X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4d9a419b6d4aba8b640b5f5fe8ea8992a6879961;hb=97de0d0525d1b7a81a7d8164fae39e6538a583e5;hp=78c175b3c062a0d42abc35657f3209469cd5667c;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 78c175b..4d9a419 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -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;
 
@@ -60,6 +61,9 @@ public class AlignFrame extends Frame implements ActionListener,
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
 
+    viewport.updateConservation(alignPanel);
+    viewport.updateConsensus(alignPanel);
+
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
     seqLimits.setState(viewport.showJVSuffix);
@@ -91,13 +95,13 @@ 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)
@@ -113,17 +117,6 @@ public class AlignFrame extends Frame implements ActionListener,
    alignPanel.scalePanel.addKeyListener(this);
    alignPanel.annotationPanel.addKeyListener(this);
 
-    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-     public void propertyChange(java.beans.PropertyChangeEvent evt)
-     {
-       if (evt.getPropertyName().equals("alignment"))
-       {
-         alignmentChanged();
-       }
-     }
-   });
-
 
    if(embedded)
    {
@@ -132,8 +125,8 @@ 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();
@@ -215,9 +208,9 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_V:
-        if (evt.isControlDown() || evt.isMetaDown())
+        if (evt.isControlDown())
         {
-          paste(true);
+          paste(evt.isShiftDown());
         }
         break;
       case KeyEvent.VK_A:
@@ -260,7 +253,10 @@ 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;
 
@@ -268,7 +264,9 @@ 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
         {
@@ -320,7 +318,6 @@ public class AlignFrame extends Frame implements ActionListener,
          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
        }
-       alignPanel.seqPanel.seqCanvas.repaint();
        break;
 
       case KeyEvent.VK_F:
@@ -329,6 +326,7 @@ public class AlignFrame extends Frame implements ActionListener,
           findMenuItem_actionPerformed();
         }
         break;
+
       case KeyEvent.VK_H:
       {
         boolean toggleSeqs = !evt.isControlDown();
@@ -358,12 +356,84 @@ public class AlignFrame extends Frame implements ActionListener,
           else if (!hide)
             viewport.showAllHiddenColumns();
         }
+        break;
+      }
 
-        alignPanel.repaint();
+      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;
+
+      case KeyEvent.VK_Z:
+        if (evt.isControlDown())
+        {
+          undoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_Y:
+        if (evt.isControlDown())
+        {
+          redoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_L:
+        if (evt.isControlDown())
+        {
+          trimAlignment(true);
+        }
+        break;
+
+      case KeyEvent.VK_R:
+        if (evt.isControlDown())
+        {
+          trimAlignment(false);
+        }
         break;
+
+      case KeyEvent.VK_E:
+        if (evt.isControlDown())
+        {
+          if (evt.isShiftDown())
+            this.removeAllGapsMenuItem_actionPerformed();
+          else
+            removeGappedColumnMenuItem_actionPerformed();
+        }
+        break;
+      case KeyEvent.VK_I:
+        if (evt.isControlDown())
+        {
+          if (evt.isAltDown())
+            viewport.invertColumnSelection();
+          else
+            this.invertSequenceMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_U:
+      if (evt.isControlDown())
+      {
+       this.deleteGroups_actionPerformed();
       }
+      break;
 
-    }
+
+      }
+      alignPanel.repaint();
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -453,9 +523,9 @@ public void itemStateChanged(ItemEvent evt)
     else if(source==invertColSel)
     { viewport.invertColumnSelection(); alignPanel.repaint(); }
     else if(source==remove2LeftMenuItem)
-            remove2LeftMenuItem_actionPerformed();
+            trimAlignment(true);
     else if(source==remove2RightMenuItem)
-            remove2RightMenuItem_actionPerformed();
+            trimAlignment(false);
     else if(source==removeGappedColumnMenuItem)
             removeGappedColumnMenuItem_actionPerformed();
     else if(source==removeAllGapsMenuItem)
@@ -553,7 +623,7 @@ 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,
@@ -583,6 +653,12 @@ public void itemStateChanged(ItemEvent evt)
       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=" +
@@ -636,16 +712,18 @@ public void itemStateChanged(ItemEvent evt)
     this.dispose();
   }
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
 
