X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c60355c6554497a5e37407297d1167d75f078c1a;hb=d3fb461d66f67625686387cb75f6e9589510a577;hp=be428fee3e4df3bd86e0c2910977986924de7d43;hpb=2e22e46f5f79840fd368858faa191e1be5f6095c;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index be428fe..c60355c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -24,20 +24,18 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
+import java.awt.dnd.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
 
 import jalview.analysis.*;
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.commands.*;
 import jalview.ws.*;
-import java.awt.dnd.*;
-import javax.swing.event.ChangeListener;
-import javax.swing.event.ChangeEvent;
 
 /**
  * DOCUMENT ME!
@@ -45,7 +43,8 @@ import javax.swing.event.ChangeEvent;
  * @author $author$
  * @version $Revision$
  */
-public class AlignFrame extends GAlignFrame implements DropTargetListener
+public class AlignFrame
+    extends GAlignFrame implements DropTargetListener
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
@@ -113,8 +112,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   void init()
   {
-    this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
-
     if (viewport.conservation == null)
     {
       BLOSUM62Colour.setEnabled(false);
@@ -128,12 +125,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
     if (sortby.equals("Id"))
+    {
       sortIDMenuItem_actionPerformed(null);
+    }
     else if (sortby.equals("Pairwise Identity"))
+    {
       sortPairwiseMenuItem_actionPerformed(null);
+    }
 
     if (Desktop.desktop != null)
    {
+     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
      addServiceListeners();
      setGUINucleotide(viewport.alignment.isNucleotide());
    }
@@ -145,6 +147,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
      wrapMenuItem_actionPerformed(null);
    }
 
+    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
+    {
+      this.overviewMenuItem_actionPerformed(null);
+    }
+
    addKeyListener();
 
   }
@@ -153,8 +160,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
      fileName = file;
      currentFileFormat = format;
-     if (!fileName.startsWith("http"))
-       reload.setEnabled(true);
+     reload.setEnabled(true);
   }
 
   void addKeyListener()
@@ -163,12 +169,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         public void keyPressed(KeyEvent evt)
         {
-          if (viewport.cursorMode
-              && evt.getKeyCode() >= KeyEvent.VK_0
-              && evt.getKeyCode() <= KeyEvent.VK_9)
-          {
+          if (viewport.cursorMode &&
+              ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
+                 evt.getKeyCode() <= KeyEvent.VK_9)
+               ||
+               (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
+                evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
+              )
+              && Character.isDigit(evt.getKeyChar()))
             alignPanel.seqPanel.numberPressed(evt.getKeyChar());
-          }
 
           switch (evt.getKeyCode())
           {
@@ -179,35 +188,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               break;
 
             case KeyEvent.VK_DOWN:
+             if (evt.isAltDown() || !viewport.cursorMode)
+              moveSelectedSequences(false);
               if (viewport.cursorMode)
-              {
                 alignPanel.seqPanel.moveCursor(0, 1);
-              }
-              else
-                moveSelectedSequences(false);
               break;
 
             case KeyEvent.VK_UP:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              moveSelectedSequences(true);
               if (viewport.cursorMode)
-              {
                 alignPanel.seqPanel.moveCursor(0, -1);
-              }
-              else
-                moveSelectedSequences(true);
+
               break;
 
             case KeyEvent.VK_LEFT:
-              if (viewport.cursorMode)
-              {
+            if (evt.isAltDown() || !viewport.cursorMode)
+              slideSequences(false,
+                             alignPanel.seqPanel.getKeyboardNo1());
+            else
                 alignPanel.seqPanel.moveCursor( -1, 0);
-              }
+
+
               break;
 
             case KeyEvent.VK_RIGHT:
-              if (viewport.cursorMode)
-              {
+            if (evt.isAltDown() || !viewport.cursorMode)
+              slideSequences(true,
+                             alignPanel.seqPanel.getKeyboardNo1());
+            else
                 alignPanel.seqPanel.moveCursor(1, 0);
-              }
               break;
 
             case KeyEvent.VK_SPACE:
@@ -226,9 +236,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 cut_actionPerformed(null);
               }
               else
+            {
                 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
                                            || evt.isShiftDown()
                                            || evt.isAltDown());
+            }
 
               break;
 
@@ -311,14 +323,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               SequenceGroup sg = viewport.getSelectionGroup();
               if (toggleSeqs)
               {
-                if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+                if (sg != null && sg.getSize() != viewport.alignment.getHeight())
                 {
                   hideSelSequences_actionPerformed(null);
                   hide = true;
                 }
-                else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+              else if (! (toggleCols &&
+                          viewport.colSel.getSelected().size() > 0))
+              {
                   showAllSeqs_actionPerformed(null);
               }
+            }
 
               if (toggleCols)
               {
@@ -326,31 +341,61 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 {
                   hideSelColumns_actionPerformed(null);
                   if (!toggleSeqs)
+                {
                     viewport.selectionGroup = sg;
                 }
+              }
                 else if (!hide)
+              {
                   showAllColumns_actionPerformed(null);
               }
+            }
               break;
             }
             case KeyEvent.VK_PAGE_UP:
               if (viewport.wrapAlignment)
+            {
                 alignPanel.scrollUp(true);
+            }
               else
+            {
                 alignPanel.setScrollValues(viewport.startRes,
                                            viewport.startSeq
                                            - viewport.endSeq + viewport.startSeq);
+            }
               break;
             case KeyEvent.VK_PAGE_DOWN:
               if (viewport.wrapAlignment)
+            {
                 alignPanel.scrollUp(false);
+            }
               else
+            {
                 alignPanel.setScrollValues(viewport.startRes,
                                            viewport.startSeq
                                            + viewport.endSeq - viewport.startSeq);
+            }
               break;
           }
         }
+
+      public void keyReleased(KeyEvent evt)
+      {
+        switch(evt.getKeyCode())
+        {
+          case KeyEvent.VK_LEFT:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              viewport.firePropertyChange("alignment", null,
+                                          viewport.getAlignment().getSequences());
+            break;
+
+          case KeyEvent.VK_RIGHT:
+            if (evt.isAltDown() || !viewport.cursorMode)
+              viewport.firePropertyChange("alignment", null,
+                                          viewport.getAlignment().getSequences());
+            break;
+        }
+      }
       });
   }
 
