X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=0bdcb55f4915cfd2f897950f624ea662c3df35f3;hb=08620e4438a99912019631c0b1c9deb341b76ae0;hp=44b163b4f67f90c8a52ec73e2404a2d4c942cf49;hpb=2202e4f29a90e65c507a8d941ce14e42af49b658;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 44b163b..0bdcb55 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,13 +1,21 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
-
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
@@ -20,11 +28,11 @@ import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
 
-
-public class AlignFrame extends GAlignFrame
+public class AlignFrame
+    extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
-  final AlignViewport  viewport;
+  final AlignViewport viewport;
   public static final int NEW_WINDOW_WIDTH = 700;
   public static final int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
@@ -53,14 +61,15 @@ public class AlignFrame extends GAlignFrame
       try
       {
         treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile( applet.getCodeBase()+treeFile, "URL");
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+            getCodeBase() + treeFile, "URL");
         fin.parse();
 
         if (fin.getTree() != null)
         {
           TreePanel tp = null;
           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase()+treeFile);
+                             fin, "FromFile", applet.getCodeBase() + treeFile);
           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
           addTreeMenuItem(tp, treeFile);
         }
@@ -76,20 +85,23 @@ public class AlignFrame extends GAlignFrame
 
   public void inputText_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500,500);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
   }
 
-
   protected void outputText_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(frame,"Alignment output - "+e.getActionCommand(),600, 500);
-     cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame,
+                                     "Alignment output - " + e.getActionCommand(),
+                                     600, 500);
+    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+                                              viewport.getAlignment().
+                                              getSequences()));
   }
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
@@ -102,24 +114,24 @@ public class AlignFrame extends GAlignFrame
 
   void updateEditMenuBar()
   {
-    if(historyList.size()>0)
-     {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.elementAt(0);
-       undoMenuItem.setLabel("Undo "+history[0]);
-     }
+    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);
-       Object [] history = (Object[])redoList.elementAt(0);
-       redoMenuItem.setLabel("Redo "+history[0]);
-     }
+    if (redoList.size() > 0)
+    {
+      redoMenuItem.setEnabled(true);
+      HistoryItem hi = (HistoryItem) redoList.peek();
+      redoMenuItem.setLabel("Redo " + hi.getDescription());
+    }
     else
     {
       redoMenuItem.setEnabled(false);
@@ -127,55 +139,83 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
-  public void addHistoryItem(String type)
+  public void addHistoryItem(HistoryItem hi)
   {
-    // 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());
-    }
-
-    historyList.addElement(new Object[]{type,  seq} );
+    historyList.push(hi);
     updateEditMenuBar();
   }
 
   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());
-    }
-    /////////
+    HistoryItem hi = (HistoryItem) historyList.pop();
+    redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
+                                  HistoryItem.HIDE));
+    restoreHistoryItem(hi);
+  }
 
-    redoList.addElement(new Object[] {history[0], seq});
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+    HistoryItem hi = (HistoryItem) redoList.pop();
+    restoreHistoryItem(hi);
+    updateEditMenuBar();
+    viewport.updateConsensus();
+    alignPanel.repaint();
+    alignPanel.repaint();
+  }
 
-      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)
+        {
+          // log.System.out.println(hi.getHidden().elementAt(i));
+          restore.setSequence(hi.getHidden().elementAt(i).toString());
+          viewport.alignment.getSequences().insertElementAt(
+              restore,
+              hi.getAlignIndex(i));
+        }
+        else
+        {
+          restore.setSequence(hi.getHidden().elementAt(i).toString());
+        }
+      }
+      if (hi.getType() == HistoryItem.PASTE)
+      {
+        for (int i = viewport.alignment.getHeight() - 1;
+             i > hi.getSequences().size() - 1; i--)
+        {
+          viewport.alignment.deleteSequence(i);
+        }
+      }
+    }
 
-      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.updateConservation();
-      viewport.updateConsensus();
-      alignPanel.repaint();
+    viewport.updateConsensus();
+    viewport.updateConservation();
+    alignPanel.repaint();
   }
 
