X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3f49cc49ca923ab2972778efa65f26fc3e9a3c15;hb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;hp=27cb9627837d84c23d549743dcc809aa94ece926;hpb=1627d5f04287be852b799ba51bf2b6ded9acecda;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 27cb962..3f49cc4 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,821 +18,1312 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
 
-public class SeqPanel
-    extends JPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqPanel extends JPanel implements MouseListener,
+    MouseMotionListener, MouseWheelListener
+
 {
-  public SeqCanvas seqCanvas;
-  public AlignmentPanel ap;
-  protected int lastres;
-  protected int startseq;
-  int startEdit = -1;
-  int endEdit = -1;
-  protected AlignViewport av;
-
-  // if character is inserted or deleted, we will need to recalculate the conservation
-  int seqEditOccurred = -1;
-  ScrollThread scrollThread = null;
-  boolean mouseDragging = false;
-  boolean editingSeqs = false;
-  boolean groupEditing = false;
-
-  //////////////////////////////////////////
-  /////Everything below this is for defining the boundary of the rubberband
-  //////////////////////////////////////////
-  int oldSeq = -1;
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
-  boolean remove = false;
-
-  public SeqPanel(AlignViewport avp, AlignmentPanel p)
-  {
-    ToolTipManager.sharedInstance().registerComponent(this);
-    ToolTipManager.sharedInstance().setInitialDelay(0);
-    ToolTipManager.sharedInstance().setDismissDelay(10000);
-    this.av = avp;
-    setBackground(Color.white);
-
-    seqCanvas = new SeqCanvas(avp);
-    setLayout(new BorderLayout());
-    add(seqCanvas, BorderLayout.CENTER);
-
-    ap = p;
-
-    addMouseMotionListener(new MouseMotionAdapter()
+    /** DOCUMENT ME!! */
+    public SeqCanvas seqCanvas;
+
+    /** DOCUMENT ME!! */
+    public AlignmentPanel ap;
+    protected int lastres;
+    protected int startseq;
+    protected AlignViewport av;
+
+    // if character is inserted or deleted, we will need to recalculate the conservation
+    boolean seqEditOccurred = false;
+    ScrollThread scrollThread = null;
+    boolean mouseDragging = false;
+    boolean editingSeqs = false;
+    boolean groupEditing = false;
+
+    //////////////////////////////////////////
+    /////Everything below this is for defining the boundary of the rubberband
+    //////////////////////////////////////////
+    int oldSeq = -1;
+    boolean changeEndSeq = false;
+    boolean changeStartSeq = false;
+    boolean changeEndRes = false;
+    boolean changeStartRes = false;
+    SequenceGroup stretchGroup = null;
+    boolean remove = false;
+
+    boolean mouseWheelPressed = false;
+
+    /**
+     * Creates a new SeqPanel object.
+     *
+     * @param avp DOCUMENT ME!
+     * @param p DOCUMENT ME!
+     */
+    public SeqPanel(AlignViewport avp, AlignmentPanel p)
     {
-      public void mouseMoved(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        this.av = avp;
+        setBackground(Color.white);
 
-        doMouseMoved(evt);
-      }
+        seqCanvas = new SeqCanvas(avp);
+        setLayout(new BorderLayout());
+        add(seqCanvas, BorderLayout.CENTER);
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
+        ap = p;
 
-        if (editingSeqs)
-        {
-          doMouseDragged(evt);
-        }
-        else
+        if(!av.isDataset())
         {
-          doMouseDraggedDefineMode(evt);
+          addMouseMotionListener(this);
+          addMouseListener(this);
+          addMouseWheelListener(this);
         }
-      }
-    });
+    }
 