+  /**
+   * DOCUMENT ME!
+   */
   void updateEditMenuBar()
   {
-    if (historyList.size() > 0)
+
+    if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) historyList.peek();
-      undoMenuItem.setLabel("Undo " + hi.getDescription());
+      CommandI command = (CommandI) viewport.historyList.peek();
+      undoMenuItem.setLabel("Undo " + command.getDescription());
     }
     else
     {
@@ -653,11 +731,12 @@ public void itemStateChanged(ItemEvent evt)
       undoMenuItem.setLabel("Undo");
     }
 
-    if (redoList.size() > 0)
+    if (viewport.redoList.size() > 0)
     {
       redoMenuItem.setEnabled(true);
-      HistoryItem hi = (HistoryItem) redoList.peek();
-      redoMenuItem.setLabel("Redo " + hi.getDescription());
+
+      CommandI command = (CommandI) viewport.redoList.peek();
+      redoMenuItem.setLabel("Redo " + command.getDescription());
     }
     else
     {
@@ -666,43 +745,81 @@ public void itemStateChanged(ItemEvent evt)
     }
   }
 
-  public void addHistoryItem(HistoryItem hi)
+  public void addHistoryItem(CommandI command)
   {
-    historyList.push(hi);
-    redoList.removeAllElements();
-    updateEditMenuBar();
+    if(command.getSize()>0)
+    {
+      viewport.historyList.push(command);
+      viewport.redoList.removeAllElements();
+      updateEditMenuBar();
+      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void undoMenuItem_actionPerformed()
   {
-    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());
+    if(viewport.historyList.size()<1)
+      return;
+
+    CommandI command = (CommandI)viewport.historyList.pop();
+    viewport.redoList.push(command);
+    command.undoCommand();
+
+    AlignViewport originalSource = getOriginatingSource(command);
+
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    updateEditMenuBar();
+    originalSource.firePropertyChange("alignment", null,null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void redoMenuItem_actionPerformed()
   {
-    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);
+    CommandI command = (CommandI) viewport.redoList.pop();
+    viewport.historyList.push(command);
+    command.doCommand();
+
+    AlignViewport originalSource = getOriginatingSource(command);
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    originalSource.firePropertyChange("alignment", null, null);
   }
 
-  // used by undo and redo
-  void restoreHistoryItem(HistoryItem hi)
+  AlignViewport getOriginatingSource(CommandI command)
   {
-    hi.restore(viewport.getColumnSelection());
-    updateEditMenuBar();
-
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    AlignViewport originalSource = viewport;
+    //For sequence removal and addition, we need to fire
+   //the property change event FROM the viewport where the
+   //original alignment was altered
+    if (command instanceof EditCommand)
+    {
+      EditCommand editCommand = (EditCommand) command;
+      AlignmentI al = editCommand.getAlignment();
+      Vector comps = (Vector) PaintRefresher.components
+          .get(viewport.getSequenceSetId());
+      for (int i = 0; i < comps.size(); i++)
+      {
+        if (comps.elementAt(i) instanceof AlignmentPanel)
+        {
+          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          {
+            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            break;
+          }
+        }
+      }
+    }
+    return originalSource;
   }
 
   public void moveSelectedSequences(boolean up)
@@ -855,8 +972,6 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void pasteThis_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
-                                   HistoryItem.PASTE));
     paste(false);
   }
 
@@ -876,26 +991,16 @@ public void itemStateChanged(ItemEvent evt)
         String name = st.nextToken();
         int start = Integer.parseInt(st.nextToken());
         int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
-
-        if (!newAlignment)
-        {
-          viewport.alignment.addSequence(sequence);
-        }
-        else
-        {
-          seqs.addElement(sequence);
-        }
+        seqs.addElement(new Sequence(name, st.nextToken(), start, end));
+      }
+      SequenceI[] newSeqs = new SequenceI[seqs.size()];
+      for (int i = 0; i < seqs.size(); i++)
+      {
+        newSeqs[i] = (SequenceI) seqs.elementAt(i);
       }
 
       if (newAlignment)
       {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        for (int i = 0; i < seqs.size(); i++)
-        {
-          newSeqs[i] = (SequenceI) seqs.elementAt(i);
-        }
-
         String newtitle = new String("Copied sequences");
         if (getTitle().startsWith("Copied sequences"))
         {
@@ -919,11 +1024,21 @@ public void itemStateChanged(ItemEvent evt)
         }
 
