From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 23 May 2005 09:27:33 +0000 (+0000)
Subject: historyitem added
X-Git-Tag: Release_2_0~238
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4c61bddcb9e367db694e3f2bde9c4d25f114f50b;p=jalview.git

historyitem added
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dd4ff38..0003d14 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -101,75 +101,94 @@ public class AlignFrame extends GAlignFrame
   Stack redoList = new Stack();
 
   void updateEditMenuBar()
-  {
-    if(historyList.size()>0)
+   {
+     if(historyList.size()>0)
+      {
+        undoMenuItem.setEnabled(true);
+        HistoryItem hi = (HistoryItem)historyList.peek();
+        undoMenuItem.setLabel("Undo "+hi.getDescription());
+      }
+     else
      {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.elementAt(0);
-       undoMenuItem.setLabel("Undo "+history[0]);
+       undoMenuItem.setEnabled(false);
+       undoMenuItem.setLabel("Undo");
      }
-    else
-    {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setLabel("Undo");
-    }
 
-    if(redoList.size()>0)
+     if(redoList.size()>0)
+      {
+        redoMenuItem.setEnabled(true);
+        HistoryItem hi = (HistoryItem)redoList.peek();
+        redoMenuItem.setLabel("Redo "+hi.getDescription());
+      }
+     else
      {
-       redoMenuItem.setEnabled(true);
-       Object [] history = (Object[])redoList.elementAt(0);
-       redoMenuItem.setLabel("Redo "+history[0]);
+       redoMenuItem.setEnabled(false);
+       redoMenuItem.setLabel("Redo");
      }
-    else
-    {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setLabel("Redo");
-    }
-  }
+   }
 
-  public void addHistoryItem(String type)
-  {
-    // must make sure we add new sequence objects her, not refs to the existing sequences
-    redoList.removeAllElements();
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for(int i=0; i<viewport.getAlignment().getHeight(); i++)
-    {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
-    }
+   public void addHistoryItem(HistoryItem hi)
+   {
+     historyList.push(hi);
+     updateEditMenuBar();
+   }
 
-    historyList.addElement(new Object[]{type,  seq} );
-    updateEditMenuBar();
-  }
+   protected void undoMenuItem_actionPerformed(ActionEvent e)
+   {
+       HistoryItem hi = (HistoryItem)historyList.pop();
+       redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
+       restoreHistoryItem(hi);
+   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
-  {
-    Object [] history = (Object[])historyList.elementAt(0);
-    historyList.removeElementAt(0);
-    // add the redo state before continuing!!
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
-    {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
-    }
-    /////////
+   protected void redoMenuItem_actionPerformed(ActionEvent e)
+   {
+      HistoryItem hi = (HistoryItem)redoList.pop();
+      restoreHistoryItem(hi);
+      updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.repaint();
+      alignPanel.repaint();
+   }
 
-    redoList.addElement(new Object[] {history[0], seq});
 
-      seq = (SequenceI[]) history[1];
+   // 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)
+          {
+            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);
+        }
+      }
 
-      AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
-      viewport.setAlignment(new Alignment(seq));
-      updateEditMenuBar();
-      for (int i = 0; i < old.length; i++)
-        viewport.alignment.addAnnotation(old[i]);
+       updateEditMenuBar();
+
+       viewport.updateConsensus();
+       viewport.updateConservation();
+       alignPanel.repaint();
+   }
 
-      viewport.updateConservation();
-      viewport.updateConsensus();
-      alignPanel.repaint();
-  }
 
   public void moveSelectedSequences(boolean up)
   {
@@ -261,7 +280,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
     paste(false);
   }
 
@@ -322,7 +341,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Delete");
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
     if (viewport.getSelectionGroup() == null)
       return;
 
@@ -355,23 +374,6 @@ public class AlignFrame extends GAlignFrame
 
 
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-     Object [] history = (Object[])redoList.pop();
-     SequenceI[] seq = (SequenceI[]) history[1];
-
-     AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
-     viewport.setAlignment(new Alignment(seq));
-     for (int i = 0; i < old.length; i++)
-       viewport.alignment.addAnnotation(old[i]);
-
-     viewport.updateConservation();
-     viewport.updateConsensus();
-     updateEditMenuBar();
-     alignPanel.repaint();
-  }
-
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -412,10 +414,11 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     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);
@@ -437,10 +440,11 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     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)
@@ -463,7 +467,9 @@ public class AlignFrame extends GAlignFrame
 