-    addMouseListener(new MouseAdapter()
+    int startWrapBlock=-1;
+    int wrappedBlock=-1;
+    int findRes(MouseEvent evt)
+   {
+     int res = 0;
+     int x = evt.getX();
+
+    if (av.wrapAlignment)
     {
-      public void mouseReleased(MouseEvent evt)
+
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+        hgap += av.charHeight;
+
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
+
+        int y = evt.getY();
+        y -= hgap;
+        x -= seqCanvas.LABEL_WEST;
+
+
+        int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+
+        wrappedBlock = y / cHeight;
+        wrappedBlock += av.getStartRes() / cwidth;
+
+        res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+    }
+    else
+    {
+        res = (x / av.getCharWidth()) + av.getStartRes();
+    }
+
+    if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+    return res;
+
+   }
+
+   int findSeq(MouseEvent evt)
+   {
+
+     int seq = 0;
+     int y = evt.getY();
+
+     if (av.wrapAlignment)
+     {
+       int hgap = av.charHeight;
+       if (av.scaleAboveWrapped)
+         hgap += av.charHeight;
+
+       int cHeight = av.getAlignment().getHeight() * av.charHeight
+           + hgap + seqCanvas.getAnnotationHeight();
+
+         y -= hgap;
+
+       seq = ( (y % cHeight) / av.getCharHeight());
+     }
+     else
+     {
+       seq = (y / av.getCharHeight()) + av.getStartSeq();
+     }
+
+     return seq;
+   }
+
+   void endEditing()
+   {
+     startseq = -1;
+     lastres = -1;
+     seqEditOccurred = false;
+     editingSeqs = false;
+     groupEditing = false;
+     keyboardGaps = null;
+    }
+
+
+    void moveCursor(int dx, int dy)
+    {
+      seqCanvas.cursorX += dx;
+      seqCanvas.cursorY += dy;
+
+      if(seqCanvas.cursorX<0)
+        seqCanvas.cursorX = 0;
+      else if(seqCanvas.cursorX>av.alignment.getWidth()-1)
+        seqCanvas.cursorX = av.alignment.getWidth()-1;
+      if(seqCanvas.cursorX<av.startRes)
+        ap.scrollRight(false);
+      else if(seqCanvas.cursorX>av.endRes)
+        ap.scrollRight(true);
+
+      if(seqCanvas.cursorY<0)
+        seqCanvas.cursorY=0;
+      else if(seqCanvas.cursorY>av.alignment.getHeight()-1)
+        seqCanvas.cursorY = av.alignment.getHeight()-1;
+      if(seqCanvas.cursorY<av.startSeq)
+        ap.scrollUp(true);
+      else if(seqCanvas.cursorY+1>av.endSeq)
+        ap.scrollUp(false);
+
+      setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+                       seqCanvas.cursorX, seqCanvas.cursorY);
+      seqCanvas.repaint();
+    }
+
+    void setSelectionAreaAtCursor(boolean topLeft)
+    {
+      SequenceI sequence =
+          (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+      if(av.getSelectionGroup()!=null)
       {
-        if (av.getWrapAlignment())
+        SequenceGroup sg = av.selectionGroup;
+        //Find the top and bottom of this group
+        int min = av.alignment.getHeight(), max = 0;
+        for(int i=0; i<sg.getSize(); i++)
         {
-          return;
+          int index = av.alignment.findIndex( sg.getSequenceAt(i) );
+          if(index > max)
+            max = index;
+          if(index < min)
+            min = index;
         }
 
-        if (editingSeqs)
+        max ++;
+
+        if(topLeft)
         {
-          doMouseReleased(evt);
+          sg.setStartRes(seqCanvas.cursorX);
+          if(sg.getEndRes()<seqCanvas.cursorX)
+            sg.setEndRes(seqCanvas.cursorX);
+
+          min = seqCanvas.cursorY;
         }
         else
         {
-          doMouseReleasedDefineMode(evt);
-        }
-      }
+          sg.setEndRes(seqCanvas.cursorX);
+          if(sg.getStartRes()>seqCanvas.cursorX)
+            sg.setStartRes(seqCanvas.cursorX);
 
-      public void mousePressed(MouseEvent evt)
-      {
-        if (av.getWrapAlignment())
-        {
-          return;
+          max = seqCanvas.cursorY+1;
         }
 
-        if (evt.isShiftDown() || evt.isAltDown() ||
-            evt.isControlDown())
+        if(min>max)
         {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
-
-          editingSeqs = true;
-          doMousePressed(evt);
+          // Only the user can do this
+          av.setSelectionGroup(null);
         }
         else
         {
-          doMousePressedDefineMode(evt);
+          // Now add any sequences between min and max
+          sg.sequences.clear();
+          for (int i = min; i < max; i++)
+          {
+            sg.addSequence(av.alignment.getSequenceAt(i), false);
+          }
         }
       }
 
-      public void mouseExited(MouseEvent evt)
+      if (av.getSelectionGroup() == null)
       {
-        if (av.getWrapAlignment() || editingSeqs)
-        {
-          return;
-        }
-
-        doMouseExitedDefineMode(evt);
+        SequenceGroup sg = new SequenceGroup();
+        sg.setStartRes(seqCanvas.cursorX);
+        sg.setEndRes(seqCanvas.cursorX);
+        sg.addSequence(sequence, false);
+        av.setSelectionGroup(sg);
       }
 
-      public void mouseEntered(MouseEvent evt)
-      {
-        if (av.getWrapAlignment() || editingSeqs)
-        {
-          return;
-        }
 
-        doMouseEnteredDefineMode(evt);
-      }
-    });
-  }
+      ap.repaint();
+    }
 
+    void insertGapAtCursor(boolean group)
+    {
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                   av.alignment, HistoryItem.EDIT));
+      groupEditing = group;
+      startseq = seqCanvas.cursorY;
+      lastres = seqCanvas.cursorX;
+      editSequence(true, seqCanvas.cursorX+getKeyboardGaps());
+      editOccurred();
+    }
 
-  public void doMouseReleased(MouseEvent evt)
-  {
-    if (seqEditOccurred > -1)
+    void deleteGapAtCursor(boolean group)
     {
-      editOccurred(seqEditOccurred);
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                   av.alignment, HistoryItem.EDIT));
+      groupEditing = group;
+      startseq = seqCanvas.cursorY;
+      lastres = seqCanvas.cursorX+getKeyboardGaps();
+      editSequence(false, seqCanvas.cursorX);
+      editOccurred();
     }
 
-    startseq = -1;
-    lastres = -1;
-    seqEditOccurred = -1;
-    editingSeqs = false;
-    groupEditing = false;
+    void numberPressed(char value)
+    {
+      if(keyboardGaps==null)
+        keyboardGaps = new StringBuffer();
+
+      keyboardGaps.append(value);
+    }
 