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                         NEW_WINDOW_HEIGHT);
+        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
+                                         DEFAULT_HEIGHT);
       }
       else
       {
+        //!newAlignment
+        addHistoryItem(new EditCommand(
+            "Add sequences",
+            EditCommand.PASTE,
+            newSeqs,
+            0,
+            viewport.alignment.getWidth(),
+            viewport.alignment)
+            );
+
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -943,62 +1058,62 @@ public void itemStateChanged(ItemEvent evt)
 
   protected void delete_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
-                                   HistoryItem.HIDE));
-    if (viewport.getSelectionGroup() == null)
+
+    SequenceGroup sg = viewport.getSelectionGroup();
+    if (sg == null)
     {
       return;
     }
 
-
-    SequenceGroup sg = viewport.getSelectionGroup();
-    boolean allSequences = false;
-    if(sg.getSize(false)==viewport.alignment.getHeight())
-          allSequences = true;
-
+    Vector seqs = new Vector();
+    SequenceI seq;
     for (int i = 0; i < sg.getSize(false); i++)
     {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+      seq = sg.getSequenceAt(i);
+      seqs.addElement(seq);
+    }
 
-      // If the cut affects all sequences, remove highlighted columns
-      if (allSequences)
-      {
-        viewport.getColumnSelection().removeElements(sg.getStartRes(),
-                                                     sg.getEndRes() + 1);
-      }
 
+   // If the cut affects all sequences, remove highlighted columns
+   if (sg.getSize(false) == viewport.alignment.getHeight())
+   {
+     viewport.getColumnSelection().removeElements(sg.getStartRes(),
+         sg.getEndRes() + 1);
+   }
+
+
+    SequenceI [] cut = new SequenceI[seqs.size()];
+    for(int i=0; i<seqs.size(); i++)
+      cut[i] = (SequenceI)seqs.elementAt(i);
+
+
+    /*
+    //ADD HISTORY ITEM
+    */
+    addHistoryItem(new EditCommand("Cut Sequences",
+                                      EditCommand.CUT,
+                                      cut,
+                                      sg.getStartRes(),
+                                      sg.getEndRes()-sg.getStartRes()+1,
+                                      viewport.alignment));
 
-      if (seq.getSequence().length() < 1)
-      {
-        viewport.getAlignment().deleteSequence(seq);
-      }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
-      }
-    }
 
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
+
+    viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+
     if (viewport.getAlignment().getHeight() < 1)
     {
-      try
-      {
         this.setVisible(false);
-      }
-      catch (Exception ex)
-      {}
     }
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-
   }
 
   protected void deleteGroups_actionPerformed()
   {
     viewport.alignment.deleteAllGroups();
+    viewport.sequenceColours=null;
     viewport.setSelectionGroup(null);
 
     alignPanel.repaint();
@@ -1014,7 +1129,7 @@ public void itemStateChanged(ItemEvent evt)
     sg.setEndRes(viewport.alignment.getWidth()-1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed()
@@ -1030,7 +1145,7 @@ public void itemStateChanged(ItemEvent evt)
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void invertSequenceMenuItem_actionPerformed()
@@ -1041,215 +1156,144 @@ public void itemStateChanged(ItemEvent evt)
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
-  public void remove2LeftMenuItem_actionPerformed()
+  void trimAlignment(boolean trimLeft)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
+    int column;
+
     if (colSel.size() > 0)
     {
-      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);
-      }
+      if(trimLeft)
+        column = colSel.getMin();
+      else
+        column = colSel.getMax();
 
-      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());
-    }
-  }
+      SequenceI [] seqs;
+      if(viewport.getSelectionGroup()!=null)
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      else
+        seqs = viewport.alignment.getSequencesArray();
 