@@ -389,7 +434,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if(newPanel)
     {
       if (ap.av.padGaps)
+      {
         ap.av.alignment.padGaps();
+      }
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
     }
@@ -473,6 +520,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     idRightAlign.setSelected(av.rightAlignIds);
     renderGapsMenuItem.setSelected(av.renderGaps);
     wrapMenuItem.setSelected(av.wrapAlignment);
+    scaleAbove.setVisible(av.wrapAlignment);
+    scaleLeft.setVisible(av.wrapAlignment);
+    scaleRight.setVisible(av.wrapAlignment);
     annotationPanelMenuItem.setState(av.showAnnotation);
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
@@ -492,7 +542,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void setProgressBar(String message, long id)
   {
     if(progressBars == null)
+    {
       progressBars = new Hashtable();
+    }
 
     JPanel progressPanel;
     GridLayout layout = (GridLayout) statusPanel.getLayout();
@@ -503,7 +555,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
        progressBars.remove( progressPanel );
        progressPanel = null;
        if(message!=null)
+      {
          statusBar.setText(message);
+      }
 
        layout.setRows(layout.getRows() - 1);
      }
@@ -566,42 +620,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               && frames[i] != this
               && ( (AlignFrame) frames[i]).fileName.equals(fileName))
           {
-            try{
+            try
+            {
               frames[i].setSelected(true);
               Desktop.instance.closeAssociatedWindows();
-            }catch(java.beans.PropertyVetoException ex){}
+          }
+            catch (java.beans.PropertyVetoException ex)
+            {}
           }
 
         }
         Desktop.instance.closeAssociatedWindows();
 
+        FileLoader loader = new FileLoader();
+        String protocol = fileName.startsWith("http:")? "URL":"File";
+        loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
       {
-        viewport.alignment.deleteAllGroups();
-        viewport.sequenceColours=null;
-        while (viewport.alignment.getHeight() > 0)
-        {
-          viewport.alignment.deleteSequence(0);
-        }
+        Rectangle bounds = this.getBounds();
 
-        viewport.historyList.clear();
-        viewport.redoList.clear();
-        Alignment dset = viewport.alignment.getDataset();
-        while (dset.getHeight() > 0)
-        {
-          dset.deleteSequence(0);
-        }
+        FileLoader loader = new FileLoader();
+        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        AlignFrame newframe =
+            loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
 
-        firePropertyChange("Alignment", null, null);
+        newframe.setBounds(bounds);
 
-        updateEditMenuBar();
+        this.closeMenuItem_actionPerformed(true);
       }
-
-      FileLoader loader = new FileLoader();
-      String protocol = fileName.startsWith("http:")? "URL":"File";
-      loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
-
     }
   }
 
@@ -619,11 +666,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public void save_actionPerformed(ActionEvent e)
   {
-    if(fileName==null || currentFileFormat==null)
+    if(fileName==null
+       || currentFileFormat==null
+       || fileName.startsWith("http")
+        )
+    {
       saveAs_actionPerformed(null);
+    }
     else
+    {
       saveAlignment(fileName, currentFileFormat);
   }
+  }
 
   /**
    * DOCUMENT ME!
@@ -674,6 +728,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   public boolean saveAlignment(String file, String format)
   {
+    boolean success = true;
+
     if (format.equalsIgnoreCase("Jalview"))
     {
       String shortName = title;
@@ -684,15 +740,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             java.io.File.separatorChar) + 1);
       }
 
-      new Jalview2XML().SaveAlignment(this, file, shortName);
+      success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
       statusBar.setText("Successfully saved to file: "
                           +fileName+" in "
                           +format +" format.");
 
-
-      // USE Jalview2XML to save this file
-      return true;
     }
     else
     {
@@ -708,8 +761,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
+        {
           omitHidden = viewport.getViewAsString(false);
       }
+      }
 
       String output = new FormatAdapter().formatSequences(
           format,
@@ -718,28 +773,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       if (output == null)
       {
-        return false;
-      }
-
-      try
-      {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-            new java.io.FileWriter(file));
-
-        out.print(output);
-        out.close();
-        this.setTitle(file);
-        statusBar.setText("Successfully saved to file: "
-                          +fileName+" in "
-                          +format +" format.");
-        return true;
+        success = false;
       }
-      catch (Exception ex)
+      else
       {
-        ex.printStackTrace();
+        try
+        {
+          java.io.PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(file));
+
+          out.print(output);
+          out.close();
+          this.setTitle(file);
+          statusBar.setText("Successfully saved to file: "
+                            + fileName + " in "
+                            + format + " format.");
+        }
+        catch (Exception ex)
+        {
+          success = false;
+          ex.printStackTrace();
+        }
       }
     }
-    return false;
+
+    if (!success)
+    {
+      JOptionPane.showInternalMessageDialog(
+          this, "Couldn't save file: " + fileName,
+          "Error Saving File",
+          JOptionPane.WARNING_MESSAGE);
+    }
+
+    return success;
   }
 