-    seqCanvas.repaint();
-  }
+    StringBuffer keyboardGaps;
+    int getKeyboardGaps()
+    {
+      if(keyboardGaps==null)
+        return 1;
+      else
+        return Integer.parseInt(keyboardGaps.toString());
+    }
 
-  public void doMousePressed(MouseEvent evt)
-  {
-    ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                 av.alignment, HistoryItem.EDIT));
 
-    int seq;
-    int res;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
+    {
+      mouseDragging = false;
+      mouseWheelPressed = false;
 
-    int x = evt.getX();
-    int y = evt.getY();
+      if (!editingSeqs)
+      {
+         doMouseReleasedDefineMode(evt);
+         return;
+      }
 
-    res = (x / av.getCharWidth()) + av.getStartRes();
-    seq = (y / av.getCharHeight()) + av.getStartSeq();
+       editOccurred();
 
-    if ( (seq < av.getAlignment().getHeight()) &&
-        (res < av.getAlignment().getSequenceAt(seq).getLength()))
-    {
-      startseq = seq;
-      lastres = res;
-    }
-    else
-    {
-      startseq = -1;
-      lastres = -1;
+       endEditing();
+       ap.repaint();
     }
 
-    startEdit = lastres;
-    endEdit = lastres;
 
-    return;
-  }
 
-  public void doMouseMoved(MouseEvent evt)
-  {
-    int res = 0;
-    int seq = 0;
-    int x = evt.getX();
-    int y = evt.getY();
-
-    if (av.wrapAlignment)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      y -= (2 * av.charHeight);
+      if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+      {
+        mouseWheelPressed = true;
+        return;
+      }
 
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+      if (evt.isShiftDown() || evt.isAltDown() ||
+          evt.isControlDown())
+      {
+        if (evt.isAltDown() || evt.isControlDown())
+        {
+          groupEditing = true;
+        }
+        editingSeqs = true;
+      }
+      else
+      {
+        doMousePressedDefineMode(evt);
+        return;
+      }
 
-      res = (int) ( (y / chunkHeight) * (getWidth() / av.charWidth)) +
-          (x / av.getCharWidth()) + av.getStartRes();
 
-      y %= chunkHeight;
-      seq = (y / av.getCharHeight()) + av.getStartSeq();
-    }
-    else
-    {
-      res = (x / av.getCharWidth()) + av.getStartRes();
-      seq = (y / av.getCharHeight()) + av.getStartSeq();
-    }
 
-    if (seq >= av.getAlignment().getHeight())
-    {
-      return;
-    }
+      int seq = findSeq(evt);
+      int res = findRes(evt);
 
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+      if(seq<0 || res<0)
+        return;
 
-    if (res > sequence.getLength())
-    {
-      return;
-    }
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                         av.alignment, HistoryItem.EDIT));
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                                                  "");
-    String aa = "";
+        if ((seq < av.getAlignment().getHeight()) &&
+                (res < av.getAlignment().getSequenceAt(seq).getLength()))
+        {
+            startseq = seq;
+            lastres = res;
+        }
+        else
+        {
+            startseq = -1;
+            lastres = -1;
+        }
 
-    if (obj != null)
-    {
-      aa = obj.toString();
+        return;
     }
 
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
-
-    if (aa != "")
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseMoved(MouseEvent evt)
     {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
-    }
+      if (editingSeqs)
+      {
+       // This is because MacOSX creates a mouseMoved
+       // If control is down, other platforms will not.
+       mouseDragged(evt);
+      }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+      int res = findRes(evt);
+      int seq = findSeq(evt);
 
-    // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
-    {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
 
-      while (e.hasMoreElements())
-      {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
+      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
+            return;
 
-        if ( (sf.getStart() <= sequence.findPosition(res)) &&
-            (sf.getEnd() >= sequence.findPosition(res)))
-        {
-          if (sbuffer.length() > 0)
-          {
-            sbuffer.append("; ");
-          }
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
+      if (res > sequence.getLength())
+      {
+        return;
+      }
 
-          if (sf.getStatus().length() > 0)
-          {
-            sbuffer.append(" (" + sf.getStatus() + ")");
-          }
-        }
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
       }
 
-      this.setToolTipText(sbuffer.toString());
-    }
-  }
+      setStatusMessage(sequence, res, seq);
 
-  public void doMouseDragged(MouseEvent evt)
-  {
-    // If we're dragging we're editing
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+        // use aa to see if the mouse pointer is on a
+        if (av.showSequenceFeatures)
+        {
+            SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
+            {
+              StringBuffer sbuffer = new StringBuffer("<html>");
 