-  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)
+      TrimRegionCommand trimRegion;
+      if(trimLeft)
       {
-        viewport.getSelectionGroup().adjustForRemoveRight(max);
+        trimRegion = new TrimRegionCommand("Remove Left",
+                                    TrimRegionCommand.TRIM_LEFT,
+                                    seqs,
+                                    column,
+                                    viewport.alignment,
+                                    viewport.colSel,
+                                    viewport.selectionGroup);
+        viewport.setStartRes(0);
       }
+     else
+     {
+       trimRegion = new TrimRegionCommand("Remove Right",
+                                   TrimRegionCommand.TRIM_RIGHT,
+                                   seqs,
+                                   column,
+                                   viewport.alignment,
+                                   viewport.colSel,
+                                   viewport.selectionGroup);
+     }
+
+     statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
+
+
+      addHistoryItem(trimRegion);
 
       Vector groups = viewport.alignment.getGroups();
+
       for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (!sg.adjustForRemoveRight(max))
+
+        if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+            || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
           viewport.alignment.deleteGroup(sg);
         }
       }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-    }
 
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
+    }
   }
 
+
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    HistoryItem edit;
-    addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
-                                   viewport.alignment,
-                                   HistoryItem.HIDE));
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
-    //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[] seqs;
+    if (viewport.getSelectionGroup() != null)
+    {
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequencesArray();
 
-    viewport.getAlignment().removeGaps();
 
-    viewport.setStartRes(seq.findIndex(startRes)-1);
+    RemoveGapColCommand removeGapCols =
+        new RemoveGapColCommand("Remove Gapped Columns",
+                                seqs,
+                                start, end,
+                                viewport.getGapCharacter());
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-  }
+    addHistoryItem(removeGapCols);
 
-  public void removeAllGapsMenuItem_actionPerformed()
-  {
-    // 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));
+    statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
 
     //This is to maintain viewport position on first residue
     //of first sequence
     SequenceI seq = viewport.alignment.getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
+   // ShiftList shifts;
+   // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+   // edit.alColumnChanges=shifts.getInverse();
+   // if (viewport.hasHiddenColumns)
+   //   viewport.getColumnSelection().compensateForEdits(shifts);
+   viewport.setStartRes(seq.findIndex(startRes)-1);
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
-    SequenceI current;
-    Vector seqs=null;
+  }
 
-    int start=0, end = viewport.alignment.getWidth();
+  public void removeAllGapsMenuItem_actionPerformed()
+  {
+    int start = 0, end = viewport.alignment.getWidth()-1;
 
-    if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().getSequences(false) != null
-        && viewport.getSelectionGroup().getSize(false)>0)
+    SequenceI[] seqs;
+    if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequences(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes()+1;
+      end = viewport.getSelectionGroup().getEndRes();
     }
     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);
-      //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());
-       }
-       }
-      }
-      }*/
+      seqs = viewport.alignment.getSequencesArray();
 
-    viewport.setStartRes(seq.findIndex(startRes)-1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-  }
-
-  public void alignmentChanged()
-  {
-    viewport.alignment.padGaps();
-    if(viewport.autocalculateConsensus)
-    {
-      viewport.updateConsensus();
-      viewport.updateConservation();
-    }
-
-    resetAllColourSchemes();
-    if(alignPanel.overviewPanel!=null)
-      alignPanel.overviewPanel.updateOverviewImage();
-
-    viewport.alignment.adjustSequenceAnnotations();
-    alignPanel.repaint();
-  }
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
 
-  void resetAllColourSchemes()
-  {
-    ColourSchemeI cs = viewport.globalColourScheme;
-    if(cs!=null)
-    {
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
-            resetClustalX(viewport.alignment.getSequences(),
-                          viewport.alignment.getWidth());
-      }
+    addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+                                           seqs,
+                                           start, end,
+                     viewport.getGapCharacter()));
 
-      cs.setConsensus(viewport.vconsensus);
-      if (cs.conservationApplied())
-      {
-        Alignment al = (Alignment) viewport.alignment;
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          al.getSequences(), 0,
-                                          al.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, viewport.ConsPercGaps);
+    viewport.setStartRes(seq.findIndex(startRes)-1);
 
-        cs.setConservation(c);
-      }
-    }
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
-    int s, sSize = viewport.alignment.getGroups().size();
-    for(s=0; s<sSize; s++)
-    {
-      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
-      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(
-            sg.getSequences(true), sg.getWidth());
-      }
-      sg.recalcConservation();
-    }
   }
 