   /**
@@ -785,7 +851,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(viewport,
+    new HTMLOutput(alignPanel,
                    alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
@@ -815,6 +881,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     alignPanel.makeEPS(f);
   }
 
+
+  public void pageSetup_actionPerformed(ActionEvent e)
+  {
+    PrinterJob printJob = PrinterJob.getPrinterJob();
+    PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -823,7 +896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     //Putting in a thread avoids Swing painting problems
-    PrintThread thread = new PrintThread();
+    PrintThread thread = new PrintThread(alignPanel);
     thread.start();
   }
 
@@ -837,7 +910,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     new AnnotationExporter().exportAnnotations(
       alignPanel,
-      viewport.alignment.getAlignmentAnnotation()
+        viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
+      viewport.alignment.getGroups()
         );
   }
 
@@ -872,20 +946,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
     if(alignPanels!=null && alignPanels.size()<2)
+    {
       closeAllTabs = true;
+    }
 
     try
     {
       if(alignPanels!=null)
       {
         if (closeAllTabs)
+        {
           for (int i = 0; i < alignPanels.size(); i++)
           {
             AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+            jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+                .removeStructureViewerListener(ap.seqPanel, null);
             PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
             PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
             PaintRefresher.RemoveComponent(ap);
+            ap.av.alignment = null;
           }
+        }
         else
         {
           int index = tabbedPane.getSelectedIndex();
@@ -894,6 +975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
           PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
           PaintRefresher.RemoveComponent(alignPanel);
+          viewport.alignment = null;
           alignPanel = null;
           viewport = null;
 
@@ -901,15 +983,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           tabbedPane.validate();
 
           if(index==tabbedPane.getTabCount())
+          {
             index --;
+          }
 
           this.tabSelectionChanged(index);
         }
       }
 
       if (closeAllTabs)
+      {
         this.setClosed(true);
     }
+    }
     catch (Exception ex)
     {
       ex.printStackTrace();
@@ -980,7 +1066,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if(originalSource!=null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-      originalSource.firePropertyChange("alignment", null,null);
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
     }
   }
 
@@ -992,7 +1080,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
     if(viewport.redoList.size()<1)
+    {
       return;
+    }
 
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
@@ -1004,7 +1094,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if(originalSource!=null)
     {
       originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-      originalSource.firePropertyChange("alignment", null,null);
+      originalSource.firePropertyChange("alignment",
+                                        null,
+                                        originalSource.alignment.getSequences());
     }
   }
 
@@ -1040,7 +1132,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       //The original view is closed, we must validate
       //the current view against the closed view first
       if (al != null)
+      {
         PaintRefresher.validateSequences(al, viewport.alignment);
+      }
 
       originalSource = viewport;
     }
@@ -1068,14 +1162,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -1090,14 +1184,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.getSequences(false).contains(seq))
+        if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
 
-        if (sg.getSequences(false).contains(temp))
+        if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
@@ -1107,11 +1201,102 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       }
     }
 
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
 
 
+
+  synchronized void slideSequences(boolean right, int size)
+  {
+    Vector sg = new Vector();
+    if(viewport.cursorMode)
+    {
+      sg.addElement(viewport.alignment.getSequenceAt(
+          alignPanel.seqPanel.seqCanvas.cursorY));
+    }
+    else if(viewport.getSelectionGroup()!=null
+        && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
+   {
+     sg = viewport.getSelectionGroup().getSequences(
+         viewport.hiddenRepSequences);
+   }
+
+    if(sg.size()<1)
+    {
+      return;
+    }
+
+    Vector invertGroup = new Vector();
+
+    for (int i = 0; i < viewport.alignment.getHeight(); i++)
+    {
+      if(!sg.contains(viewport.alignment.getSequenceAt(i)))
+         invertGroup.add(viewport.alignment.getSequenceAt(i));
+    }
+
+    SequenceI[] seqs1 = new SequenceI[sg.size()];
+    for (int i = 0; i < sg.size(); i++)
+      seqs1[i] = (SequenceI) sg.elementAt(i);
+
+    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+    for (int i = 0; i < invertGroup.size(); i++)
+      seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+
+    SlideSequencesCommand ssc;
+    if (right)
+      ssc = new SlideSequencesCommand("Slide Sequences",
+                                      seqs2, seqs1, size,
+                                      viewport.getGapCharacter()
+          );
+    else
+      ssc = new SlideSequencesCommand("Slide Sequences",
+                                      seqs1, seqs2, size,
+                                      viewport.getGapCharacter()
+          );
+
+    int groupAdjustment = 0;
+    if (ssc.getGapsInsertedBegin() && right)
+    {
+      if (viewport.cursorMode)
+        alignPanel.seqPanel.moveCursor(size, 0);
+      else
+        groupAdjustment = size;
+    }
+    else if (!ssc.getGapsInsertedBegin() && !right)
+    {
+      if (viewport.cursorMode)
+        alignPanel.seqPanel.moveCursor( -size, 0);
+      else
+        groupAdjustment = -size;
+    }
+
+    if (groupAdjustment != 0)
+    {
+      viewport.getSelectionGroup().setStartRes(
+          viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+      viewport.getSelectionGroup().setEndRes(
+          viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+    }
+
+
+    boolean appendHistoryItem = false;
+    if(viewport.historyList!=null
+       && viewport.historyList.size()>0
+      && viewport.historyList.peek() instanceof SlideSequencesCommand)
+    {
+      appendHistoryItem = ssc.appendSlideCommand(
+          (SlideSequencesCommand)viewport.historyList.peek())
+          ;
+    }
+
+    if(!appendHistoryItem)
+      addHistoryItem(ssc);
+
+    repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1124,8 +1309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       return;
     }
-
-    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    //  TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();  
     String[] omitHidden = null;
 