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete gapped columns");
+    addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                                   viewport.alignment,
+                                   HistoryItem.HIDE));
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
@@ -472,7 +478,9 @@ public class AlignFrame extends GAlignFrame
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete all gaps");
+    addHistoryItem(new HistoryItem("Remove Gaps",
+                                   viewport.alignment,
+                                   HistoryItem.HIDE));
     SequenceI current;
     int jSize;
     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
@@ -860,21 +868,21 @@ public class AlignFrame extends GAlignFrame
 
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByID( viewport.getAlignment() );
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.repaint();
@@ -976,7 +984,8 @@ public class AlignFrame extends GAlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        addHistoryItem("sort");
+        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+                                       HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index e6e02c5..27250cd 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -15,6 +15,8 @@ public class SeqPanel extends Panel
 
   protected int lastres;
   protected int startseq;
+  int startEdit=-1;
+  int endEdit=-1;
 
   protected AlignViewport av;
 
@@ -24,6 +26,10 @@ public class SeqPanel extends Panel
   ScrollThread scrollThread = null;
   boolean mouseDragging = false;
 
+  boolean editingSeqs = false;
+  boolean groupEditing = false;
+
+
 
   public SeqPanel(AlignViewport avp, AlignmentPanel p) {
     this.av         = avp;
@@ -46,7 +52,7 @@ public class SeqPanel extends Panel
       {
         if(av.getWrapAlignment())
          return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        if( editingSeqs )
           doMouseDragged(evt);
         else
           doMouseDraggedDefineMode(evt);
@@ -59,32 +65,38 @@ public class SeqPanel extends Panel
       {
         if(av.getWrapAlignment())
          return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        if(editingSeqs)
           doMouseReleased(evt);
         else
           doMouseReleasedDefineMode(evt);
+
       }
       public void mousePressed(MouseEvent evt)
       {
         if(av.getWrapAlignment())
          return;
+       System.out.println("here");
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        {
+          if(evt.isAltDown() || evt.isControlDown())
+            groupEditing = true;
+
+          editingSeqs = true;
           doMousePressed(evt);
+        }
         else
           doMousePressedDefineMode(evt);
       }
       public void mouseExited(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
-                  evt.isControlDown())
+        if (av.getWrapAlignment() || editingSeqs)
                 return;
               doMouseExitedDefineMode(evt);
 
       }
       public void mouseEntered(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
-            evt.isControlDown())
+        if (av.getWrapAlignment() || editingSeqs)
           return;
         doMouseEnteredDefineMode(evt);
       }
@@ -96,18 +108,20 @@ public class SeqPanel extends Panel
 
   public void doMouseReleased(MouseEvent evt) {
 
-    startseq = -1;
-    lastres  = -1;
     if(seqEditOccurred>-1)
-      updateConservation(seqEditOccurred);
+      editOccurred(seqEditOccurred);
 
+    startseq = -1;
+    lastres  = -1;
     seqEditOccurred = -1;
-
+    editingSeqs  = false;
+    groupEditing = false;
     ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt) {
-    ap.alignFrame.addHistoryItem("sequence edit");
+    ap.alignFrame.addHistoryItem( new HistoryItem(
+        "Edit Sequence",av.alignment, HistoryItem.EDIT));
     int seq;
     int res;
 
