From 577f505f54fe343e89f581461e780ea8308c20ec Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 15 Mar 2005 16:06:54 +0000
Subject: [PATCH] selection removed, now SelectionGroup does same job as id
 select and residue select

---
 src/jalview/gui/AlignFrame.java         |   43 ++++---
 src/jalview/gui/AlignViewport.java      |   16 ++-
 src/jalview/gui/AlignmentPanel.java     |  100 ++++++++++++----
 src/jalview/gui/Desktop.java            |    3 +-
 src/jalview/gui/Finder.java             |    8 +-
 src/jalview/gui/GroupEditor.java        |   10 +-
 src/jalview/gui/IdCanvas.java           |   28 +++--
 src/jalview/gui/IdPanel.java            |  197 +++++++++++++++++++++----------
 src/jalview/gui/PCAPanel.java           |    6 +-
 src/jalview/gui/PairwiseAlignPanel.java |    5 +-
 src/jalview/gui/PopupMenu.java          |   12 +-
 src/jalview/gui/RedundancyPanel.java    |   13 +-
 src/jalview/gui/RotatableCanvas.java    |   29 +++--
 src/jalview/gui/ScalePanel.java         |    6 +-
 src/jalview/gui/Selection.java          |   73 ------------
 src/jalview/gui/SeqCanvas.java          |    2 +-
 src/jalview/gui/SeqPanel.java           |  105 +++++++++++++++-
 src/jalview/gui/SequenceRenderer.java   |    5 +-
 src/jalview/gui/SplashScreen.java       |    2 +-
 src/jalview/gui/TreeCanvas.java         |   47 ++++----
 src/jalview/gui/UserDefinedColours.java |    2 +
 21 files changed, 429 insertions(+), 283 deletions(-)
 delete mode 100755 src/jalview/gui/Selection.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4209455..c679559 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,6 +64,7 @@ public class AlignFrame extends GAlignFrame
   protected void saveAs_actionPerformed(ActionEvent e)
   {
     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
@@ -222,7 +223,7 @@ public class AlignFrame extends GAlignFrame
 
   public void moveSelectedSequences(boolean up)
   {
-    SequenceGroup sg = viewport.getRubberbandGroup();
+    SequenceGroup sg = viewport.getSelectionGroup();
     if (sg == null)
       return;
 
@@ -266,10 +267,10 @@ public class AlignFrame extends GAlignFrame
 
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getRubberbandGroup()==null)
+   if(viewport.getSelectionGroup()==null)
      return;
 
-   SequenceGroup sg = viewport.getRubberbandGroup();
+   SequenceGroup sg = viewport.getSelectionGroup();
 
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      StringBuffer buffer= new StringBuffer();
@@ -352,10 +353,10 @@ public class AlignFrame extends GAlignFrame
   protected void delete_actionPerformed(ActionEvent e)
   {
     addHistoryItem("Delete");
-    if (viewport.getRubberbandGroup() == null)
+    if (viewport.getSelectionGroup() == null)
       return;
 
-     SequenceGroup sg = viewport.getRubberbandGroup();
+     SequenceGroup sg = viewport.getSelectionGroup();
      for (int i=0;i < sg.sequences.size(); i++)
      {
        SequenceI seq = sg.getSequenceAt(i);
@@ -368,7 +369,7 @@ public class AlignFrame extends GAlignFrame
           viewport.getAlignment().getSequences().setElementAt(seq, index);
      }
 
-     viewport.setRubberbandGroup(null);
+     viewport.setSelectionGroup(null);
      viewport.alignment.deleteGroup(sg);
      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
      if(viewport.getAlignment().getHeight()<1)
@@ -404,7 +405,7 @@ public class AlignFrame extends GAlignFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
 
     alignPanel.RefreshPanels();
   }
@@ -413,29 +414,26 @@ public class AlignFrame extends GAlignFrame
 
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
+    SequenceGroup sg = new SequenceGroup();
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
+      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
     PaintRefresher.Refresh(null);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setRubberbandGroup(null);
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
+    SequenceGroup sg = viewport.getSelectionGroup();
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-    {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
-      else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
-    }
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+
     PaintRefresher.Refresh(null);
   }
 
@@ -870,7 +868,7 @@ if ( viewport.getConservationSelected() )
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()<2)
+    if(viewport.getSelectionGroup().getSize()<2)
       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
@@ -882,7 +880,8 @@ if ( viewport.getConservationSelected() )
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
+
+    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
        || viewport.getAlignment().getHeight()<4)
     {
       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
@@ -938,9 +937,9 @@ if ( viewport.getConservationSelected() )
     }
 
     TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
+   if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
    {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
+     tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
                          0, viewport.alignment.getWidth());
    }
    else
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7719f02..2f40de4 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -28,7 +28,7 @@ public class AlignViewport
   boolean conservationColourSelected = false;
   boolean abovePIDThreshold = false;
 
-  SequenceGroup rubberbandGroup = null;
+  SequenceGroup selectionGroup = new SequenceGroup();
 