     if (viewport.hasHiddenColumns)
@@ -1142,6 +1327,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     try
     {
+      jalview.gui.Desktop.internalCopy = true;
       //Its really worth setting the clipboard contents
       //to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()
@@ -1174,19 +1360,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     {
       hiddenColumns =new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
+      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
+           i++)
       {
         int[] region = (int[])
             viewport.getColumnSelection().getHiddenColumns().elementAt(i);
 
-        hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
+        hiddenColumns.addElement(new int[]
+                                 {region[0] - hiddenOffset,
                           region[1]-hiddenOffset});
       }
     }
 
-
-
-    Desktop.jalviewClipboard = new Object[]{ seqs,
+    Desktop.jalviewClipboard = new Object[]
+        {
+        seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
     statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
@@ -1219,6 +1407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   void paste(boolean newAlignment)
   {
+    boolean externalPaste=true;
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -1234,7 +1423,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
         if (str.length() < 1)
+        {
           return;
+        }
 
         format = new IdentifyFile().Identify(str, "Paste");
 
@@ -1259,96 +1450,149 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       }
 
       SequenceI[] sequences;
-
+      boolean annotationAdded = false;
+      AlignmentI alignment = null;
 
      if(Desktop.jalviewClipboard!=null)
      {
        // The clipboard was filled from within Jalview, we must use the sequences
        // And dataset from the copied alignment
-       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+       SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
+       // be doubly sure that we create *new* sequence objects.
+       sequences = new SequenceI[newseq.length];
+       for (int i=0;i<newseq.length;i++) {
+         sequences[i] = new Sequence(newseq[i]);
+       }
+       alignment = new Alignment(sequences);
+       externalPaste = false;
      }
      else
      {
-       sequences = new FormatAdapter().readFile(str, "Paste", format);
+       // parse the clipboard as an alignment.
+       alignment = new FormatAdapter().readFile(str, "Paste", format);
+       sequences = alignment.getSequencesArray();
      }
 
-     AlignmentI alignment = null;
-
-      if (newAlignment)
-      {
-          alignment = new Alignment(sequences);
-
-          if (Desktop.jalviewClipboard != null)
-            alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
-          else
-            alignment.setDataset(null);
-      }
-      else
-      {
-        alignment = viewport.getAlignment();
+     int alwidth=0;
 
-        //!newAlignment
-        SequenceI [] newseqs = new SequenceI[sequences.length];
+     if (newAlignment)
+     {
+       
+       if (Desktop.jalviewClipboard != null)
+       {
+         // dataset is inherited
+         alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+       }
+       else
+       {
+         // new dataset is constructed
+         alignment.setDataset(null);
+       }
+       alwidth = alignment.getWidth()+1;
+     }
+     else
+     {
+       AlignmentI pastedal = alignment; // preserve pasted alignment object
+       // Add pasted sequences and dataset into existing alignment.
+       alignment = viewport.getAlignment();
+       alwidth = alignment.getWidth()+1;
+        // decide if we need to import sequences from an existing dataset
+        boolean importDs = Desktop.jalviewClipboard != null
+                && Desktop.jalviewClipboard[1] != alignment.getDataset();
+        // importDs==true instructs us to copy over new dataset sequences from
+        // an existing alignment
+        Vector newDs = (importDs) ? new Vector() : null; // used to create
+                                                          // minimum dataset set
+        
         for (int i = 0; i < sequences.length; i++)
         {
-          newseqs[i] = new Sequence(sequences[i].getName(),
-              sequences[i].getSequence(), sequences[i].getStart(),
-              sequences[i].getEnd());
-
-          alignment.addSequence(newseqs[i]);
+          if (importDs) 
+          {
+            newDs.addElement(null);
+          }
+          SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
+                                                            // paste
+          if (importDs && ds != null)
+          {
+            if (!newDs.contains(ds))
+            {
+              newDs.setElementAt(ds, i); 
+              ds = new Sequence(ds);
+              // update with new dataset sequence
+              sequences[i].setDatasetSequence(ds);
+            }
+            else
+            {
+              ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
+            }
+          }
+          else
+          {
+            // copy and derive new dataset sequence
+            sequences[i] = sequences[i].deriveSequence();
+            alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
+            // TODO: avoid creation of duplicate dataset sequences with a
+            // 'contains' method using SequenceI.equals()/SequenceI.contains()
+          }
+          alignment.addSequence(sequences[i]); // merges dataset
         }
-
-        /*
-         //ADD HISTORY ITEM
-         */
-        addHistoryItem(new EditCommand(
-            "Add sequences",
-            EditCommand.PASTE,
-            newseqs,
-            0,
-            alignment.getWidth(),
-            alignment)
-            );
-
-
-        viewport.setEndSeq(alignment.getHeight());
-        alignment.getWidth();
-        viewport.firePropertyChange("alignment", null, alignment.getSequences());
-      }
-
-
-
-      // Add any annotations attached to sequences
-      for (int i = 0; i < sequences.length; i++)
+        if (newDs != null)
+        {
+          newDs.clear(); // tidy up
+        }
+        if (pastedal.getAlignmentAnnotation()!=null) {
+          // Add any annotation attached to alignment.
+          AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
+          for (int i=0; i<alann.length; i++)
+          {
+            annotationAdded=true;
+            if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
+              AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              newann.padAnnotation(alwidth);
+              alignment.addAnnotation(newann);
+            }
+          }
+        }
+     }
+     if (!newAlignment) {
+       ///////
+       // ADD HISTORY ITEM
+       //
+       addHistoryItem(new EditCommand(
+               "Add sequences",
+               EditCommand.PASTE,
+               sequences,
+               0,
+               alignment.getWidth(),
+               alignment)
+              );
+     }
+     // Add any annotations attached to sequences
+     for (int i = 0; i < sequences.length; i++)
      {
        if (sequences[i].getAnnotation() != null)
        {
          for (int a = 0; a < sequences[i].getAnnotation().length; a++)
          {
-           AlignmentAnnotation newAnnot =
-               new AlignmentAnnotation(
-                   sequences[i].getAnnotation()[a].label,
-                   sequences[i].getAnnotation()[a].description,
-                   sequences[i].getAnnotation()[a].annotations,
-                   sequences[i].getAnnotation()[a].graphMin,
-                   sequences[i].getAnnotation()[a].graphMax,
-                   sequences[i].getAnnotation()[a].graph);
-
-           sequences[i].getAnnotation()[a] = newAnnot;
-           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
-               sequenceMapping;
-           newAnnot.sequenceRef = sequences[i];
-           newAnnot.adjustForAlignment();
-           alignment.addAnnotation(newAnnot);
-           alignment.setAnnotationIndex(newAnnot, a);
+           annotationAdded=true;
+           sequences[i].getAnnotation()[a].adjustForAlignment();
+           sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+           alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
+           alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
          }
 