@@ -221,98 +235,107 @@ public class SeqPanel extends Panel
 
 
       if (res != lastres)
-      {
-          // Group editing
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            SequenceGroup sg = av.getSelectionGroup();
-            if(sg==null)
-            {
-              lastres=-1;
-              return;
-            }
-
-              // drag to right
-              if(dragRight)
-                  sg.setEndRes(sg.getEndRes() + (res-lastres));
-
-              // drag to left
-              else
-              {
-                 /// Are we able to delete?
-                 // ie are all columns blank?
-                 boolean deleteAllowed = false;
-                for (int s = 0; s < sg.getSize(); s++)
-                {
-                  SequenceI seq = sg.getSequenceAt(s);
-                  for (int j=res; j<lastres; j++)
-                  {
-                    if(seq.getSequence().length()<=j)
-                      continue;
-
-                    if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
-                    {
-                      // Not a gap, block edit not valid
-                      res=j+1;
-                      deleteAllowed = false;
-                      continue;
-                    }
-                    deleteAllowed = true;
-                  }
-                }
-
-                if(!deleteAllowed)
-                {
-                  lastres = -1;
-                  return;
-                }
-
-                sg.setEndRes(sg.getEndRes() - (lastres-res));
-              }
-
-
-              for (int i = 0; i < sg.getSize(); i++)
-              {
-                SequenceI s = sg.getSequenceAt(i);
-                int k = av.alignment.findIndex(s);
-
-                // drag to right
-                if (dragRight)
-                  for (int j = lastres; j < res; j++)
-                    insertChar(j, k);
-
-                // drag to left
-                else
-                {
-                  for (int j = res; j < lastres; j++)
-                  {
-                    if(s.getLength()>j)
-                      deleteChar(res, k);
-                  }
-                }
-              }
-          }
-          else /////Editing a single sequence///////////
-          {
-            if (res < av.getAlignment().getWidth() && res > lastres)
-            {
-              // dragging to the right
-              for (int j = lastres; j < res; j++)
-                insertChar(j, startseq);
-            }
-            else if (res < av.getAlignment().getWidth() && res < lastres)
-            {
-              // dragging to the left
-              for (int j = lastres; j > res; j--)
-              {
-                deleteChar(res, startseq);
-              }
-            }
-
-          }
-      }
+     {
+         // Group editing
+         if (groupEditing)
+         {
+           SequenceGroup sg = av.getSelectionGroup();
+           if(sg==null)
+           {
+             lastres=-1;
+             return;
+           }
 
-      lastres = res;
+             // drag to right
+             if(dragRight)
+                 sg.setEndRes(sg.getEndRes() + (res-lastres));
+
+             // drag to left
+             else
+             {
+                /// Are we able to delete?
+                // ie are all columns blank?
+                boolean deleteAllowed = false;
+               for (int s = 0; s < sg.getSize(); s++)
+               {
+                 SequenceI seq = sg.getSequenceAt(s);
+                 for (int j=res; j<lastres; j++)
+                 {
+                   if(seq.getSequence().length()<=j)
+                     continue;
+
+                   if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
+                   {
+                     // Not a gap, block edit not valid
+                     res=j+1;
+                     deleteAllowed = false;
+                     continue;
+                   }
+                   deleteAllowed = true;
+                 }
+               }
+
+               if(!deleteAllowed)
+               {
+                 lastres = -1;
+                 return;
+               }
+
+               sg.setEndRes(sg.getEndRes() - (lastres-res));
+             }
+
+
+             for (int i = 0; i < sg.getSize(); i++)
+             {
+               SequenceI s = sg.getSequenceAt(i);
+               int k = av.alignment.findIndex(s);
+
+               // drag to right
+               if (dragRight)
+                 for (int j = lastres; j < res; j++)
+                   insertChar(j, k);
+
+               // drag to left
+               else
+               {
+                 for (int j = res; j < lastres; j++)
+                 {
+                   if(s.getLength()>j)
+                     deleteChar(res, k);
+                 }
+               }
+             }
+         }
+         else /////Editing a single sequence///////////
+         {
+           if (res < av.getAlignment().getWidth() && res > lastres)
+           {
+             // dragging to the right
+             for (int j = lastres; j < res; j++)
+               insertChar(j, startseq);
+           }
+           else if (res < av.getAlignment().getWidth() && res < lastres)
+           {
+             // dragging to the left
+             for (int j = lastres; j > res; j--)
+             {
+               if( jalview.util.Comparison.isGap(
+                 av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
+
+               deleteChar(res, startseq);
+               else
+               {
+
+                 break;
+               }
+             }
+           }
+
+         }
+     }
+
+     endEdit = res;
+     lastres = res;
       seqCanvas.repaint();
   }
 
@@ -330,17 +353,21 @@ public class SeqPanel extends Panel
   public void deleteChar(int j, int seq)
   {
 