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
     if (sg == null)
+    {
       return;
+    }
 
     if (up)
     {
@@ -183,11 +223,15 @@ public class AlignFrame extends GAlignFrame
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
         if (!sg.sequences.contains(seq))
+        {
           continue;
+        }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
         if (sg.sequences.contains(temp))
+        {
           continue;
+        }
 
         viewport.alignment.getSequences().setElementAt(temp, i);
         viewport.alignment.getSequences().setElementAt(seq, i - 1);
@@ -199,11 +243,15 @@ public class AlignFrame extends GAlignFrame
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
         if (!sg.sequences.contains(seq))
+        {
           continue;
+        }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
         if (sg.sequences.contains(temp))
+        {
           continue;
+        }
 
         viewport.alignment.getSequences().setElementAt(temp, i);
         viewport.alignment.getSequences().setElementAt(seq, i + 1);
@@ -213,26 +261,76 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-
   StringBuffer copiedSequences;
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getSelectionGroup()==null)
-     return;
+    if (viewport.getSelectionGroup() == null)
+    {
+      return;
+    }
 
-   SequenceGroup sg = viewport.getSelectionGroup();
-   copiedSequences = new StringBuffer();
+    SequenceGroup sg = viewport.getSelectionGroup();
+    copiedSequences = new StringBuffer();
+    Hashtable orderedSeqs = new Hashtable();
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+      SequenceI seq = sg.getSequenceAt(i);
+      int index = viewport.alignment.findIndex(seq);
+      orderedSeqs.put(index + "", seq);
+    }
 
-       for(int i=0; i<sg.getSize(); i++)
-       {
-         SequenceI seq = sg.getSequenceAt(i);
-         copiedSequences.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
-                        +seq.findPosition( sg.getEndRes() )+ "\t"
-                        +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
-       }
+    int index = 0, startRes, endRes;
+    char ch;
 
-  }
+    for (int i = 0; i < sg.getSize(); i++)
+    {
+        SequenceI seq = null;
+
+        while (seq == null)
+        {
+            if (orderedSeqs.containsKey(index + ""))
+            {
+                seq = (SequenceI) orderedSeqs.get(index + "");
+                index++;
+
+                break;
+            }
+            else
+            {
+                index++;
+            }
+        }
+
+        //FIND START RES
+        //Returns residue following index if gap
+        startRes = seq.findPosition(sg.getStartRes());
+
+        //FIND END RES
+        //Need to find the residue preceeding index if gap
+        endRes = 0;
+
+        for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
+        {
+          ch = seq.getCharAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
 
+        if(endRes>0)
+        {
+          endRes += seq.getStart() -1;
+        }
+
+        copiedSequences.append(seq.getName() + "\t" +
+            startRes + "\t" +
+            endRes + "\t" +
+            seq.getSequence(sg.getStartRes(),
+                sg.getEndRes() + 1) + "\n");
+    }
+
+  }
 
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
@@ -241,15 +339,19 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+                                   HistoryItem.PASTE));
     paste(false);
   }
 
   void paste(boolean newAlignment)
   {
-    try{
+    try
+    {
       if (copiedSequences == null)
+      {
         return;
+      }
 
       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
       Vector seqs = new Vector();
@@ -258,27 +360,38 @@ public class AlignFrame extends GAlignFrame
         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);
+        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
 
-        if(!newAlignment)
+        if (!newAlignment)
+        {
           viewport.alignment.addSequence(sequence);
+        }
         else
+        {
           seqs.addElement(sequence);
+        }
       }
 
-      if(newAlignment)
+      if (newAlignment)
       {
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        for(int i=0; i<seqs.size(); i++)
-         newSeqs[i] = (SequenceI)seqs.elementAt(i);
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          newSeqs[i] = (SequenceI) seqs.elementAt(i);
+        }
 
         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);
         String newtitle = new String("Copied sequences");
-        if( getTitle().startsWith("Copied sequences"))
-         newtitle = getTitle();
-       else
-         newtitle = newtitle.concat("- from "+getTitle());
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+        if (getTitle().startsWith("Copied sequences"))
+        {
+          newtitle = getTitle();
+        }
+        else
+        {
+          newtitle = newtitle.concat("- from " + getTitle());
+        }
+        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                                         NEW_WINDOW_HEIGHT);
       }
       else
       {
@@ -289,11 +402,12 @@ public class AlignFrame extends GAlignFrame
         alignPanel.repaint();
       }
 
-    }catch(Exception ex){}// could be anything being pasted in here
+    }
+    catch (Exception ex)
+    {} // could be anything being pasted in here
 
   }
 
-
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
@@ -302,56 +416,61 @@ 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;
+    }
 