-         alignPanel.annotationPanel.adjustPanelHeight();
+         
        }
      }
-
-     if(newAlignment)
-     {
+     if (!newAlignment) {
+       // propagate alignment changed.
+       viewport.setEndSeq(alignment.getHeight());
+       if (annotationAdded)
+       {
+         alignPanel.annotationPanel.adjustPanelHeight();
+       }
+       viewport.firePropertyChange("alignment", null, alignment.getSequences());
+     } else {
        AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
        String newtitle = new String("Copied sequences");
 
@@ -1366,15 +1610,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
        //>>>This is a fix for the moment, until a better solution is found!!<<<
        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
-
-       if (title.startsWith("Copied sequences"))
-       {
-         newtitle = title;
-       }
-       else
-       {
-         newtitle = newtitle.concat("- from " + title);
+       
+       // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
+       if (!externalPaste) {
+         if (title.startsWith("Copied sequences"))
+         {
+           newtitle = title;
+         }
+         else
+         {
+           newtitle = newtitle.concat("- from " + title);
+         }
+       } else {
+         newtitle = new String("Pasted sequences");
        }
 
        Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
@@ -1421,7 +1669,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     Vector seqs = new Vector();
     SequenceI seq;
-    for (int i = 0; i < sg.getSize(false); i++)
+    for (int i = 0; i < sg.getSize(); i++)
     {
       seq = sg.getSequenceAt(i);
       seqs.addElement(seq);
@@ -1429,7 +1677,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
    // If the cut affects all sequences, remove highlighted columns
-   if (sg.getSize(false) == viewport.alignment.getHeight())
+   if (sg.getSize() == viewport.alignment.getHeight())
    {
      viewport.getColumnSelection().removeElements(sg.getStartRes(),
          sg.getEndRes() + 1);
@@ -1438,7 +1686,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     SequenceI [] cut = new SequenceI[seqs.size()];
     for(int i=0; i<seqs.size(); i++)
+    {
       cut[i] = (SequenceI)seqs.elementAt(i);
+    }
 
 
     /*
@@ -1481,7 +1731,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1501,7 +1751,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
     sg.setEndRes(viewport.alignment.getWidth() - 1);
     viewport.setSelectionGroup(sg);
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -1522,7 +1772,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     viewport.setSelectionGroup(null);
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -1548,13 +1798,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
+    alignPanel.paintAlignment(true);
+
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
 
@@ -1586,15 +1838,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if (colSel.size() > 0)
     {
       if(trimLeft)
+      {
         column = colSel.getMin();
+      }
       else
+      {
         column = colSel.getMax();
+      }
 
       SequenceI [] seqs;
       if(viewport.getSelectionGroup()!=null)
-        seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      {
+        seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+            hiddenRepSequences);
+      }
       else
+      {
         seqs = viewport.alignment.getSequencesArray();
+      }
 
 
       TrimRegionCommand trimRegion;
@@ -1655,19 +1916,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+          hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
     else
+    {
       seqs = viewport.alignment.getSequencesArray();
+    }
 
 
     RemoveGapColCommand removeGapCols =
         new RemoveGapColCommand("Remove Gapped Columns",
                                 seqs,
                                 start, end,
-                                viewport.getGapCharacter());
+                                viewport.alignment);
 
     addHistoryItem(removeGapCols);
 
@@ -1683,7 +1947,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    // if (viewport.hasHiddenColumns)
    //   viewport.getColumnSelection().compensateForEdits(shifts);
    viewport.setStartRes(seq.findIndex(startRes)-1);
-   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
 
   }
 
@@ -1699,12 +1964,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
-      seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
+      seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+          hiddenRepSequences);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
     else
+    {
       seqs = viewport.alignment.getSequencesArray();
+    }
 