-    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-      av.alignment.getSequenceAt(seq).deleteCharAt(j);
-
+    av.alignment.getSequenceAt(seq).deleteCharAt(j);
+    seqEditOccurred=seq;
     av.alignment.getWidth();
     repaint();
-    seqEditOccurred=seq;
   }
 
 
-  void updateConservation(int i)
+  void editOccurred(int i)
   {
+    if(endEdit==startEdit)
+    {
+      ap.alignFrame.historyList.pop();
+      ap.alignFrame.updateEditMenuBar();
+    }
+
     av.updateConservation();
     av.updateConsensus();
 
@@ -352,6 +379,7 @@ public class SeqPanel extends Panel
       cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
 
     ap.alignFrame.changeColour(cs);
+
   }
 
 //////////////////////////////////////////
diff --git a/src/jalview/datamodel/HistoryItem.java b/src/jalview/datamodel/HistoryItem.java
new file mode 100755
index 0000000..3a5b180
--- /dev/null
+++ b/src/jalview/datamodel/HistoryItem.java
@@ -0,0 +1,52 @@
+package jalview.datamodel;
+
+import java.util.*;
+
+public class HistoryItem
+{
+  public static final int EDIT = 0;
+  public static final int SORT = 1;
+  public static final int HIDE = 2;
+  public static final int PASTE= 3;
+
+  final int type;
+  Vector sequences;
+  Vector alignIndex;
+  String description;
+  Vector hiddenSeqs;
+
+  public HistoryItem(String description, AlignmentI al, int type)
+  {
+    this.type = type;
+    this.description = description;
+    sequences = new Vector();
+    alignIndex = new Vector();
+    hiddenSeqs = new Vector();
+
+    for (int i = 0; i < al.getHeight(); i++)
+    {
+      SequenceI seq = al.getSequenceAt(i);
+      sequences.addElement(seq);
+      alignIndex.addElement(i + "");
+      hiddenSeqs.addElement(seq.getSequence().toString());
+    }
+  }
+
+  public int getType()
+  {return type;}
+
+  public Vector getSequences()
+  {return sequences;}
+
+  public String getDescription()
+  {return description; }
+
+  public Vector getHidden()
+  { return hiddenSeqs; }
+
+  public int getAlignIndex(int seq)
+  {
+    return Integer.parseInt(alignIndex.elementAt(seq).toString());
+  }
+
+}
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b60ee62..63b3787 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -171,75 +171,94 @@ public class AlignFrame extends GAlignFrame
   Stack redoList = new Stack();
 
   void updateEditMenuBar()
-  {
-    if(historyList.size()>0)
+   {
+     if(historyList.size()>0)
+      {
+        undoMenuItem.setEnabled(true);
+        HistoryItem hi = (HistoryItem)historyList.peek();
+        undoMenuItem.setText("Undo "+hi.getDescription());
+      }
+     else
      {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.get(0);
-       undoMenuItem.setText("Undo "+history[0]);
+       undoMenuItem.setEnabled(false);
+       undoMenuItem.setText("Undo");
      }
-    else
-    {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setText("Undo");
-    }
 
-    if(redoList.size()>0)
+     if(redoList.size()>0)
+      {
+        redoMenuItem.setEnabled(true);
+        HistoryItem hi = (HistoryItem)redoList.peek();
+        redoMenuItem.setText("Redo "+hi.getDescription());
+      }
+     else
      {
-       redoMenuItem.setEnabled(true);
-       Object [] history = (Object[])redoList.get(0);
-       redoMenuItem.setText("Redo "+history[0]);
+       redoMenuItem.setEnabled(false);
+       redoMenuItem.setText("Redo");
      }
-    else
-    {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setText("Redo");
-    }
-  }
-
-  public void addHistoryItem(String type)
-  {
-    // must make sure we add new sequence objects her, not refs to the existing sequences
-    redoList.clear();
-
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for(int i=0; i<viewport.getAlignment().getHeight(); i++)
-    {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
-    }
-
+   }
 
-    historyList.add(0, new Object[]{type,  seq} );
-    updateEditMenuBar();
-  }
+   public void addHistoryItem(HistoryItem hi)
+   {
+     historyList.push(hi);
+     updateEditMenuBar();
+   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
-  {
-    Object [] history = (Object[])historyList.remove(0);
-    // add the redo state before continuing!!
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
-    {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
-    }
-    /////////
+   protected void undoMenuItem_actionPerformed(ActionEvent e)
+   {
+       HistoryItem hi = (HistoryItem)historyList.pop();
+       redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
+       restoreHistoryItem(hi);
+   }
 