   RendererI renderer = new SequenceRenderer(this);
 
@@ -40,7 +40,6 @@ public class AlignViewport
   Font            font = new Font("SansSerif",Font.PLAIN,10);
   AlignmentI      alignment;
 
-  Selection       sel    = new Selection(this);
   ColumnSelection colSel = new ColumnSelection();
 
   String visibleConsensus;
@@ -116,16 +115,17 @@ public class AlignViewport
     return consensus;
   }
 
-  public SequenceGroup getRubberbandGroup()
+  public SequenceGroup getSelectionGroup()
   {
-    return rubberbandGroup;
+    return selectionGroup;
   }
 
-  public void setRubberbandGroup(SequenceGroup sg)
+  public void setSelectionGroup(SequenceGroup sg)
   {
-    rubberbandGroup = sg;
+    selectionGroup = sg;
   }
 
+
  public boolean getConservationSelected()
  {
    return conservationColourSelected;
@@ -325,9 +325,7 @@ public class AlignViewport
     }
     return -1;
   }
-  public Selection getSelection() {
-    return sel;
-  }
+
   public ColumnSelection getColumnSelection() {
     return colSel;
   }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fafcdcd..15f1a1f 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -55,8 +55,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    });
 
 
-   hscroll.setFocusable(false);
-   vscroll.setFocusable(false);
+  // hscroll.setFocusable(false);
+  // vscroll.setFocusable(false);
    setFocusable(true);
 
    addKeyListener(new KeyAdapter()
@@ -66,8 +66,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        switch(evt.getKeyCode())
        {
          case  27: // escape key
-           av.setRubberbandGroup(null);
-           av.getSelection().clear();
+           av.setSelectionGroup(null);
            RefreshPanels();
            break;
          case KeyEvent.VK_X:
@@ -180,33 +179,83 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void RefreshPanels()
   {
-    requestFocus();
-    invalidate();
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(500, av.charHeight/2 +12));
-    scalePanelHolder.setPreferredSize(new Dimension(500, av.charHeight/2 +12));
-    if(av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+
+              requestFocus();
+              invalidate();
+              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
+              hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.
+                  getPreferredSize().width, 12));
+              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
+                  av.charHeight / 2 + 12));
+              scalePanelHolder.setPreferredSize(new Dimension(500,
+                  av.charHeight / 2 + 12));
+              if (av.getWrapAlignment())
+              {
+                int max = av.alignment.getWidth() /
+                    (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
+
+                int h = (av.alignment.getHeight() + 2) * av.charHeight;
+                vextent = seqPanel.seqCanvas.getHeight() / h;
+                vscroll.setValues(0, vextent, 0, max);
+              }
+              else
+
+                setScrollValues(av.getStartRes(), av.getStartSeq());
+              av.getConsensus(true);
+              if (overviewPanel != null)
+                overviewPanel.updateOverviewImage();
+
+            }
+          });
+
+          validate();
+          repaint();
+  }
+  int hextent = 0;
+  int vextent = 0;
+
 
-      int h  = (av.alignment.getHeight() + 2)*av.charHeight;
-      vextent = seqPanel.seqCanvas.getHeight()/h;
-      vscroll.setValues(0,vextent,0,max);
+  // return value is true if the scroll is valid
+  public boolean scrollUp(boolean up)
+  {
+    if(up)
+    {
+      if(vscroll.getValue()<1)
+        return false;
+      vscroll.setValue(vscroll.getValue() - 1);
     }
     else
+    {
+     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
+       return false;
+      vscroll.setValue(vscroll.getValue() + 1);
+    }
 
-    setScrollValues(av.getStartRes(), av.getStartSeq());
-    av.getConsensus(true);
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
+    return true;
+  }
 
-    validate();
-    repaint();
+  public boolean scrollRight(boolean right)
+  {
+    if(right)
+   {
+     if(hscroll.getValue()<1)
+       return false;
+     hscroll.setValue(hscroll.getValue() - 1);
+   }
+   else
+   {
+    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
+      return false;
+     hscroll.setValue(hscroll.getValue() + 1);
+   }
 
-  }
+   return true;
+ }
 
-  int hextent = 0;
-  int vextent = 0;
 
   public void setScrollValues(int x, int y)
   {
@@ -324,7 +373,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     Color currentTextColor=null;
     for(int i=startSeq; i<endSeq; i++)
     {
-      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
+      if (av.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -431,6 +480,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(
           "LAST_DIRECTORY"));
+      chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle("Create JPG image from alignment");
       chooser.setToolTipText("Save");
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 25bfa52..efa283c 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -48,7 +48,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
 