-     SequenceGroup sg = viewport.getSelectionGroup();
-     for (int i=0;i < sg.sequences.size(); i++)
-     {
-       SequenceI seq = sg.getSequenceAt(i);
-       int index = viewport.getAlignment().findIndex(seq);
-       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
-
-       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);
-     if(viewport.getAlignment().getHeight()<1)
-     try
-     {
-       this.setVisible(false);
-     }catch(Exception ex){}
-   viewport.updateConservation();
-   viewport.updateConsensus();
-     alignPanel.repaint();
+    SequenceGroup sg = viewport.getSelectionGroup();
+    boolean allSequences = false;
+    if(sg.sequences.size()==viewport.alignment.getHeight())
+          allSequences = true;
 
-  }
+    for (int i = 0; i < sg.sequences.size(); i++)
+    {
+      SequenceI seq = sg.getSequenceAt(i);
+      int index = viewport.getAlignment().findIndex(seq);
+      seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
+      // If the cut affects all sequences, remove highlighted columns
+      if (allSequences)
+      {
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),
+                                                     sg.getEndRes() + 1);
+      }
 
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-     Object [] history = (Object[])redoList.pop();
-     SequenceI[] seq = (SequenceI[]) history[1];
+      if (seq.getSequence().length() < 1)
+      {
+        viewport.getAlignment().deleteSequence(seq);
+      }
+      else
+      {
+        viewport.getAlignment().getSequences().setElementAt(seq, index);
+      }
+    }
 
-     AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
-     viewport.setAlignment(new Alignment(seq));
-     for (int i = 0; i < old.length; i++)
-       viewport.alignment.addAnnotation(old[i]);
+    viewport.setSelectionGroup(null);
+    viewport.alignment.deleteGroup(sg);
+    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
+    if (viewport.getAlignment().getHeight() < 1)
+    {
+      try
+      {
+        this.setVisible(false);
+      }
+      catch (Exception ex)
+      {}
+    }
+    viewport.updateConservation();
+    viewport.updateConsensus();
+    alignPanel.repaint();
 
-     viewport.updateConservation();
-     viewport.updateConsensus();
-     updateEditMenuBar();
-     alignPanel.repaint();
   }
 
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -360,13 +479,13 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-
-
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+    {
+      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+    }
     sg.setEndRes(viewport.alignment.getWidth());
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
@@ -384,31 +503,38 @@ public class AlignFrame extends GAlignFrame
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
-    for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+    {
+      sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+    }
 
     PaintRefresher.Refresh(null);
   }
 
   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);
+      colSel.compensateForEdit(0, min);
 
-      if(viewport.getSelectionGroup()!=null)
+      if (viewport.getSelectionGroup() != null)
+      {
         viewport.getSelectionGroup().adjustForRemoveLeft(min);
+      }
 
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if(!sg.adjustForRemoveLeft(min))
+        if (!sg.adjustForRemoveLeft(min))
+        {
           viewport.alignment.deleteGroup(sg);
+        }
       }
 
       alignPanel.repaint();
@@ -417,25 +543,28 @@ 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)
+      if (viewport.getSelectionGroup() != null)
+      {
         viewport.getSelectionGroup().adjustForRemoveRight(max);
+      }
 
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if(!sg.adjustForRemoveRight(max))
+        if (!sg.adjustForRemoveRight(max))
+        {
           viewport.alignment.deleteGroup(sg);
+        }
       }
 
-
-
       alignPanel.repaint();
     }
 
@@ -443,7 +572,9 @@ 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();
@@ -452,21 +583,46 @@ 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++)
+
+    Vector seqs=null;
+
+    int start=0, end = viewport.alignment.getWidth();
+
+    if (viewport.getSelectionGroup() != null
+        && viewport.getSelectionGroup().sequences != null
+        && viewport.getSelectionGroup().sequences.size()>0)
     {
-      current = viewport.getAlignment().getSequenceAt(i);
+      seqs = viewport.getSelectionGroup().sequences;
+      start = viewport.getSelectionGroup().getStartRes();
+      end = viewport.getSelectionGroup().getEndRes();
+    }
+    else
+      seqs = viewport.alignment.getSequences();
+
+    for (int i = 0; i <seqs.size(); i++)
+    {
+      current = (SequenceI)seqs.elementAt(i);
       jSize = current.getLength();
-      for (int j=0; j < jSize; j++)
-        if(jalview.util.Comparison.isGap(current.getCharAt(j)))
+
+      int j = start;
+      do
+      {
+        if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
           current.deleteCharAt(j);
           j--;
           jSize--;
         }
+        j++;
+      }
+      while(j < end && j < jSize) ;
     }
+
     viewport.updateConservation();
     viewport.updateConsensus();
     alignPanel.repaint();
@@ -478,36 +634,35 @@ public class AlignFrame extends GAlignFrame
     Finder finder = new Finder(alignPanel);
   }
 