-    redoList.add(0, new Object[] {history[0], seq});
 
-      seq = (SequenceI[]) history[1];
-      AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
-      viewport.setAlignment( new Alignment(seq) );
-      viewport.alignment.setGapCharacter( Preferences.gapSymbol );
+   protected void redoMenuItem_actionPerformed(ActionEvent e)
+   {
+      HistoryItem hi = (HistoryItem)redoList.pop();
+      restoreHistoryItem(hi);
       updateEditMenuBar();
-      for(int i=0; i<old.length; i++)
-        viewport.alignment.addAnnotation(old[i]);
       viewport.updateConsensus();
-      viewport.updateConservation();
       alignPanel.repaint();
-  }
+      alignPanel.repaint();
+   }
+
+
+   // 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)
+          {
+            System.out.println(hi.getHidden().elementAt(i));
+            restore.setSequence(hi.getHidden().elementAt(i).toString());
+            viewport.alignment.getSequences().insertElementAt(
+               restore,
+               hi.getAlignIndex(i));
+          }
+          else
+            restore.setSequence(hi.getHidden().elementAt(i).toString());
+        }
+        if(hi.getType()==HistoryItem.PASTE)
+        {
+          for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
+            viewport.alignment.deleteSequence(i);
+        }
+      }
+
+       updateEditMenuBar();
+
+       viewport.updateConsensus();
+       viewport.updateConservation();
+       alignPanel.repaint();
+   }
 
   public void moveSelectedSequences(boolean up)
   {
@@ -335,7 +354,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
     paste(false);
   }
 
@@ -398,7 +417,8 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Delete");
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+
     if (viewport.getSelectionGroup() == null)
       return;
 
@@ -430,20 +450,6 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-     Object [] history = (Object[])redoList.remove(0);
-     SequenceI[] seq = (SequenceI[]) history[1];
-     viewport.setAlignment( new Alignment(seq) );
-     viewport.alignment.setGapCharacter( Preferences.gapSymbol );
-     updateEditMenuBar();
-     viewport.updateConsensus();
-     alignPanel.repaint();
-     alignPanel.repaint();
-  }
-
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -482,10 +488,11 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     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);
@@ -507,10 +514,12 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     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)
@@ -533,7 +542,9 @@ public class AlignFrame extends GAlignFrame
 
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete gapped columns");
+    addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                                   viewport.alignment,
+                                   HistoryItem.HIDE));
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
@@ -542,7 +553,9 @@ public class AlignFrame extends GAlignFrame
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete all gaps");
+    addHistoryItem(new HistoryItem("Remove Gaps",
+                                   viewport.alignment,
+                                   HistoryItem.HIDE));
     SequenceI current;
     int jSize;
     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
@@ -936,21 +949,21 @@ public class AlignFrame extends GAlignFrame
 
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByID( viewport.getAlignment() );
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.repaint();
@@ -1061,7 +1074,8 @@ public class AlignFrame extends GAlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        addHistoryItem("sort");
+        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+                                       HistoryItem.SORT));
         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
         alignPanel.repaint();
@@ -1077,7 +1091,8 @@ public class AlignFrame extends GAlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        addHistoryItem("sort");
+        addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
+                                       HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c43acf9..ca09c97 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -15,6 +15,8 @@ public class SeqPanel extends JPanel
 
   protected int lastres;
   protected int startseq;
+  int startEdit=-1;
+  int endEdit=-1;
 
   protected AlignViewport av;
 
@@ -24,6 +26,9 @@ public class SeqPanel extends JPanel
   ScrollThread scrollThread = null;
   boolean mouseDragging = false;
 