-    if (res < 0)
-    {
-      res = 0;
+              for (int i = 0; i < features.length; i++)
+              {
+
+                if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
+                    (features[i].getEnd() >= sequence.findPosition(res)))
+                {
+                  if(av.featuresDisplayed==null
+                    || !av.featuresDisplayed.containsKey(features[i].getType()))
+                  continue;
+
+
+                  if (features[i].getType().equals("disulfide bond"))
+                  {
+                    if (features[i].getBegin() == sequence.findPosition(res)
+                        || features[i].getEnd() == sequence.findPosition(res))
+                    {
+                      if (sbuffer.length() > 6)
+                        sbuffer.append("<br>");
+                      sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
+                                     features[i].getEnd());
+                    }
+                  }
+                  else
+                  {
+                    if (sbuffer.length() > 6)
+                      sbuffer.append("<br>");
+                    if(features[i].featureGroup!=null)
+                      sbuffer.append(features[i].featureGroup+";");
+
+                    sbuffer.append(features[i].getType());
+
+                    if (features[i].getDescription() != null
+                        && !features[i].description.equals(features[i].getType()))
+                      sbuffer.append("; " + features[i].getDescription());
+
+                    if (features[i].getStatus() != null && features[i].getStatus().length()>0)
+                    {
+                      sbuffer.append("; (" + features[i].getStatus() + ")");
+                    }
+                  }
+                }
+
+              }
+
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
+            }
+            else
+              setToolTipText("");
+        }
     }
 
-    if ( (lastres == -1) || (lastres == res))
+    void setStatusMessage(SequenceI sequence, int res, int seq)
     {
-      return;
-    }
+      StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                                           sequence.getName());
 
-    boolean dragRight = true;
+      Object obj = null;
+      if (av.alignment.isNucleotide())
+      {
+        obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+                                                   "");
+        if (obj != null)
+          text.append(" Nucleotide: ");
+      }
+      else
+      {
+        obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+        if (obj != null)
+          text.append("  Residue: ");
+      }
+
+      if (obj != null)
+      {
+
+        if (obj != "")
+        {
+          text.append(obj + " (" + sequence.findPosition(res) +
+                      ")");
+        }
+      }
+      ap.alignFrame.statusBar.setText(text.toString());
 
-    if ( (res < av.getAlignment().getWidth()) && (res < lastres))
-    {
-      dragRight = false;
     }
 
-    if (res != lastres)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseDragged(MouseEvent evt)
     {
-      // Group editing
-      if (groupEditing)
+      if (!editingSeqs)
       {
-        SequenceGroup sg = av.getSelectionGroup();
+        doMouseDraggedDefineMode(evt);
+        return;
+      }
+
+        int res = findRes(evt);
 
-        if (sg == null)
+        if (res < 0)
         {
-          lastres = -1;
+            res = 0;
+        }
 
-          return;
+        if ((lastres == -1) || (lastres == res))
+        {
+            return;
         }
 
-        // drag to right
-        if (dragRight)
+        if ( (res < av.getAlignment().getWidth()) && (res < lastres))
         {
-          sg.setEndRes(sg.getEndRes() + (res - lastres));
+          // dragLeft, delete gap
+          editSequence(false, res);
         }
-        // drag to left
         else
-        {
-          /// Are we able to delete?
-          // ie are all columns blank?
-          boolean deleteAllowed = false;
+          editSequence(true, res);
 
-          for (int s = 0; s < sg.getSize(); s++)
-          {
-            SequenceI seq = sg.getSequenceAt(s);
+        mouseDragging = true;
+        if(scrollThread!=null)
+          scrollThread.setEvent(evt);
 
-            for (int j = res; j < lastres; j++)
-            {
-              if (seq.getSequence().length() <= j)
-              {
-                continue;
-              }
-
-              if (!jalview.util.Comparison.isGap(
-                  seq.getSequence().charAt(j)))
-              {
-                // Not a gap, block edit not valid
-                res = j + 1;
-                deleteAllowed = false;
+    }
 
-                continue;
-              }
+    void editSequence(boolean insertGap, int startres)
+    {
+      int fixedLeft = -1;
+      int fixedRight = -1;
+      boolean fixedColumns = false;
 
-              deleteAllowed = true;
+       if(insertGap && av.hasHiddenColumns)
+        {
+          //Stop editing if the user has dragged beyond hiddenBoundary
+          fixedRight = av.getColumnSelection().getHiddenRegionBoundary(lastres);
+          if( fixedRight < lastres)
+          {
+            if(lastres!=fixedRight)
+            {
+              endEditing();
+              return;
             }
           }
+        }
 
-          if (!deleteAllowed)
+        if (!groupEditing && av.hasHiddenRows)
+        {
+          if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
           {
-            lastres = -1;
+            groupEditing = true;
+          }
+        }
+
+
+        SequenceI seq = av.alignment.getSequenceAt(startseq);
+        StringBuffer message = new StringBuffer();
+        if (groupEditing)
+          message.append("Edit group:");
+       else
+            message.append("Edit sequence: "+seq.getName());
+
+       if(insertGap)
+         message.append(" insert ");
+       else
+         message.append(" delete ");
+
+       message.append(Math.abs(startres-lastres)+" gaps.");
+       ap.alignFrame.statusBar.setText(message.toString());
+
+
+        //Are we editing within a selection group?
+        if (groupEditing
+            || (av.getSelectionGroup() != null &&
+                av.getSelectionGroup().sequences.contains(seq)))
+        {
+          fixedColumns = true;
+
+          fixedLeft = av.getSelectionGroup().getStartRes();
+          fixedRight = av.getSelectionGroup().getEndRes();
 