     //This is to maintain viewport position on first residue
     //of first sequence
@@ -1712,13 +1980,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     int startRes = seq.findPosition(viewport.startRes);
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps",
-                                           seqs,
-                                           start, end,
-                     viewport.getGapCharacter()));
+                                         seqs,
+                                         start, end,
+                                         viewport.alignment));
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    viewport.firePropertyChange("alignment", null,
+                                viewport.getAlignment().getSequences());
 
   }
 
@@ -1751,8 +2020,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignmentPanel newap =
         new Jalview2XML().copyAlignPanel(alignPanel, true);
 
+    newap.av.gatherViewsHere = false;
+
     if (viewport.viewName == null)
+    {
       viewport.viewName = "Original";
+    }
 
     newap.av.historyList = viewport.historyList;
     newap.av.redoList = viewport.redoList;
@@ -1760,7 +2033,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
     String newViewName = "View " +index;
 
-    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport.
+        getSequenceSetId());
     Vector existingNames = new Vector();
     for(int i=0; i<comps.size(); i++)
     {
@@ -1768,9 +2042,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       {
         AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
         if(!existingNames.contains(ap.av.viewName))
+        {
           existingNames.addElement(ap.av.viewName);
       }
     }
+    }
 
     while(existingNames.contains(newViewName))
     {
@@ -1821,13 +2097,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
     viewport.rightAlignIds = idRightAlign.isSelected();
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
 
@@ -1840,7 +2116,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1871,13 +2147,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   public void hiddenMarkers_actionPerformed(ActionEvent e)
@@ -1894,7 +2170,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1905,7 +2181,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1916,7 +2192,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1927,7 +2203,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1938,7 +2214,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -1949,7 +2225,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
 
@@ -1972,7 +2248,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
@@ -2214,7 +2490,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -2239,18 +2515,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 viewport.getIgnoreGapsConsensus());
 
          sg.cs.setConsensus(AAFrequency.calculate(
-             sg.getSequences(true), sg.getStartRes(),
+             sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
              sg.getEndRes()+1));
        }
         else
+        {
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+        }
 
 
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.getSequences(true),
+                                            sg.getSequences(viewport.
+              hiddenRepSequences),
                                             sg.getStartRes(),
                                             sg.getEndRes()+1);
           c.calculate();
@@ -2258,16 +2537,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           sg.cs.setConservation(c);
         }
         else
+        {
           sg.cs.setConservation(null);
       }
     }
+    }
 
     if (alignPanel.getOverviewPanel() != null)
     {
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
 
-    alignPanel.repaint();
+
+
+
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -2377,7 +2661,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+            userColours.
             nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
@@ -2388,16 +2673,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 {
                   radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
+                  Desktop.desktop,
                       "Remove from default list?",
                       "Remove user defined colour",
                       JOptionPane.YES_NO_OPTION);
                   if(option == JOptionPane.YES_OPTION)
                   {
-                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(
+                    radioItem.getText());
                     colourMenu.remove(radioItem);
                   }
                   else
+              {
                     radioItem.addActionListener(new ActionListener()
                     {
                       public void actionPerformed(ActionEvent evt)
@@ -2407,6 +2695,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                     });
                 }
               }
+          }
             });
         radioItem.addActionListener(new ActionListener()
         {
@@ -2452,8 +2741,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
                               viewport.getAlignment().getSequenceAt(0));
-    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
-    alignPanel.repaint();
+    addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+                                    viewport.alignment));
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -2466,7 +2756,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -2480,7 +2770,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
 
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -2502,7 +2792,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ( (viewport.getSelectionGroup() == null) ||
-        (viewport.getSelectionGroup().getSize(false) < 2))
+        (viewport.getSelectionGroup().getSize() < 2))
     {
       JOptionPane.showInternalMessageDialog(this,
                                             "You must select at least 2 sequences.",
@@ -2525,8 +2815,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if ( ( (viewport.getSelectionGroup() != null) &&
-          (viewport.getSelectionGroup().getSize(false) < 4) &&
-          (viewport.getSelectionGroup().getSize(false) > 0)) ||
+          (viewport.getSelectionGroup().getSize() < 4) &&
+          (viewport.getSelectionGroup().getSize() > 0)) ||
         (viewport.getAlignment().getHeight() < 4))
     {
       JOptionPane.showInternalMessageDialog(this,
@@ -2605,8 +2895,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null) {
-      if (viewport.getSelectionGroup().getSize(false) < 3) {
+    if (viewport.getSelectionGroup() != null)
+    {
+      if (viewport.getSelectionGroup().getSize() < 3)
+      {
         JOptionPane.showMessageDialog(Desktop.desktop,
                                       "You need to have more than two sequences selected to build a tree!",
                                       "Not enough sequences",
@@ -2618,9 +2910,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      while (s < sg.getSize(false))
+      while (s < sg.getSize())
       {
-        if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
+        if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
             sg.getEndRes())
         {
           JOptionPane.showMessageDialog(Desktop.desktop,
@@ -2653,14 +2945,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       }
 
       if(viewport.alignment.getHeight()<2)
+      {
         return;
+      }
 
       tp = new TreePanel(alignPanel, type, pwType);
     }
 
-    title = title + " from " + this.title;
+    title += " from ";
+
     if(viewport.viewName!=null)
-      title+= " ("+viewport.viewName+")";
+    {
+      title+= viewport.viewName+" of ";
+    }
+
+    title += this.title;
 