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    int width = 1200, height = 800;
+    int width = 900, height = 650;
     if(screenSize.getWidth()<width)
       width = screenSize.width;
     if(screenSize.getHeight()<height)
@@ -126,6 +126,7 @@ public class Desktop extends jalview.jbgui.GDesktop
  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
  {
    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+   chooser.setFileView(new JalviewFileView());
    chooser.setDialogTitle("Open local file");
    chooser.setToolTipText("Open");
    int value = chooser.showOpenDialog(this);
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 2311a9f..8567451 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -99,8 +99,8 @@ public class Finder extends GFinder
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if(av.getSelection().size()>0)
-        seq = (Sequence)(av.getSelection().sequenceAt(0));
+      if(av.getSelectionGroup().getSize()>0)
+        seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
       else
         seq = (Sequence)av.getAlignment().getSequenceAt(0);
 
@@ -122,7 +122,7 @@ public class Finder extends GFinder
     int end = av.alignment.getHeight();
 
 
-    SequenceGroup rubberband = av.getRubberbandGroup();
+    SequenceGroup rubberband = av.getSelectionGroup();
     if(rubberband!=null)
       end = rubberband.getEndRes();
 
@@ -132,7 +132,7 @@ public class Finder extends GFinder
     {
       seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
 
-      if(   av.getSelection().size()>0 && !av.getSelection().contains(seq)
+      if(   av.getSelectionGroup().getSize()>0 && !av.getSelectionGroup().sequences.contains(seq)
             || (rubberband!=null && !rubberband.sequences.contains(seq))  )
       {
         // if a selection has been made, only search within that selection
diff --git a/src/jalview/gui/GroupEditor.java b/src/jalview/gui/GroupEditor.java
index 3ee186b..e3c49d6 100755
--- a/src/jalview/gui/GroupEditor.java
+++ b/src/jalview/gui/GroupEditor.java
@@ -198,10 +198,10 @@ public class GroupEditor extends GGroupEditor
       return;
 
     SequenceGroup sg = (SequenceGroup)groups.elementAt(selectedGroupIndex);
-    Selection sel = av.getSelection();
-    for(int i=0; i<sel.size(); i++)
+
+    for(int i=0; i<av.getSelectionGroup().getSize(); i++)
     {
-      int index = unassignedVector.indexOf( sel.sequenceAt(i).getDisplayId() );
+      int index = unassignedVector.indexOf( av.getSelectionGroup().getSequenceAt(i).getDisplayId() );
       if(index!=-1)
       {
         sg.addSequence( (SequenceI) sequenceHash.get( unassignedVector.elementAt(index) ));
@@ -267,7 +267,7 @@ public class GroupEditor extends GGroupEditor
 
       unassignedVector.addElement(assignedVector.elementAt(indices[i]-i));
       SequenceI removeSequence = (SequenceI)sequenceHash.get( assignedVector.elementAt(indices[i]-i) );
-      av.getSelection().removeElement( removeSequence );
+      av.getSelectionGroup().deleteSequence( removeSequence );
       sg.deleteSequence( removeSequence );
       assignedVector.removeElementAt(indices[i]-i);
 
@@ -288,7 +288,7 @@ public class GroupEditor extends GGroupEditor
       String id = (String)enum.nextElement();
       unassignedVector.addElement( id );
       SequenceI removeSequence = (SequenceI)sequenceHash.get( id );
-      av.getSelection().removeElement( removeSequence );
+      av.getSelectionGroup().deleteSequence( removeSequence );
       sg.deleteSequence( removeSequence );
     }
 
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index f68d967..9e64b1e 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -10,7 +10,6 @@ public class IdCanvas extends JPanel
 {
   protected AlignViewport av;
 
-  public boolean paintFlag   = false;
   protected boolean showScores  = true;
 
   protected int     maxIdLength = -1;
@@ -23,28 +22,29 @@ public class IdCanvas extends JPanel
     PaintRefresher.Register(this);
   }
 
-  public void drawIdString(Graphics gg,SequenceI ds,int i, int starty, int ypos) {
+  public void drawIdString(Graphics gg,SequenceI s,int i, int starty, int ypos) {
       int charHeight = av.getCharHeight();
 
-      if (av.getSelection().contains(ds)) {
+
+      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {
 	  gg.setColor(Color.lightGray);
 	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
 	  gg.setColor(Color.white);
       } else {
-	  gg.setColor(ds.getColor());
+	  gg.setColor(s.getColor());
 	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
 	  gg.setColor(Color.black);
       }
 
-      String string = ds.getName() + "/" + ds.getStart() + "-" + ds.getEnd();
+      String string = s.getName() + "/" + s.getStart() + "-" + s.getEnd();
 
       gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
 
   }
 
   public void paintComponent(Graphics gg) {
-    AlignmentI da         = av.getAlignment();
-    int        charHeight = av.getCharHeight();
+    AlignmentI al         = av.alignment;
+    int        charHeight = av.charHeight;
     gg.setFont(av.getFont());
 