+          if (   (startres < fixedLeft && lastres >= fixedLeft)
+              || (startres >= fixedLeft && lastres < fixedLeft)
+              || (startres > fixedRight && lastres <=fixedRight)
+              || (startres <= fixedRight && lastres > fixedRight))
+          {
+            endEditing();
             return;
           }
 
-          sg.setEndRes(sg.getEndRes() - (lastres - res));
+          if (fixedLeft > startres)
+          {
+            fixedRight = fixedLeft - 1;
+            fixedLeft = 0;
+          }
+          else if (fixedRight < startres)
+          {
+            fixedLeft = fixedRight;
+            fixedRight = -1;
+          }
         }
 
-        for (int i = 0; i < sg.getSize(); i++)
+        if (groupEditing)
         {
-          SequenceI s = sg.getSequenceAt(i);
-          int k = av.alignment.findIndex(s);
+          SequenceGroup sg = av.getSelectionGroup();
+          if(fixedLeft>sg.getEndRes()
+          ||fixedRight<sg.getStartRes())
+       {
+         endEditing();
+         return;
+       }
+
+          if (av.hasHiddenRows)
+          {
+            //sg might be null as the user may only see 1 sequence
+            if (sg == null)
+            {
+              sg = new SequenceGroup();
+              sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+            }
+
+            SequenceGroup tmp = new SequenceGroup();
+
+            //Do any of the sequences have hidden associates?
+            for (int s = 0; s < sg.getSize(); s++)
+            {
+              seq = sg.getSequenceAt(s);
+              tmp.addSequence(seq, false);
+              if (seq.getHiddenSequences() != null)
+              {
+                for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
+                  tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
+                                  false);
+              }
+            }
+
+            sg = tmp;
+          }
+
+          if (sg == null)
+          {
+            endEditing();
+            return;
+          }
+
+         // int blankColumn = -1;
 
           // drag to right
-          if (dragRight)
+          if (insertGap)
           {
-            for (int j = lastres; j < res; j++)
+            // Is it valid??
+            // Find the next gap before the end
+            // of the visible region boundary
+            if (av.hasHiddenColumns)
             {
-              insertChar(j, k);
+             // int lastCol = av.getColumnSelection().
+             //     getHiddenRegionBoundary(res);
+
             }
-          }
+
+              if (fixedRight != startres && fixedRight<av.alignment.getWidth()-1)
+              {
+                for (fixedRight = fixedRight;
+                     fixedRight > lastres;
+                     fixedRight --)
+                {
+                  boolean blank = true;
+                  for (int s = 0; s < sg.getSize(); s++)
+                  {
+                    seq = sg.getSequenceAt(s);
+
+                    if (seq.getSequence().length() <= fixedRight)
+                    {
+                      continue;
+                    }
+
+                    if (!jalview.util.Comparison.isGap(
+                        seq.getCharAt(fixedRight)))
+                    {
+                      blank = false;
+                      continue;
+                    }
+                  }
+                  if (blank)
+                    break;
+                }
+              }
+
+              if (fixedRight <= startres)
+              {
+                endEditing();
+                return;
+              }
+            }
+
+
           // drag to left
           else
           {
-            for (int j = res; j < lastres; j++)
+            /// Are we able to delete?
+            // ie are all columns blank?
+
+            for (int s = 0; s < sg.getSize(); s++)
             {
-              if (s.getLength() > j)
+              seq = sg.getSequenceAt(s);
+
+              for (int j = startres; j < lastres; j++)
               {
-                deleteChar(res, k);
+                if (seq.getSequence().length() <= j)
+                {
+                  continue;
+                }
+
+                if (!jalview.util.Comparison.isGap(
+                    seq.getSequence().charAt(j)))
+                {
+                  // Not a gap, block edit not valid
+                  endEditing();
+                  return;
+                }
               }
             }
           }
-        }
-      }
-      else /////Editing a single sequence///////////
-      {
-        if ( (res < av.getAlignment().getWidth()) && (res > lastres))
-        {
-          // dragging to the right
-          for (int j = lastres; j < res; j++)
+
+
+          for (int i = 0; i < sg.getSize(); i++)
           {
-            insertChar(j, startseq);
+            seq = sg.getSequenceAt(i);
+
+            if (insertGap)
+            {
+              // dragging to the right
+              for (int j = lastres; j < startres; j++)
+              {
+                if (fixedColumns && fixedRight != -1)
+                {
+                  insertChar(j, seq, fixedRight);
+                }
+                else
+                  insertChar(j, seq);
+              }
+            }
+            else
+            {
+              // dragging to the left
+              for (int j = lastres; j > startres; j--)
+              {
+                if (fixedColumns && fixedRight != -1)
+                {
+                  deleteChar(startres, seq, fixedRight);
+                }
+                else
+                {
+                  deleteChar(startres, seq);
+                }
+              }
+            }
           }
         }
-        else if ( (res < av.getAlignment().getWidth()) &&
-                 (res < lastres))
+        else /////Editing a single sequence///////////
         {
-          // dragging to the left
-          for (int j = lastres; j > res; j--)
+
+          if (insertGap)
           {
-            if (jalview.util.Comparison.isGap(
-                av.alignment.getSequenceAt(startseq)
-                .getSequence().charAt(res)))
+            // dragging to the right
+            for (int j = lastres; j < startres; j++)
             {
-              deleteChar(res, startseq);
+              if (fixedColumns && fixedRight != -1)
+                insertChar(j, seq, fixedRight);
+              else
+                insertChar(j, seq);
             }
-            else
+          }
+          else
+          {
+            // dragging to the left
+            for (int j = lastres; j > startres; j--)
             {
-              break;
+              if (fixedColumns && fixedRight != -1)
+              {
+                deleteChar(startres, seq, fixedRight);
+              }
+              else
+              {
+                deleteChar(startres, seq);
+              }
             }
           }
         }
-      }
-    }
 