-
   public void font_actionPerformed(ActionEvent e)
   {
     Frame frame = new Frame();
-    FontChooser fc = new FontChooser( alignPanel, frame);
+    FontChooser fc = new FontChooser(alignPanel, frame);
     frame.add(fc);
-    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440,100);
+    jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);
 
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
   {
-    viewport.setShowFullId( fullSeqId.getState() );
-    alignPanel.idPanel.idCanvas.setSize( alignPanel.calculateIdWidth() );
+    viewport.setShowFullId(fullSeqId.getState());
+    alignPanel.fontChanged();
     alignPanel.repaint();
   }
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-      viewport.setColourText( colourTextMenuItem.getState() );
-      alignPanel.repaint();
+    viewport.setColourText(colourTextMenuItem.getState());
+    alignPanel.repaint();
   }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment( wrapMenuItem.getState() );
-    alignPanel.setWrapAlignment( wrapMenuItem.getState() );
-    scaleAbove.setEnabled( wrapMenuItem.getState() );
-    scaleLeft.setEnabled( wrapMenuItem.getState());
-    scaleRight.setEnabled( wrapMenuItem.getState());
+    viewport.setWrapAlignment(wrapMenuItem.getState());
+    alignPanel.setWrapAlignment(wrapMenuItem.getState());
+    scaleAbove.setEnabled(wrapMenuItem.getState());
+    scaleLeft.setEnabled(wrapMenuItem.getState());
+    scaleRight.setEnabled(wrapMenuItem.getState());
     alignPanel.repaint();
   }
 
@@ -529,74 +684,73 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-
-
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowBoxes( viewBoxesMenuItem.getState() );
+    viewport.setShowBoxes(viewBoxesMenuItem.getState());
     alignPanel.repaint();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowText( viewTextMenuItem.getState() );
+    viewport.setShowText(viewTextMenuItem.getState());
     alignPanel.repaint();
   }
 
-
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.getState());
     alignPanel.repaint();
   }
 
-
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    if(annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
+    if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())
     {
       annotationPanelMenuItem.setState(false);
       return;
     }
-    viewport.setShowAnnotation( annotationPanelMenuItem.getState() );
-    alignPanel.setAnnotationVisible( annotationPanelMenuItem.getState() );
+    viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+    alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
-   if (alignPanel.overviewPanel != null)
+    if (alignPanel.overviewPanel != null)
+    {
       return;
+    }
 
     Frame frame = new Frame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.add(overview);
     // +50 must allow for applet frame window
     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
-                             overview.preferredSize().width, overview.preferredSize().height+50);
+                                     overview.preferredSize().width,
+                                     overview.preferredSize().height + 50);
 
     frame.pack();
     frame.addWindowListener(new WindowAdapter()
-    { public void windowClosing(WindowEvent e)
+    {
+      public void windowClosing(WindowEvent e)
       {
-            alignPanel.setOverviewPanel(null);
+        alignPanel.setOverviewPanel(null);
       };
     });
 
-    alignPanel.setOverviewPanel( overview );
-
+    alignPanel.setOverviewPanel(overview);
 
   }
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    changeColour( null );
+    changeColour(null);
   }
 
-
   public void clustalColour_actionPerformed(ActionEvent e)
   {
     abovePIDThreshold.setState(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
+                                          viewport.alignment.getWidth()));
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
@@ -609,33 +763,29 @@ public class AlignFrame extends GAlignFrame
     changeColour(new TaylorColourScheme());
   }
 
-
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new HydrophobicColourScheme() );
+    changeColour(new HydrophobicColourScheme());
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new HelixColourScheme() );
+    changeColour(new HelixColourScheme());
   }
 
-
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
   }
 
-
   public void turnColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TurnColourScheme());
   }
 