     //Fill in the background
@@ -61,15 +61,15 @@ public class IdCanvas extends JPanel
     if (av.getWrapAlignment())
     {
           // Draw the rest of the panels
-          int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
+          int chunkHeight =  (al.getHeight() + 2)*av.charHeight;
           int row = av.getStartRes() / av.chunkWidth ;
           for(int ypos=2*av.charHeight;
-              ypos <= getHeight() && row*av.chunkWidth<da.getWidth();
+              ypos <= getHeight() && row*av.chunkWidth<al.getWidth();
               ypos += chunkHeight, row++ )
           {
             for (int i = starty; i < av.alignment.getHeight(); i++)
             {
-              SequenceI s = da.getSequenceAt(i);
+              SequenceI s = al.getSequenceAt(i);
               drawIdString(gg, s, i, 0, ypos);
             }
           }
@@ -82,14 +82,16 @@ public class IdCanvas extends JPanel
       for (int i = starty; i < endy; i++)
       {
         // Selected sequence colours
-        if (av.getSelection().contains(da.getSequenceAt(i)))
+
+        if (av.getSelectionGroup()!= null && av.getSelectionGroup().sequences.contains(al.getSequenceAt(i)))
         {
+       //   if(av.alignment.findGroup(al.getSequenceAt(i)).getEndRes()==
           currentColor = Color.lightGray;
           currentTextColor = Color.black;
         }
         else
         {
-          currentColor = da.getSequenceAt(i).getColor();
+          currentColor = al.getSequenceAt(i).getColor();
           currentTextColor = Color.black;
         }
 
@@ -101,7 +103,7 @@ public class IdCanvas extends JPanel
                     charHeight);
 
         gg.setColor(currentTextColor);
-        String string = da.getSequenceAt(i).getDisplayId();
+        String string = al.getSequenceAt(i).getDisplayId();
         gg.drawString(string, 0,
                       AlignmentUtil.getPixelHeight(starty, i, charHeight) +
                       charHeight - (charHeight / 5));
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 32f3425..1889eb6 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -12,12 +12,12 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
   protected IdCanvas       idCanvas;
   protected AlignViewport  av;
   protected AlignmentPanel alignPanel;
+  ScrollThread scrollThread = null;
 
-  protected int            offy;
-  public    int            width;
-  public    int            lastid;
-
-  SequenceGroup selectedSequenceGroup;
+  int            offy;
+  int            width;
+  int lastid = -1;
+  boolean mouseDragging = false;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -32,59 +32,25 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
 
   public void mouseMoved(MouseEvent e) {}
 
-  public void selectSeqs(int start, int end) {
-     if (end < start)
-     {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-     }
-
-     for (int i = start; i <= end; i++)
-     {
-       SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);
-       if (av.getSelection().contains(pickedSeq))
-       {
-         av.getSelection().removeElement(pickedSeq);
-         selectedSequenceGroup.deleteSequence(pickedSeq);
-       }
-       else
-       {
-         av.getSelection().addElement(pickedSeq);
-         if(selectedSequenceGroup==null)
-         {
-           selectedSequenceGroup = new SequenceGroup();
-           av.setRubberbandGroup( selectedSequenceGroup );
-          // av.alignment.addGroup( selectedSequenceGroup );
-           selectedSequenceGroup.setStartRes(0);
-           selectedSequenceGroup.setEndRes( pickedSeq.getSequence().length());
-         }
-
-         selectedSequenceGroup.addSequence( pickedSeq );
-       }
-
-     }
-
-     alignPanel.seqPanel.seqCanvas.paintFlag=true;
-     alignPanel.repaint();
-     repaint();
-
-   }
 
   public void mouseDragged(MouseEvent e) {
+    mouseDragging = true;
+
     int y = e.getY();
     if(av.getWrapAlignment())
       y-=2*av.charHeight;
     int seq = av.getIndex(y);
 
+    if(seq<0)
+      return;
+
     if (seq < lastid)
       selectSeqs(lastid - 1, seq);
     else if (seq > lastid)
       selectSeqs(lastid + 1, seq);
 
     lastid = seq;
-
-    return;
+    alignPanel.repaint();
   }
 
   public void mouseClicked(MouseEvent e)
@@ -106,8 +72,28 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     }
 
   }
-  public void mouseEntered(MouseEvent e) { }
-  public void mouseExited (MouseEvent e) { }
+  public void mouseEntered(MouseEvent e)
+  {
+    if(scrollThread!=null)
+      scrollThread.running = false;
+  }
+
+  public void mouseExited (MouseEvent e)
+  {
+    if(av.getWrapAlignment())
+      return;
+
+    if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)
+    {
+      scrollThread = new ScrollThread(true);
+    }
+
+    if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq())
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
 
   public void mousePressed(MouseEvent e) {
     if (e.getClickCount() == 2)
@@ -118,6 +104,8 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
       y-=2*av.charHeight;
 
     int seq = av.getIndex(y);
+    if (seq == -1)
+      return;
 
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
@@ -127,34 +115,117 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
       return;
     }
 
+    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
+    {
 
+      SequenceGroup selection = new SequenceGroup();
+      SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
+      selection.setStartRes(0);
+      selection.setEndRes(av.alignment.getWidth());
+      for (int i =0; i< sg.getSize(); i++)
+        selection.addSequence(sg.getSequenceAt(i));
 