-    endEdit = res;
-    lastres = res;
-    seqCanvas.repaint();
-  }
-
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
-                        seqend, av.getStartRes(), av.getStartSeq(), 0);
-    seqCanvas.repaint();
-  }
-
-  public void insertChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred = seq;
-  }
-
-  public void deleteChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred = seq;
-
-    av.alignment.getWidth();
-    seqCanvas.repaint();
-  }
-
-  void editOccurred(int i)
-  {
-    if (endEdit == startEdit)
-    {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
+        lastres = startres;
+        seqCanvas.repaint();
     }
 
-    av.updateConservation();
-    av.updateConsensus();
 
-    // Y O Y CLUSTALX
-    ColourSchemeI cs = av.getGlobalColourScheme();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    void insertChar(int j, SequenceI seq)
+    {
+        seq.insertCharAt(j, av.getGapCharacter());
+        seqEditOccurred = true;
+    }
 
-    if (cs instanceof ConservationColourScheme)
+    void insertChar(int j, SequenceI seq, int fixedColumn)
+    {
+      //Find the next gap before the end of the visible region boundary
+      //If lastCol > j, theres a boundary after the gap insertion
+      int blankColumn = fixedColumn;
+      for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
+          //Theres a space, so break and insert the gap
+          break;
+        }
+      }
+
+      if (blankColumn <= j)
+      {
+        endEditing();
+        return;
+      }
 
-      if (ccs.cs instanceof ClustalxColourScheme)
+      if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
       {
-        Conservation c = new Conservation("All",
-                                          ResidueProperties.propHash, 3,
-                                          av.alignment.getSequences(), 0,
-                                          av.alignment.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, av.ConsPercGaps);
-
-        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(),
-                          av.alignment.getWidth());
-        ccs = new ConservationColourScheme(c, cxs);
-        av.setGlobalColourScheme(ccs);
+        //Just Checking
+        System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
+        return;
       }
+
+      seq.deleteCharAt(blankColumn);
+      seq.insertCharAt(j, av.getGapCharacter());
+      seqEditOccurred = true;
     }
 
-    if (cs instanceof ClustalxColourScheme)
+    void deleteChar(int j, SequenceI seq, int fixedColumn)
     {
-      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                 av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
+      if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+      {
+        ap.alignFrame.statusBar.setText(
+            "End editing: Tried removing residue " + seq.getCharAt(j));
+        return;
+      }
+
+      seq.deleteCharAt(j);
+      seq.insertCharAt(fixedColumn, av.getGapCharacter());
+      seqEditOccurred = true;
     }
-  }
 
-  public void doMousePressedDefineMode(MouseEvent evt)
-  {
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
-    oldSeq = seq;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    void deleteChar(int j, SequenceI seq)
+    {
+      if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+      {
+        ap.alignFrame.statusBar.setText(
+            "End editing: Tried removing residue " + seq.getCharAt(j));
+        return;
+      }
 
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+        seq.deleteCharAt(j);
+        seqEditOccurred = true;
+        seqCanvas.repaint();
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent e)
+    {
+        if(oldSeq < 0)
+          oldSeq = 0;
 
-    if ( (sequence == null) || (res > sequence.getLength()))
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+            scrollThread = null;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
     {
-      return;
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
+
+        if (mouseDragging)
+        {
+            scrollThread = new ScrollThread();
+        }
     }
 
-    stretchGroup = av.getSelectionGroup();
+    public void mouseClicked(MouseEvent evt)
+    {}
 
-    if (stretchGroup == null)
+    public void mouseWheelMoved(MouseWheelEvent e)
     {
-      stretchGroup = av.alignment.findGroup(sequence);
-
-      if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
-          (res < stretchGroup.getEndRes()))
+      e.consume();
+      if (mouseWheelPressed)
       {
-        av.setSelectionGroup(stretchGroup);
+        Font font = av.getFont();
+        int fontSize = font.getSize();
+        if (e.getWheelRotation() > 0 && fontSize < 51)
+          fontSize++;
+        else if (fontSize > 1)
+          fontSize--;
+
+        av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+        ap.fontChanged();
       }
       else
       {
-        stretchGroup = null;
+        if (e.getWheelRotation() > 0)
+          ap.scrollUp(false);
+        else
+          ap.scrollUp(true);
       }
+
     }
-    else if (!stretchGroup.sequences.contains(sequence) ||
-             (stretchGroup.getStartRes() > res) ||
-             (stretchGroup.getEndRes() < res))
-    {
-      stretchGroup = null;
 