     Desktop.addInternalFrame(tp, title, 600, 500);
   }
@@ -2684,9 +2983,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         // TODO: JBPNote - have to map order entries to curent SequenceI pointers
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
 
-        addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
+        addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+                                        viewport.alignment));
 
-        alignPanel.repaint();
+        alignPanel.paintAlignment(true);
       }
     });
   }
@@ -2704,7 +3004,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     sortByTreeMenu.removeAll();
 
-    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    Vector comps = (Vector) PaintRefresher.components.get(viewport.
+        getSequenceSetId());
     Vector treePanels = new Vector();
     int i, iSize = comps.size();
     for(i=0; i<iSize; i++)
@@ -2741,7 +3042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                                           oldOrder,
                                           viewport.alignment));
 
-          alignPanel.repaint();
+          alignPanel.paintAlignment(true);
         }
       });
 
@@ -2760,7 +3061,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     AlignmentView msa = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 1))
+        (viewport.getSelectionGroup().getSize() > 1))
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       /*SequenceGroup seqs = viewport.getSelectionGroup();
@@ -2802,7 +3103,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    AlignmentView seqs = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 0))
+        (viewport.getSelectionGroup().getSize() > 0))
     {
       seqs = viewport.getAlignmentView(true);
     }
@@ -2814,7 +3115,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
     if (!viewport.alignment.isAligned())
     {
-      seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
+      seqs.setSequences(new SeqCigar[]
+                        {seqs.getSequences()[0]});
     }
     return seqs;
   }
@@ -2862,11 +3164,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     return ShowNewickTree(nf,title,600,500,4,5);
   }
-  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input)
   {
     return ShowNewickTree(nf,title, input, 600,500,4,5);
   }
-  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
+                                  int x, int y)
+  {
     return ShowNewickTree(nf, title, null, w, h, x, y);
   }
   /**
@@ -2881,7 +3188,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    * @param y position
    * @return TreePanel handle
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
+  public TreePanel ShowNewickTree(NewickFile nf, String title,
+                                  AlignmentView input, int w, int h, int x,
+                                  int y)
+  {
     TreePanel tp = null;
 
     try
@@ -2898,7 +3208,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         tp.setSize(w,h);
 
         if(x>0 && y>0)
+        {
           tp.setLocation(x,y);
+        }
 
 
         Desktop.addInternalFrame(tp, title, w, h);
@@ -2912,28 +3224,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     return tp;
   }
 
-  class PrintThread
-      extends Thread
-  {
-    public void run()
-    {
-      PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
-      printJob.setPrintable(alignPanel, pf);
-
-      if (printJob.printDialog())
-      {
-        try
-        {
-          printJob.print();
-        }
-        catch (Exception PrintException)
-        {
-          PrintException.printStackTrace();
-        }
-      }
-    }
-  }
 
   /**
    * Generates menu items and listener event actions for web service clients
@@ -2963,7 +3253,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
             {
               AlignmentView msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset(), af);
+                                         false, true,
+                                         viewport.getAlignment().getDataset(),
+                                         af);
 
             }
 
@@ -2980,7 +3272,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
               {
                 AlignmentView msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset(), af);
+                                           true, true,
+                                           viewport.getAlignment().getDataset(),
+                                           af);
 
               }
 
@@ -3025,7 +3319,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
         wsmenu.add(secstrmenu);
       }
-      this.webService.removeAll();
+      resetWebServiceMenu();
       for (int i = 0, j = wsmenu.size(); i < j; i++)
       {
         webService.add( (JMenu) wsmenu.get(i));
@@ -3033,7 +3327,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
     else
     {
-      this.webService.removeAll();
+      resetWebServiceMenu();
       this.webService.add(this.webServiceNoServices);
     }
     // TODO: add in rediscovery function
@@ -3041,6 +3335,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     // TODO: group services by location as well as function.
   }
 
+
+  /**
+   * empty the web service menu and add any ad-hoc functions
+   * not dynamically discovered.
+   *
+   */
+  private void resetWebServiceMenu()
+  {
+    webService.removeAll();
+    // Temporary hack - DBRef Fetcher always top level ws entry.
+    JMenuItem rfetch = new JMenuItem("Fetch DB References");
+    rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
+    webService.add(rfetch);
+    rfetch.addActionListener(new ActionListener() {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        new jalview.io.DBRefFetcher(
+                alignPanel.av.getSequenceSelection(),
+                alignPanel.alignFrame).fetchDBRefs(false);
+      }
+      
+    });
+  }
+
  /* public void vamsasStore_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
@@ -3062,95 +3381,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
 