-
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new BuriedColourScheme() );
+    changeColour(new BuriedColourScheme());
   }
 
   public void nucleotideColour_actionPerformed(ActionEvent e)
@@ -643,35 +793,30 @@ public class AlignFrame extends GAlignFrame
     changeColour(new NucleotideColourScheme());
   }
 
-
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
   }
 
-
-
   void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
-    if ( viewport.getAbovePIDThreshold() )
+    if (viewport.getAbovePIDThreshold())
     {
       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
       if (cs instanceof ResidueColourScheme)
+      {
         ( (ResidueColourScheme) cs).setThreshold(threshold);
-      else if (cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) cs).setThreshold(threshold);
+      }
 
       viewport.setGlobalColourScheme(cs);
     }
     else if (cs instanceof ResidueColourScheme)
+    {
       ( (ResidueColourScheme) cs).setThreshold(0);
-    else if (cs instanceof ScoreColourScheme)
-      ( (ScoreColourScheme) cs).setThreshold(0);
-
-
+    }
 
     if (viewport.getConservationSelected())
     {
@@ -689,7 +834,7 @@ public class AlignFrame extends GAlignFrame
       ccs = new ConservationColourScheme(c, cs);
 
       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus( viewport.vconsensus );
+      ccs.setConsensus(viewport.vconsensus);
       viewport.setGlobalColourScheme(ccs);
 
       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
@@ -697,25 +842,34 @@ public class AlignFrame extends GAlignFrame
     }
     else
     {
-        // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-        if (cs != null)
-          cs.setConsensus(viewport.vconsensus);
-        viewport.setGlobalColourScheme(cs);
+      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
+      if (cs != null)
+      {
+        cs.setConsensus(viewport.vconsensus);
+      }
+      viewport.setGlobalColourScheme(cs);
     }
 
-
-    if(viewport.getColourAppliesToAllGroups())
+    if (viewport.getColourAppliesToAllGroups())
     {
       Vector groups = viewport.alignment.getGroups();
-      for(int i=0; i<groups.size(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
-        SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
+        if(cs==null)
+        {
+          sg.cs = null;
+          continue;
+        }
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
+          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
+          sg.cs = cxs;
         }
         else
+        {
           try
           {
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
@@ -725,28 +879,30 @@ public class AlignFrame extends GAlignFrame
             ex.printStackTrace();
             sg.cs = cs;
           }
+        }
 
-        if(viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold())
         {
           if (sg.cs instanceof ResidueColourScheme)
+          {
             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
-          else if (sg.cs instanceof ScoreColourScheme)
-            ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+          }
 
-           sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );
+          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
 
-        if( viewport.getConservationSelected() )
+        if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.sequences, 0, viewport.alignment.getWidth()-1);
+                                            sg.sequences, 0,
+                                            viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
           sg.cs = ccs;
         }
         else
@@ -758,25 +914,27 @@ public class AlignFrame extends GAlignFrame
       }
     }
 
-    if(alignPanel.getOverviewPanel()!=null)
+    if (alignPanel.getOverviewPanel() != null)
+    {
       alignPanel.getOverviewPanel().updateOverviewImage();
+    }
 
     alignPanel.repaint();
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-      if(viewport.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
-                                   "Background");
-        SliderPanel.showPIDSlider();
-      }
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
+                                     "Background");
+      SliderPanel.showPIDSlider();
+    }
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if(viewport.getConservationSelected())
+    if (viewport.getConservationSelected())
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
@@ -784,19 +942,22 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
-
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.getState());
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setState(false);
 
-   ColourSchemeI cs = viewport.getGlobalColourScheme();
-   if(cs instanceof ConservationColourScheme )
-     changeColour( ((ConservationColourScheme)cs).cs );
+    ColourSchemeI cs = viewport.getGlobalColourScheme();
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
     else
-      changeColour( cs );
+    {
+      changeColour(cs);
+    }
 
     modifyConservation_actionPerformed(null);
   }
@@ -810,54 +971,57 @@ public class AlignFrame extends GAlignFrame
 
     ColourSchemeI cs = viewport.getGlobalColourScheme();
 
-    if(cs instanceof ConservationColourScheme )
-        changeColour( ((ConservationColourScheme)cs).cs );
+    if (cs instanceof ConservationColourScheme)
+    {
+      changeColour( ( (ConservationColourScheme) cs).cs);
+    }
     else
-        changeColour( cs );
+    {
+      changeColour(cs);
+    }
 
     modifyPID_actionPerformed(null);
   }
 
-
-
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+    UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    changeColour( new PIDColourScheme() );
+    changeColour(new PIDColourScheme());
   }
 