-      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
 
-      if (allGroups != null)
-      {
-        for (int i = 0; i < allGroups.length; i++)
-        {
-          if ( (allGroups[i].getStartRes() <= res) &&
-              (allGroups[i].getEndRes() >= res))
-          {
-            stretchGroup = allGroups[i];
-            av.setSelectionGroup(stretchGroup);
 
-            break;
-          }
-        }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    void editOccurred()
+    {
+      if (!seqEditOccurred)
+      {
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
       }
+
+      endEditing();
+
+      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+
     }
 
-    if (stretchGroup == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressedDefineMode(MouseEvent evt)
     {
-      // define a new group here
-      SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      sg.addSequence(sequence, false);
-      av.setSelectionGroup(sg);
-      stretchGroup = sg;
-
-      if (av.getConservationSelected())
-      {
-        SliderPanel.setConservationSlider(ap,
-                                          av.getGlobalColourScheme(),
-                                          "Background");
-      }
+      int res = findRes(evt);
+      int seq = findSeq(evt);
+      oldSeq = seq;
+
+      startWrapBlock=wrappedBlock;
 
-      if (av.getAbovePIDThreshold())
+      if(av.wrapAlignment && seq>av.alignment.getHeight())
       {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Cannot edit annotations in wrapped view.",
+              "Wrapped view - no edit",
+              JOptionPane.WARNING_MESSAGE);
+        return;
       }
-    }
-    else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
-    {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
-      pop.show(this, evt.getX(), evt.getY());
 
-      // edit the properties of existing group
-    }
+      if(seq<0 || res<0)
+            return;
 
-    if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
-    {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
-    else if ( (stretchGroup != null) && (stretchGroup.getStartRes() == res))
-    {
-      // Edit end res position of selected group
-      changeStartRes = true;
-    }
+        SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
-    stretchGroup.getWidth();
+        if ((sequence == null) || (res > sequence.getLength()))
+        {
+            return;
+        }
 
-    seqCanvas.repaint();
-  }
+        stretchGroup = av.getSelectionGroup();
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
-  {
-    if(mouseDragging)
-    {
-      stretchGroup.recalcConservation();
-      mouseDragging = false;
-    }
+        if (stretchGroup == null)
+        {
+            stretchGroup = av.alignment.findGroup(sequence);
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+            if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
+                    (res < stretchGroup.getEndRes()))
+            {
+                av.setSelectionGroup(stretchGroup);
+            }
+            else
+            {
+                stretchGroup = null;
+            }
+        }
+        else if (!stretchGroup.sequences.contains(sequence) ||
+                (stretchGroup.getStartRes() > res) ||
+                (stretchGroup.getEndRes() < res))
+        {
+            stretchGroup = null;
 
-    if (stretchGroup.cs instanceof ClustalxColourScheme)
-    {
-      ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
-                                                     stretchGroup.getWidth());
-    }
+            SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
 
-    if (stretchGroup.cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
-      stretchGroup.cs = ccs;
-      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                        stretchGroup.getName());
+            if (allGroups != null)
+            {
+                for (int i = 0; i < allGroups.length; i++)
+                {
+                    if ((allGroups[i].getStartRes() <= res) &&
+                            (allGroups[i].getEndRes() >= res))
+                    {
+                        stretchGroup = allGroups[i];
+                        av.setSelectionGroup(stretchGroup);
+
+                        break;
+                    }
+                }
+            }
+        }
 
-    }
-    else
-    {
-      SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                                     stretchGroup.getName());
-    }
+        if (av.cursorMode)
+        {
+          seqCanvas.cursorX = findRes(evt);
+          seqCanvas.cursorY = findSeq(evt);
+          seqCanvas.repaint();
+          return;
+        }
 
-    changeEndRes = false;
-    changeStartRes = false;
-    stretchGroup = null;
-    seqCanvas.repaint();
-    ap.idPanel.repaint();
-  }
 
-  public void doMouseDraggedDefineMode(MouseEvent evt)
-  {
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
+        if (stretchGroup == null)
+        {
+            // define a new group here
+            SequenceGroup sg = new SequenceGroup();
+            sg.setStartRes(res);
+            sg.setEndRes(res);
+            sg.addSequence(sequence, false);
+            av.setSelectionGroup(sg);
+            stretchGroup = sg;
+
+            if (av.getConservationSelected())
+            {
+                SliderPanel.setConservationSlider(ap,
+                    av.getGlobalColourScheme(), "Background");
+            }
 
-    if (stretchGroup == null)
-    {
-      return;
-    }
+            if (av.getAbovePIDThreshold())
+            {
+                SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                    "Background");
+            }
+        }
+        else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+        {
+            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
+            pop.show(this, evt.getX(), evt.getY());
 
-    if (res > av.alignment.getWidth())
-    {
-      res = av.alignment.getWidth() - 1;
-    }
+            // edit the properties of existing group
+        }
 
-    if (stretchGroup.getEndRes() == res)
-    {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
-    else if (stretchGroup.getStartRes() == res)
-    {
-      // Edit start res position of selected group
-      changeStartRes = true;
-    }
+        if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+        {
+            // Edit end res position of selected group
+            changeEndRes = true;
+        }
+        else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+        {
+            // Edit end res position of selected group
+            changeStartRes = true;
+        }
 