-    if(av.getRubberbandGroup()!=null && (av.getRubberbandGroup().getSize() == av.getSelection().size()))
-          selectedSequenceGroup = av.getRubberbandGroup();
-
-    if (selectedSequenceGroup == null)
-    {
-      selectedSequenceGroup = new SequenceGroup();
-      av.setRubberbandGroup(selectedSequenceGroup);
-      av.getSelection().clear();
+      av.setSelectionGroup(selection);
+      return;
     }
 
-    selectedSequenceGroup.setStartRes(0);
-    selectedSequenceGroup.setEndRes(av.getAlignment().getWidth() - 1);
+    if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))
+      av.setSelectionGroup(new SequenceGroup());
 
-    if (seq != -1)
-      selectSeqs(seq, seq);
+    av.getSelectionGroup().setStartRes(0);
+    av.getSelectionGroup().setEndRes(av.alignment.getWidth());
 
-    lastid = seq;
+    if(e.isShiftDown() && lastid!=-1)
+      selectSeqs(lastid, seq);
+    else
+      selectSeq(seq);
 
+    alignPanel.seqPanel.seqCanvas.paintFlag=true;
+    alignPanel.repaint();
+    repaint();
+  }
 
-    return;
+  void selectSeq(int seq)
+  {
+    lastid = seq;
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq);
   }
 
+  void selectSeqs(int start, int end) {
+
+    lastid = start;
+    if (end < start)
+     {
+       int tmp = start;
+       start = end;
+       end   = tmp;
+       lastid = end;
+     }
+
+     for (int i = start; i <= end; i++)
+        av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+
+   }
+
+
   public void mouseReleased(MouseEvent e)
   {
-    lastid = -1;
+    if(scrollThread!=null)
+      scrollThread.running = false;
+
+    mouseDragging = false;
     PaintRefresher.Refresh(this);
-    selectedSequenceGroup = null;
   }
+
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread
+      extends Thread
+  {
+    boolean running = false;
+    boolean up = true;
+    public ScrollThread(boolean up)
+    {
+      this.up = up;
+      start();
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if(alignPanel.scrollUp(up))
+        {
+          // scroll was ok, so add new sequence to selection
+          int seq = av.getStartSeq();
+          if(!up)
+            seq = av.getEndSeq();
+
+          if (seq < lastid)
+            selectSeqs(lastid - 1, seq);
+          else if (seq > lastid)
+            selectSeqs(lastid + 1, seq);
+
+          lastid = seq;
+        }
+        else
+          running = false;
+
+        alignPanel.repaint();
+        try
+        {
+          Thread.sleep(100);
+        }
+        catch (Exception ex)
+        {}
+      }
+    }
+}
+
 }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 7fe3835..8e0bc37 100755
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -23,11 +23,11 @@ public class PCAPanel extends GPCAPanel implements Runnable
   public PCAPanel(AlignViewport av, SequenceI[] s) {
 
     this.av = av;
-    if(av.getSelection().size()>3)
+    if(av.getSelectionGroup().getSize()>3)
     {
-      s = new Sequence[av.getSelection().size()];
+      s = new Sequence[av.getSelectionGroup().getSize()];
       for(int i=0; i<s.length; i++)
-        s[i] = av.getSelection().sequenceAt(i);
+        s[i] = av.getSelectionGroup().getSequenceAt(i);
     }
 
 
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index b85cb94..0d3b0f3 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -19,7 +19,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       this.av = av;
       float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
       double totscore = 0;
-      int count = av.getSelection().size();
+      int count = av.getSelectionGroup().getSize();
 
       int acount = 0;
         for (int i = 1; i < count; i++)
@@ -27,7 +27,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           for (int j = 0; j < i; j++)
           {
             acount++;
-            AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");
+            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
+                                       av.getSelectionGroup().getSequenceAt(j),"pep");
 
             as.calcScoreMatrix();
             as.traceAlignment();
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index c09093b..abd5093 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -73,7 +73,7 @@ public class PopupMenu extends JPopupMenu
     catch(Exception e)
     {    e.printStackTrace();    }
 
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
     if(sg!=null)
     {
       groupName.setText(sg.getName());
@@ -324,10 +324,6 @@ public class PopupMenu extends JPopupMenu
     if( superG !=null)
       superG.setSuperGroupProperties( sg );
 
-
-    //once group is defined, remove selection rubberband
-    ap.av.setRubberbandGroup(null);
-
     ap.seqPanel.seqCanvas.paintFlag=true;
     ap.seqPanel.repaint();
   }
@@ -490,7 +486,7 @@ public class PopupMenu extends JPopupMenu
 
   SequenceGroup getGroup()
   {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
     ap.av.alignment.addGroup(sg);
@@ -520,9 +516,9 @@ public class PopupMenu extends JPopupMenu
 
   void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-     SequenceGroup sg = ap.av.getRubberbandGroup();
+     SequenceGroup sg = ap.av.getSelectionGroup();
      ap.av.alignment.deleteGroup(sg);
-     ap.av.setRubberbandGroup(null);
+     ap.av.setSelectionGroup(null);
      ap.RefreshPanels();
   }
 
