1;
-          }
-          else
-            j++;
-        }
-      }
-      while (j < end && j < jSize);
-      if(rangeStart>-1)
-      {
-       current.deleteChars(rangeStart, rangeEnd);
-      }
-    }
-    viewport.setStartRes(seq.findIndex(startRes)-1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void alignmentChanged()
@@ -1128,7 +1070,7 @@ public void itemStateChanged(ItemEvent evt)
                           viewport.alignment.getWidth());
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
       if (cs.conservationApplied())
       {
         Alignment al = (Alignment) viewport.alignment;
@@ -1193,6 +1135,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.repaint();
   }
 
+
   protected void scaleAbove_actionPerformed()
   {
     viewport.setScaleAboveWrapped(scaleAbove.getState());
@@ -1367,7 +1310,7 @@ public void itemStateChanged(ItemEvent evt)
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
 
     }
     viewport.setGlobalColourScheme(cs);
@@ -1502,8 +1445,8 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+   //                                HistoryItem.SORT));
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
@@ -1511,16 +1454,16 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortIDMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+   //                                HistoryItem.SORT));
     AlignmentSorter.sortByID(viewport.getAlignment());
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+  //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+  //                                 HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     alignPanel.repaint();
 
@@ -1533,7 +1476,8 @@ public void itemStateChanged(ItemEvent evt)
 
   public void pairwiseAlignmentMenuItem_actionPerformed()
   {
-    if (viewport.getSelectionGroup().getSize(false) > 1)
+    if (viewport.getSelectionGroup()!=null
+        && viewport.getSelectionGroup().getSize(false) > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
@@ -1622,13 +1566,19 @@ public void itemStateChanged(ItemEvent evt)
 
     }
 
-    final TreePanel tp = new TreePanel(viewport,
-                         type,
-                         pwType);
+    if ( (viewport.getSelectionGroup() != null &&
+          viewport.getSelectionGroup().getSize(false) > 1)
+      || (viewport.getSelectionGroup() == null
+          && viewport.alignment.getHeight() > 1))
+    {
+      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()
@@ -1659,8 +1609,8 @@ public void itemStateChanged(ItemEvent evt)
     {
       public void actionPerformed(ActionEvent evt)
       {
-        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
-                                       HistoryItem.SORT));
+      //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+      //                                 HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }
@@ -1866,12 +1816,11 @@ public void itemStateChanged(ItemEvent evt)
       MenuItem item;
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
+      for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
 
-        item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
-                            elementAt(
-                                i));
+        item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -2039,6 +1988,20 @@ 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);
@@ -2064,7 +2027,8 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(selectAllSequenceMenuItem);
         editMenu.add(deselectAllSequenceMenuItem);
         editMenu.add(invertSequenceMenuItem);
-        editMenu.add(deleteGroups);
+    editMenu.add(invertColSel);
+    editMenu.add(deleteGroups);
         editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
@@ -2074,13 +2038,15 @@ 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);
@@ -2131,6 +2097,10 @@ public void itemStateChanged(ItemEvent evt)
         calculate.add(njTreeBlosumMenuItem);
         helpMenu.add(documentation);
         helpMenu.add(about);
+    menu1.add(showColumns);
+    menu1.add(showSeqs);
+    menu2.add(hideColumns);
+    menu2.add(hideSequences);
   }
 
   public void setEmbedded()
@@ -2203,6 +2173,13 @@ 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)
   {