 
-
 public void showTranslation_actionPerformed(ActionEvent e)
 {
-  SequenceI [] selection = viewport.getSelectionAsNewSequence();
-  String [] seqstring = viewport.getViewAsString(true);
-
-  int s, sSize = selection.length;
-  SequenceI [] newSeq = new SequenceI[sSize];
-
-  int res, resSize;
-  StringBuffer protein;
-  String seq;
-  for(s=0; s<sSize; s++)
-  {
-    protein = new StringBuffer();
-    seq = AlignSeq.extractGaps("-. ", seqstring[s]);
-    resSize = seq.length();
-    resSize -= resSize%3;
-
-    for(res = 0; res < resSize; res+=3)
-    {
-      String codon = seq.substring(res, res+3);
-      codon = codon.replace('U', 'T');
-      String aa = ResidueProperties.codonTranslate(codon);
-      if(aa==null)
-        protein.append(viewport.getGapCharacter());
-      else if(aa.equals("STOP"))
-        protein.append("X");
-      else
-        protein.append( aa );
-    }
-    newSeq[s] = new Sequence(selection[s].getName(),
-                             protein.toString());
-  }
-
-
-  AlignmentI al = new Alignment(newSeq);
-  al.setDataset(null);
-
-
-  ////////////////////////////////
-  // Copy annotations across
-  jalview.datamodel.AlignmentAnnotation[] annotations
-      = viewport.alignment.getAlignmentAnnotation();
-  int a, aSize;
-  if(annotations!=null)
-  {
-    for (int i = 0; i < annotations.length; i++)
-    {
-      if (annotations[i].label.equals("Quality") ||
-          annotations[i].label.equals("Conservation") ||
-          annotations[i].label.equals("Consensus"))
-      {
-        continue;
-      }
-
-      aSize = viewport.alignment.getWidth() / 3;
-      jalview.datamodel.Annotation[] anots =
-          new jalview.datamodel.Annotation[aSize];
-
-      for (a = 0; a < viewport.alignment.getWidth(); a++)
-      {
-        if (annotations[i].annotations[a] == null
-            || annotations[i].annotations[a] == null)
-          continue;
-
-        anots[a / 3] = new Annotation(
-            annotations[i].annotations[a].displayCharacter,
-            annotations[i].annotations[a].description,
-            annotations[i].annotations[a].secondaryStructure,
-            annotations[i].annotations[a].value,
-            annotations[i].annotations[a].colour);
-      }
-
-      jalview.datamodel.AlignmentAnnotation aa
-          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-          annotations[i].description, anots);
-      al.addAnnotation(aa);
-    }
-  }
+  ///////////////////////////////
+  // Collect Data to be translated/transferred
 
+  SequenceI [] selection = viewport.getSequenceSelection();
+  String [] seqstring = viewport.getViewAsString(true);
+  AlignmentI al  = null;
+  try {
+    al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
+        viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
+        viewport.alignment.getWidth());
+  } catch (Exception ex) {
+    al = null;
+    jalview.bin.Cache.log.debug("Exception during translation.",ex);
+  }
+  if (al==null)
+  {
+    JOptionPane.showMessageDialog(Desktop.desktop,
+        "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+        "Translation Failed",
+        JOptionPane.WARNING_MESSAGE);
+  } else {
     AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              DEFAULT_WIDTH,
                              DEFAULT_HEIGHT);
-
-
-
-
+  }
 }
 
 /**
@@ -3161,8 +3419,10 @@ public void showTranslation_actionPerformed(ActionEvent e)
 public boolean parseFeaturesFile(String file, String type)
 {
     boolean featuresFile = false;
-    try{
-      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
+    try
+    {
+      featuresFile = new FeaturesFile(file,
+          type).parse(viewport.alignment.getDataset(),
                                          alignPanel.seqPanel.seqCanvas.
                                          getFeatureRenderer().featureColours,
                                          false);
@@ -3176,7 +3436,7 @@ public boolean parseFeaturesFile(String file, String type)
     {
       viewport.showSequenceFeatures = true;
       showSeqFeatures.setSelected(true);
-      alignPanel.repaint();
+      alignPanel.paintAlignment(true);
     }
 
     return featuresFile;
@@ -3201,12 +3461,14 @@ public void drop(DropTargetDropEvent evt)
 
     try
     {
-      DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+      DataFlavor uriListFlavor = new DataFlavor(
+          "text/uri-list;class=java.lang.String");
       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
         //Works on Windows and MacOSX
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+        files = (java.util.List) t.getTransferData(DataFlavor.
+            javaFileListFlavor);
       }
       else if (t.isDataFlavorSupported(uriListFlavor))
       {
@@ -3259,7 +3521,8 @@ public void drop(DropTargetDropEvent evt)
   // AlignFrame
    public void loadJalviewDataFile(String file)
   {
-    try{
+    try
+    {
       String protocol = "File";
 
       if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
@@ -3268,7 +3531,7 @@ public void drop(DropTargetDropEvent evt)
       }
 
       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
-          alignment, file);
+          alignment, file, protocol);
 
       if (!isAnnotation)
       {
@@ -3285,19 +3548,22 @@ public void drop(DropTargetDropEvent evt)
                 viewport.getAlignment(),
                 0, false);
             alignPanel.adjustAnnotationHeight();
-            alignPanel.repaint();
+            alignPanel.paintAlignment(true);
           }
           else
+          {
             new FileLoader().LoadFile(viewport, file, protocol, format);
         }
       }
+      }
       else
       {
         // (isAnnotation)
         alignPanel.adjustAnnotationHeight();
       }
 
-    }catch(Exception ex)
+    }
+    catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -3336,3 +3602,39 @@ public void drop(DropTargetDropEvent evt)
     return viewport;
   }
 }
+
+class PrintThread
+    extends Thread
+{
+  AlignmentPanel ap;
+  public PrintThread(AlignmentPanel ap)
+  {
+   this.ap = ap;
+  }
+  static PageFormat pf;
+  public void run()
+  {
+    PrinterJob printJob = PrinterJob.getPrinterJob();
+
+    if (pf != null)
+    {
+      printJob.setPrintable(ap, pf);
+    }
+    else
+    {
+      printJob.setPrintable(ap);
+    }
+
+    if (printJob.printDialog())
+    {
+      try
+      {
+        printJob.print();
+      }
+      catch (Exception PrintException)
+      {
+        PrintException.printStackTrace();
+      }
+    }
+  }
+}