-
-
   public void findMenuItem_actionPerformed()
   {
     new Finder(alignPanel);
@@ -1460,7 +1504,7 @@ public void itemStateChanged(ItemEvent evt)
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
 
     }
     viewport.setGlobalColourScheme(cs);
@@ -1595,25 +1639,25 @@ public void itemStateChanged(ItemEvent evt)
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
-    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
-                                   HistoryItem.SORT));
+    SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
     alignPanel.repaint();
   }
 
   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();
 
@@ -1759,8 +1803,8 @@ 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();
       }
@@ -1922,8 +1966,7 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
     MenuItem findMenuItem = new MenuItem();
-    Menu searchMenu = new Menu();
-    protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
     protected MenuItem nucleotideColour = new MenuItem();
     MenuItem deleteGroups = new MenuItem();
     MenuItem delete = new MenuItem();
@@ -1951,8 +1994,9 @@ public void itemStateChanged(ItemEvent evt)
     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
   Panel embeddedMenu;
   Label embeddedEdit;
-  Label embeddedSearch;
+  Label embeddedSelect;
   Label embeddedView;
+  Label embeddedFormat;
   Label embeddedColour;
   Label embeddedFile;
   Label embeddedHelp;
@@ -2075,9 +2119,7 @@ public void itemStateChanged(ItemEvent evt)
         renderGapsMenuItem.addItemListener(this);
         findMenuItem.setLabel("Find...");
         findMenuItem.addActionListener(this);
-        searchMenu.setLabel("Search");
-
-        abovePIDThreshold.setLabel("Above Identity Threshold");
+    abovePIDThreshold.setLabel("Above Identity Threshold");
         abovePIDThreshold.addItemListener(this);
         nucleotideColour.setLabel("Nucleotide");
         nucleotideColour.addActionListener(this);
@@ -2151,13 +2193,14 @@ public void itemStateChanged(ItemEvent evt)
     showSeqs.addActionListener(this);
     hideColumns.addActionListener(this);
     hideSequences.addActionListener(this);
-
-
+    formatMenu.setLabel("Format");
+    selectMenu.setLabel("Select");
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
-        alignFrameMenuBar.add(searchMenu);
-        alignFrameMenuBar.add(viewMenu);
-        alignFrameMenuBar.add(colourMenu);
+    alignFrameMenuBar.add(selectMenu);
+    alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(formatMenu);
+    alignFrameMenuBar.add(colourMenu);
         alignFrameMenuBar.add(calculateMenu);
         alignFrameMenuBar.add(helpMenu);
         fileMenu.add(inputText);
@@ -2173,35 +2216,16 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(copy);
         editMenu.add(pasteMenu);
         editMenu.add(delete);
-        editMenu.addSeparator();
-        editMenu.add(selectAllSequenceMenuItem);
-        editMenu.add(deselectAllSequenceMenuItem);
-        editMenu.add(invertSequenceMenuItem);
-    editMenu.add(invertColSel);
-    editMenu.add(deleteGroups);
-        editMenu.addSeparator();
+    editMenu.addSeparator();
         editMenu.add(remove2LeftMenuItem);
         editMenu.add(remove2RightMenuItem);
         editMenu.add(removeGappedColumnMenuItem);
         editMenu.add(removeAllGapsMenuItem);
         editMenu.add(removeRedundancyMenuItem);
-        searchMenu.add(findMenuItem);
-        viewMenu.add(font);
-        viewMenu.addSeparator();
     viewMenu.add(menu1);
     viewMenu.add(menu2);
     viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-        viewMenu.add(scaleAbove);
-        viewMenu.add(scaleLeft);
-        viewMenu.add(scaleRight);
-        viewMenu.addSeparator();
-    viewMenu.add(seqLimits);
-    viewMenu.add(viewBoxesMenuItem);
-        viewMenu.add(viewTextMenuItem);
-        viewMenu.add(colourTextMenuItem);
-        viewMenu.add(renderGapsMenuItem);
-        viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
         viewMenu.add(sequenceFeatures);
         viewMenu.add(featureSettings);
@@ -2251,40 +2275,53 @@ public void itemStateChanged(ItemEvent evt)
     menu1.add(showSeqs);
     menu2.add(hideColumns);
     menu2.add(hideSequences);
+    formatMenu.add(font);
+    formatMenu.add(seqLimits);
+    formatMenu.add(wrapMenuItem);
+    formatMenu.add(scaleAbove);
+    formatMenu.add(scaleLeft);
+    formatMenu.add(scaleRight);
+    formatMenu.add(viewBoxesMenuItem);
+    formatMenu.add(viewTextMenuItem);
+    formatMenu.add(colourTextMenuItem);
+    formatMenu.add(renderGapsMenuItem);
+    selectMenu.add(findMenuItem);
+    selectMenu.addSeparator();
+    selectMenu.add(selectAllSequenceMenuItem);
+    selectMenu.add(deselectAllSequenceMenuItem);
+    selectMenu.add(invertSequenceMenuItem);
+    selectMenu.add(invertColSel);
+    selectMenu.add(deleteGroups);
   }
 