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 6cb2c22..3eec476 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -48,13 +48,14 @@ public class RedundancyPanel extends GSliderPanel
 
         undoButton.setEnabled(true);
 
-       if (ap.av.sel != null && ap.av.sel.size() > 1)
+        SequenceGroup sg = ap.av.getSelectionGroup();
+       if (sg != null && sg.getSize() > 1)
        {
 
-         del = ap.av.alignment.removeRedundancy(threshold, ap.av.sel.asVector());
+         del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
          for (int i = 0; i < del.size(); i++)
-           if (ap.av.sel.contains( (SequenceI) del.elementAt(i)))
-             ap.av.sel.removeElement( (SequenceI) del.elementAt(i));
+           if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
+             sg.deleteSequence( (SequenceI) del.elementAt(i));
 
          }
          else
@@ -69,8 +70,8 @@ public class RedundancyPanel extends GSliderPanel
             del = ap.av.alignment.removeRedundancy(threshold,s);
            for (int j=0; j < del.size(); j++)
            {
-               if (ap.av.sel.contains((SequenceI)del.elementAt(j)))
-               ap.av.sel.removeElement((SequenceI)del.elementAt(j));
+               if (sg.sequences.contains((SequenceI)del.elementAt(j)))
+               sg.deleteSequence((SequenceI)del.elementAt(j));
 
            }
          }
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index bd03629..b4af354 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -294,9 +294,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
           g.setColor(sp.sequence.getColor());
 
 
-      if (av != null)
+      if (av.getSelectionGroup() != null)
       {
-        if (av.getSelection().contains(((SequencePoint)points.elementAt(i)).sequence))
+        if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))
           g.setColor(Color.gray);
       }
       if (z < 0)
@@ -380,16 +380,20 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     SequenceI found = findPoint(x,y);
 
-    if (found != null) {
-      if (av != null) {
-
-        if (av.getSelection().contains(found)) {
-          av.getSelection().removeElement(found);
-        } else {
-          av.getSelection().addElement(found);
-        }
+    if (found != null)
+    {
+      if (av.getSelectionGroup() != null)
+      {
+        av.getSelectionGroup().addOrRemove(found);
         PaintRefresher.Refresh(this);
       }
+      else
+      {
+          av.setSelectionGroup(new SequenceGroup());
+          av.getSelectionGroup().addOrRemove(found);
+          av.getSelectionGroup().setEndRes(av.alignment.getWidth());
+
+      }
     }
     repaint();
   }
@@ -455,9 +459,10 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
       if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {
         if (av != null) {
-          if (!av.getSelection().contains(sp.sequence)) {
+          if (!av.getSelectionGroup().sequences.contains(sp.sequence))
+          {
             changedSel = true;
-            av.getSelection().addElement(sp.sequence);
+            av.getSelectionGroup().addSequence(sp.sequence);
           }
         }
       }
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 8d6e331..dc80d1b 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -62,7 +62,7 @@ public class ScalePanel extends JPanel
       sg.setStartRes(res);
       sg.setEndRes(res);
     }
-    av.setRubberbandGroup(sg);
+    av.setSelectionGroup(sg);
     ap.RefreshPanels();
   }
 
@@ -77,7 +77,7 @@ public class ScalePanel extends JPanel
    if (! av.getColumnSelection().contains(res))
      av.getColumnSelection().addElement(res);
 
-   SequenceGroup sg = av.getRubberbandGroup();
+   SequenceGroup sg = av.getSelectionGroup();
 
    if(res>sg.getStartRes())
      sg.setEndRes(res);
@@ -93,7 +93,7 @@ public class ScalePanel extends JPanel
     int x = evt.getX();
     int res = x/av.getCharWidth() + av.getStartRes();
 
-    SequenceGroup sg = av.getRubberbandGroup();
+    SequenceGroup sg = av.getSelectionGroup();
     if(sg!=null)
     {
       stretchingGroup = true;
diff --git a/src/jalview/gui/Selection.java b/src/jalview/gui/Selection.java
deleted file mode 100755
index 0ac9389..0000000
--- a/src/jalview/gui/Selection.java
+++ /dev/null
@@ -1,73 +0,0 @@
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import java.util.*;
-
-public class Selection
-{
-
-  Vector selected = new Vector();
-  AlignViewport av;
-
-  public Selection(AlignViewport av)
-  {
-    this.av = av;
-  }
-
-  public void addElement(SequenceI seq) {
-    selected.addElement(seq);
-    SequenceGroup sg = av.getRubberbandGroup();
-    if(sg==null)
-    {
-      sg = new SequenceGroup();
-      sg.setEndRes(av.alignment.getWidth()-1);
-      av.setRubberbandGroup(sg);
-    }
-
-    sg.addSequence(seq);
-
-  }
-
-  public void clear() {
-    selected.removeAllElements();
-  }
-
-  public void removeElement(SequenceI seq) {
-    if (selected.contains(seq))
-      selected.removeElement(seq);
-    else
-      System.err.println("WARNING: Tried to remove SequenceI NOT in Selection");
-
-    SequenceGroup sg = av.getRubberbandGroup();
-    if (sg != null)
-      sg.deleteSequence(seq);
-
-
-  }
-
-  public boolean contains(SequenceI seq) {
-    return selected.contains(seq);
-  }
-
-  public SequenceI sequenceAt(int i) {
-    return (SequenceI)selected.elementAt(i);
-  }
-
-  public int size() {
-    return selected.size();
-  }
-
-  public Vector asVector() {
-    return selected;
-  }
-
-  public void selectAll(AlignmentI align) {
-    for (int i=0;i<align.getSequences().size();i++) {
-      SequenceI seq = align.getSequenceAt(i);
-      if (!contains(seq)) {
-        addElement(seq);
-      }
-    }
-  }
-}
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 507b7b0..96dea90 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -223,7 +223,7 @@ public class SeqCanvas extends JPanel
      else
        inGroup = false;
 