-
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    changeColour(new Blosum62ColourScheme() );
+    changeColour(new Blosum62ColourScheme());
   }
 
-
-
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
-    AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
+    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");
-    AlignmentSorter.sortByID( viewport.getAlignment() );
+    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();
+
   }
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
@@ -865,13 +1029,14 @@ public class AlignFrame extends GAlignFrame
     RedundancyPanel sp = new RedundancyPanel(alignPanel);
     Frame frame = new Frame();
     frame.add(sp);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", 400, 120);
+    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
+                                     400, 120);
 
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelectionGroup().getSize()>1)
+    if (viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(viewport));
@@ -882,21 +1047,25 @@ public class AlignFrame extends GAlignFrame
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
 
-    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
-       || viewport.getAlignment().getHeight()<4)
+    if ( (viewport.getSelectionGroup() != null &&
+          viewport.getSelectionGroup().getSize() < 4 &&
+          viewport.getSelectionGroup().getSize() > 0)
+        || viewport.getAlignment().getHeight() < 4)
     {
       return;
     }
 
-    try{
+    try
+    {
       PCAPanel pcaPanel = new PCAPanel(viewport, null);
       Frame frame = new Frame();
       frame.add(pcaPanel);
-      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", 400, 400);
-   }catch(java.lang.OutOfMemoryError ex)
-   {
-   }
-
+      jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",
+                                       400, 400);
+    }
+    catch (java.lang.OutOfMemoryError ex)
+    {
+    }
 
   }
 
@@ -910,7 +1079,6 @@ public class AlignFrame extends GAlignFrame
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
   }
 
-
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -924,9 +1092,23 @@ public class AlignFrame extends GAlignFrame
   void NewTreePanel(String type, String pwType, String title)
   {
     //are the sequences aligned?
-    if(!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned())
     {
-      return;
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth();
+
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();
+           i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());
+        }
+      }
+      alignPanel.repaint();
+
     }
 
     final TreePanel tp;
@@ -943,9 +1125,9 @@ public class AlignFrame extends GAlignFrame
                          type, pwType, 0, viewport.alignment.getWidth());
     }
 
-   addTreeMenuItem(tp, title);
+    addTreeMenuItem(tp, title);
 
-   jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+    jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
   }
 
   void addTreeMenuItem(final TreePanel treePanel, String title)
@@ -956,7 +1138,8 @@ 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();
       }
@@ -971,40 +1154,45 @@ public class AlignFrame extends GAlignFrame
     });
   }
 
-  protected void documentation_actionPerformed(ActionEvent e) {
-
-    jalview.bin.JalviewLite.showURL("http://www.jalview.org");
-
+  protected void documentation_actionPerformed(ActionEvent e)
+  {
+    jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");
   }
 
   protected void about_actionPerformed(ActionEvent e)
   {
-    class AboutPanel extends Canvas
+    class AboutPanel
+        extends Canvas
     {
       public void paint(Graphics g)
       {
         g.setColor(Color.white);
-        g.fillRect(0,0,getSize().width, getSize().height);
+        g.fillRect(0, 0, getSize().width, getSize().height);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
         FontMetrics fm = g.getFontMetrics();
         int fh = fm.getHeight();
-        int y=20, x=7;
+        int y = 5, x = 7;
         g.setColor(Color.black);
         g.setFont(new Font("Helvetica", Font.BOLD, 14));
-        g.drawString("JalView - Release 2.0", 200,y+=fh);
+        g.drawString("JalView - Release 2.02", 200, y += fh);
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
-        g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",x,y+=fh*2);
-        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",x,y+=fh);
-        g.drawString("If  you use JalView, please cite:",x,y+=fh+8);
-        g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",x,y+=fh);
-        g.drawString("Bioinformatics,  2004 12;426-7.",x,y+=fh);
+        g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
+                     x, y += fh * 2);
+        g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
+                     x, y += fh);
+        g.drawString(
+            "For any issues relating to Jalview, email help@jalview.org", x,
+            y += fh);
+        g.drawString("If  you use JalView, please cite:", x, y += fh + 8);
+        g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
+                     x, y += fh);
+        g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);
       }
     }
+
     Frame frame = new Frame();
     frame.add(new AboutPanel());
-    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580,200);
-
-
+    jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
 
   }
 }