   public void setEmbedded()
   {
 
     embeddedMenu = new Panel();
-    embeddedEdit = new Label();
-    embeddedSearch = new Label();
-    embeddedView = new Label();
-    embeddedColour = new Label();
-    embeddedFile = new Label();
-    embeddedHelp = new Label();
-    embeddedCalculate = new Label();
+    embeddedEdit = new Label("Edit");
+    embeddedSelect = new Label("Select");
+    embeddedView = new Label("View");
+    embeddedFormat = new Label("Format");
+    embeddedColour = new Label("Colour");
+    embeddedFile = new Label("File");
+    embeddedHelp = new Label("Help");
+    embeddedCalculate = new Label("Calculate");
     flowLayout1 = new FlowLayout();
     embeddedMenu.setBackground(Color.lightGray);
     embeddedMenu.setLayout(flowLayout1);
-    embeddedEdit.setText("Edit");
     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedSearch.setText("Search");
-    embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedView.setText("View");
+    embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedColour.setText("Colour");
+    embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedFile.setText("File");
     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedHelp.setText("Help");
     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
-    embeddedCalculate.setText("Calculate");
     embeddedMenu.add(embeddedFile);
     embeddedMenu.add(embeddedEdit);
-    embeddedMenu.add(embeddedSearch);
+    embeddedMenu.add(embeddedSelect);
     embeddedMenu.add(embeddedView);
+    embeddedMenu.add(embeddedFormat);
     embeddedMenu.add(embeddedColour);
     embeddedMenu.add(embeddedCalculate);
     embeddedMenu.add(embeddedHelp);
@@ -2293,8 +2330,9 @@ public void itemStateChanged(ItemEvent evt)
     flowLayout1.setVgap(0);
     embeddedFile.addMouseListener(this);
     embeddedEdit.addMouseListener(this);
-    embeddedSearch.addMouseListener(this);
+    embeddedSelect.addMouseListener(this);
     embeddedView.addMouseListener(this);
+    embeddedFormat.addMouseListener(this);
     embeddedColour.addMouseListener(this);
     embeddedCalculate.addMouseListener(this);
     embeddedHelp.addMouseListener(this);
@@ -2319,7 +2357,7 @@ public void itemStateChanged(ItemEvent evt)
 
 
   PopupMenu filePopup, editPopup, searchPopup,
-      viewPopup, colourPopup, calculatePopup, helpPopup;
+      viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
   MenuItem annotationColour = new MenuItem();
@@ -2330,6 +2368,8 @@ public void itemStateChanged(ItemEvent evt)
   Menu menu2 = new Menu();
   MenuItem hideColumns = new MenuItem();
   MenuItem hideSequences = new MenuItem();
+  Menu formatMenu = new Menu();
+  Menu selectMenu = new Menu();
 
   public void mousePressed(MouseEvent evt)
   {
@@ -2343,14 +2383,18 @@ public void itemStateChanged(ItemEvent evt)
     {
       popup = editPopup = genPopupMenu(editPopup, editMenu);
     }
-    else if(source==embeddedSearch)
+    else if(source==embeddedSelect)
     {
-      popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
+      popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
     }
     else if(source==embeddedView)
     {
       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
     }
+    else if (source ==embeddedFormat)
+    {
+      popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
+    }
     else if(source==embeddedColour)
     {
       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);