-     group = av.getRubberbandGroup();
+     group = av.getSelectionGroup();
      if( group != null && group.sequences.contains(nextSeq) )
      {
          g.setColor(Color.RED.brighter());
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 35c5aef..255be5d 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,10 @@ public class SeqPanel extends JPanel
   // if character is inserted or deleted, we will need to recalculate the conservation
   int seqEditOccurred = -1;
 
+  ScrollThread scrollThread = null;
+  boolean mouseDragging = false;
+
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p) {
     this.av         = avp;
 
@@ -75,6 +79,21 @@ public class SeqPanel extends JPanel
         else
           doMousePressedDefineMode(evt);
       }
+      public void mouseExited(MouseEvent evt)
+      {
+        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
+                  evt.isControlDown())
+                return;
+              doMouseExitedDefineMode(evt);
+
+      }
+      public void mouseEntered(MouseEvent evt)
+      {
+        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
+            evt.isControlDown())
+          return;
+        doMouseEnteredDefineMode(evt);
+      }
 
     });
     repaint();
@@ -372,12 +391,12 @@ public class SeqPanel extends JPanel
     if(res>sequence.getLength())
       return;
 
-    stretchGroup = av.getRubberbandGroup();
+    stretchGroup = av.getSelectionGroup();
 
     if(stretchGroup == null)
      {
        stretchGroup = av.alignment.findGroup( sequence );
-       av.setRubberbandGroup( stretchGroup );
+       av.setSelectionGroup( stretchGroup );
      }
 
     else if(!stretchGroup.sequences.contains(sequence)
@@ -394,7 +413,7 @@ public class SeqPanel extends JPanel
                allGroups[i].getEndRes() >= res)
            {
              stretchGroup = allGroups[i];
-             av.setRubberbandGroup(stretchGroup);
+             av.setSelectionGroup(stretchGroup);
              break;
            }
      }
@@ -406,7 +425,7 @@ public class SeqPanel extends JPanel
       sg.setStartRes(res);
       sg.setEndRes(res);
       sg.addSequence( sequence );
-      av.setRubberbandGroup( sg );
+      av.setSelectionGroup( sg );
       stretchGroup = sg;
 
       if(av.getConservationSelected())
@@ -450,6 +469,8 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
+    mouseDragging = false;
+
     if(stretchGroup==null)
       return;
 
@@ -496,6 +517,7 @@ public class SeqPanel extends JPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
+    ap.idPanel.repaint();
   }
 
 
@@ -533,14 +555,13 @@ public class SeqPanel extends JPanel
         stretchGroup.setStartRes( res );
     }
 
-
     int dragDirection = 0;
     if (y > oldSeq)
       dragDirection = 1;
     else if (y < oldSeq)
       dragDirection = -1;
 
-    while (y != oldSeq)
+    while (y != oldSeq && oldSeq>0)
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -561,11 +582,83 @@ public class SeqPanel extends JPanel
       }
     }
     oldSeq = y;
+    mouseDragging = true;
+    if(scrollThread!=null)
+      scrollThread.setEvent(evt);
 
     seqCanvas.paintFlag = true;
     repaint();
   }
 
+  public void doMouseEnteredDefineMode(MouseEvent e)
+  {
+    if (scrollThread != null)
+      scrollThread.running = false;
+  }
+
+  public void doMouseExitedDefineMode(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+      return;
+
+    if(mouseDragging)
+      scrollThread = new ScrollThread();
+
+  }
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread extends Thread
+  {
+    MouseEvent evt;
+    boolean running = false;
+    public ScrollThread()
+    {
+      start();
+    }
+
+    public void setEvent(MouseEvent e)
+    {
+      evt = e;
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if(evt!=null)
+        {
+
+          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+            running = ap.scrollUp(true);
+
+          if (mouseDragging && evt.getY() >= getHeight() &&
+              av.alignment.getHeight() > av.getEndSeq())
+            running = ap.scrollUp(false);
+
+          if (mouseDragging && evt.getX() < 0)
+            running = ap.scrollRight(true);
+
+          else if (mouseDragging && evt.getX() >= getWidth())
+            running = ap.scrollRight(false);
+        }
+
+        ap.repaint();
+        try
+        {
+          Thread.sleep(75);
+        }
+        catch (Exception ex)
+        {}
+      }
+    }
+}
+
+
 