+  boolean editingSeqs = false;
+  boolean groupEditing = false;
+
 
   public SeqPanel(AlignViewport avp, AlignmentPanel p) {
     this.av         = avp;
@@ -46,7 +51,7 @@ public class SeqPanel extends JPanel
       {
         if(av.getWrapAlignment())
          return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        if( editingSeqs )
           doMouseDragged(evt);
         else
           doMouseDraggedDefineMode(evt);
@@ -59,32 +64,37 @@ public class SeqPanel extends JPanel
       {
         if(av.getWrapAlignment())
          return;
-        if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        if(editingSeqs)
           doMouseReleased(evt);
         else
           doMouseReleasedDefineMode(evt);
+
       }
       public void mousePressed(MouseEvent evt)
       {
         if(av.getWrapAlignment())
          return;
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+        {
+          if(evt.isAltDown() || evt.isControlDown())
+            groupEditing = true;
+
+          editingSeqs = true;
           doMousePressed(evt);
+        }
         else
           doMousePressedDefineMode(evt);
       }
       public void mouseExited(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
-                  evt.isControlDown())
+        if (av.getWrapAlignment() || editingSeqs)
                 return;
               doMouseExitedDefineMode(evt);
 
       }
       public void mouseEntered(MouseEvent evt)
       {
-        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
-            evt.isControlDown())
+        if (av.getWrapAlignment() || editingSeqs)
           return;
         doMouseEnteredDefineMode(evt);
       }
@@ -96,18 +106,23 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleased(MouseEvent evt) {
 
-    startseq = -1;
-    lastres  = -1;
     if(seqEditOccurred>-1)
-      updateConservation(seqEditOccurred);
+      editOccurred(seqEditOccurred);
 
+    startseq = -1;
+    lastres  = -1;
     seqEditOccurred = -1;
+    editingSeqs  = false;
+    groupEditing = false;
 
     ap.repaint();
   }
 
   public void doMousePressed(MouseEvent evt) {
-    ap.alignFrame.addHistoryItem("sequence edit");
+
+    ap.alignFrame.addHistoryItem( new HistoryItem(
+        "Edit Sequence",av.alignment, HistoryItem.EDIT));
+
     int seq;
     int res;
 
@@ -120,14 +135,8 @@ public class SeqPanel extends JPanel
     if (seq < av.getAlignment().getHeight() &&
         res < av.getAlignment().getSequenceAt(seq).getLength())
     {
-      //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
-      // Find the residue's position in the sequence (res is the position
-      // in the alignment
-
       startseq = seq;
-
       lastres = res;
-
     }
     else
     {
@@ -135,6 +144,9 @@ public class SeqPanel extends JPanel
       lastres = -1;
     }
 
+    startEdit = lastres;
+    endEdit = lastres;
+
     return;
   }
 
@@ -227,10 +239,10 @@ public class SeqPanel extends JPanel
 
     if (res != lastres)
     {
-	// Group editing
-	if (evt.isAltDown() || evt.isControlDown())
+        // Group editing
+        if (groupEditing)
         {
-	  SequenceGroup sg = av.getSelectionGroup();
+          SequenceGroup sg = av.getSelectionGroup();
           if(sg==null)
           {
             lastres=-1;
@@ -310,13 +322,22 @@ public class SeqPanel extends JPanel
             // dragging to the left
             for (int j = lastres; j > res; j--)
             {
+              if( jalview.util.Comparison.isGap(
+                av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
+
               deleteChar(res, startseq);
+              else
+              {
+
+                break;
+              }
             }
-	  }
+          }
 
-	}
+        }
     }
 
+    endEdit = res;
     lastres = res;
     repaint();
   }
@@ -334,21 +355,22 @@ public class SeqPanel extends JPanel
 
   public void deleteChar(int j, int seq)
   {
+    av.alignment.getSequenceAt(seq).deleteCharAt(j);
+    seqEditOccurred=seq;
 
-    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-    {  av.alignment.getSequenceAt(seq).deleteCharAt(j);
-
-    }
-    else System.out.println("err "+seq+" "+j);
     av.alignment.getWidth();
     repaint();
-    seqEditOccurred=seq;
-
   }
 
 
-  void updateConservation(int i)
+  void editOccurred(int i)
   {
+    if(endEdit==startEdit)
+    {
+      ap.alignFrame.historyList.pop();
+      ap.alignFrame.updateEditMenuBar();
+    }
+
     av.updateConservation();
     av.updateConsensus();
 
@@ -440,6 +462,7 @@ public class SeqPanel extends JPanel
       // Edit end res position of selected group
       changeStartRes = true;
 
+    stretchGroup.getWidth();
 
     repaint();