 }
 
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5b5a392..442239d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -131,7 +131,10 @@ public class SequenceRenderer implements RendererI
           if(av.getColourText())
            {
              getBoxColour(av.getGlobalColourScheme(), seq, i);
-             graphics.setColor(resBoxColour.darker());
+             if(av.getShowBoxes())
+              graphics.setColor(resBoxColour.darker());
+            else
+              graphics.setColor(resBoxColour);
            }
         }
 
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index a5199ab..f013dc4 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -34,7 +34,7 @@ public class SplashScreen extends JPanel implements Runnable
 
     while( visible )
     {
-      if( System.currentTimeMillis()/1000 - startTime > 8)
+      if( System.currentTimeMillis()/1000 - startTime > 5)
         visible = false;
 
       try{
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index de84902..ed9677a 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -34,7 +34,6 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
 
   //RubberbandRectangle rubberband;
 
-  Selection selected;
   Vector    listeners;
 
   Hashtable nameHash = new Hashtable();
@@ -44,7 +43,6 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
   {
     this.av = av;
     this.tree     = tree;
-    selected = av.getSelection();
     scrollPane = scroller;
     addMouseListener(this);
     tree.findHeight(tree.getTopNode());
@@ -54,23 +52,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
   }
   public void TreeSelectionChanged(Sequence sequence)
  {
-    selected = av.getSelection();
+    SequenceGroup selected = av.getSelectionGroup();
+    if(selected == null)
+    {
+      selected = new SequenceGroup();
+      av.setSelectionGroup(selected);
+    }
+
+    selected.setEndRes(av.alignment.getWidth());
+    selected.addOrRemove(sequence);
 
-    if (selected.contains(sequence))
-        selected.removeElement(sequence);
-    else
-        selected.addElement(sequence);
 
-    setSelected(selected);
     PaintRefresher.Refresh(this);
     repaint();
  }
 
 
-  public void setSelected(Selection selected)
-  {
-        this.selected = selected;
-  }
 
   public void setTree(NJTree tree) {
     this.tree = tree;
@@ -136,7 +133,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
 
       nameHash.put((SequenceI)node.element(),rect);
 
-      if (selected.contains((SequenceI)node.element())) {
+      SequenceGroup selected = av.getSelectionGroup();
+      if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
         g.setColor(Color.gray);
 
         g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
@@ -203,7 +201,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
 
   }
 
-  public void pickNodes(Rectangle pickBox, Selection sel) {
+  public void pickNodes(Rectangle pickBox) {
     int width  = getWidth();
     int height = getHeight();
 
@@ -216,10 +214,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
     }
     float chunk = (float)(height-offy*2)/top.count;
 
-    pickNode(pickBox,sel,top,chunk,wscale,width,offx,offy);
+    pickNode(pickBox,top,chunk,wscale,width,offx,offy);
   }
 
-  public void pickNode(Rectangle pickBox, Selection sel, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
+  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
     if (node == null) {
       return;
     }
@@ -236,16 +234,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
       if (pickBox.contains(new Point(xend,ypos))) {
         if (node.element() instanceof SequenceI) {
           SequenceI seq = (SequenceI)node.element();
-          if (sel.contains(seq)) {
-            sel.removeElement(seq);
-          } else {
-            sel.addElement(seq);
-          }
+          SequenceGroup sg = av.getSelectionGroup();
+          if(sg!=null)
+            sg.addOrRemove(seq);
         }
       }
     } else {
-      pickNode(pickBox,sel,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
-      pickNode(pickBox,sel,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
+      pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
+      pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
     }
   }
 
@@ -323,6 +319,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
 
   public void paintComponent(Graphics g)
   {
+
     font = new Font("Verdana",Font.PLAIN,fontSize);
     g.setFont(font);
 
@@ -411,7 +408,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
               tree.groupNodes(tree.getTopNode(),fthreshold);
               setColor(tree.getTopNode(),Color.black);
 
-              av.sel.clear();
+              av.setSelectionGroup(null);
               av.alignment.deleteAllGroups();
 
               for (int i=0; i < tree.getGroups().size(); i++)
@@ -428,7 +425,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
                   {
                     SequenceNode sn = (SequenceNode) l.elementAt(j);
                     if(sg==null)
-                       sg  = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
+                       sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
 
                     sg.addSequence( (Sequence) sn.element());
                   }
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a409549..a96cf52 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -124,6 +124,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
   protected void loadbutton_actionPerformed(ActionEvent e)
   {
     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load colour scheme");
     chooser.setToolTipText("Load");
     int value = chooser.showOpenDialog(this);
@@ -156,6 +157,7 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
   protected void savebutton_actionPerformed(ActionEvent e)
   {
     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save colour scheme");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-- 
1.7.10.2