-    if (res < av.getStartRes())
-    {
-      res = av.getStartRes();
-    }
-    else if (res > av.getEndRes())
-    {
-      res = av.getEndRes();
-    }
+        stretchGroup.getWidth();
 
-    if (changeEndRes)
-    {
-      if (res > (stretchGroup.getStartRes() - 1))
-      {
-        stretchGroup.setEndRes(res);
-      }
+        seqCanvas.repaint();
     }
-    else if (changeStartRes)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleasedDefineMode(MouseEvent evt)
     {
-      if (res < (stretchGroup.getEndRes() + 1))
-      {
-        stretchGroup.setStartRes(res);
-      }
-    }
+        if (stretchGroup == null)
+        {
+            return;
+        }
 
-    int dragDirection = 0;
 
-    if (y > oldSeq)
-    {
-      dragDirection = 1;
-    }
-    else if (y < oldSeq)
-    {
-      dragDirection = -1;
+        if(stretchGroup.cs!=null)
+        {
+          if (stretchGroup.cs instanceof ClustalxColourScheme)
+          {
+            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
+                sequences,
+                stretchGroup.getWidth());
+          }
+
+          if (stretchGroup.cs.conservationApplied())
+          {
+            SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                              stretchGroup.getName());
+            stretchGroup.recalcConservation();
+          }
+          else
+          {
+            SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                                           stretchGroup.getName());
+          }
+        }
+        changeEndRes = false;
+        changeStartRes = false;
+        stretchGroup = null;
+        PaintRefresher.Refresh(av.alignment);
     }
 
-    while ( (y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDraggedDefineMode(MouseEvent evt)
     {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+      int res = findRes(evt);
+      int y = findSeq(evt);
 
-      oldSeq += dragDirection;
+      if(wrappedBlock!=startWrapBlock)
+        return;
 
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+       if (stretchGroup == null)
+       {
+            return;
+       }
 
-      if (stretchGroup.sequences.contains(nextSeq))
-      {
-        stretchGroup.deleteSequence(seq, false);
-        stretchGroup.deleteSequence(nextSeq, false);
-      }
-      else
-      {
-        if (seq != null)
+
+        if(y > av.alignment.getHeight())
         {
-          stretchGroup.addSequence(seq, false);
+          y = av.alignment.getHeight() -1;
         }
 
-        stretchGroup.addSequence(nextSeq, false);
-      }
-    }
+        if (stretchGroup.getEndRes() == res)
+        {
+            // Edit end res position of selected group
+            changeEndRes = true;
+        }
+        else if (stretchGroup.getStartRes() == res)
+        {
+            // Edit start res position of selected group
+            changeStartRes = true;
+        }
 
-    oldSeq = y;
-    mouseDragging = true;
+        if (res < av.getStartRes())
+        {
+            res = av.getStartRes();
+        }
 
-    if (scrollThread != null)
-    {
-      scrollThread.setEvent(evt);
-    }
+        if (changeEndRes)
+        {
+            if (res > (stretchGroup.getStartRes() - 1))
+            {
+                stretchGroup.setEndRes(res);
+            }
+        }
+        else if (changeStartRes)
+        {
+            if (res < (stretchGroup.getEndRes() + 1))
+            {
+                stretchGroup.setStartRes(res);
+            }
+        }
 
-    seqCanvas.repaint();
-  }
+        int dragDirection = 0;
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-  }
+        if (y > oldSeq)
+        {
+            dragDirection = 1;
+        }
+        else if (y < oldSeq)
+        {
+            dragDirection = -1;
+        }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
-  {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
 
-    if (mouseDragging)
-    {
-      scrollThread = new ScrollThread();
-    }
-  }
+        while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+        {
+            // This routine ensures we don't skip any sequences, as the
+            // selection is quite slow.
+            Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-  // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
-  {
-    MouseEvent evt;
-    boolean running = false;
+            oldSeq += dragDirection;
 
-    public ScrollThread()
-    {
-      start();
-    }
+            if(oldSeq<0)
+              break;
 
-    public void setEvent(MouseEvent e)
-    {
-      evt = e;
-    }
+            Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-    public void stopScrolling()
-    {
-      running = false;
+            if (stretchGroup.sequences.contains(nextSeq))
+            {
+                stretchGroup.deleteSequence(seq, false);
+            }
+            else
+            {
+                if (seq != null)
+                {
+                    stretchGroup.addSequence(seq, false);
+                }
+
+                stretchGroup.addSequence(nextSeq, false);
+            }
+        }
+
+        if(oldSeq < 0)
+          oldSeq = -1;
+
+        mouseDragging = true;
+
+        if (scrollThread != null)
+        {
+            scrollThread.setEvent(evt);
+        }
+
+        seqCanvas.repaint();
     }
 
-    public void run()
+
+
+    // this class allows scrolling off the bottom of the visible alignment
+    class ScrollThread extends Thread
     {
-      running = true;
+        MouseEvent evt;
+        boolean running = false;
 
-      while (running)
-      {
-        if (evt != null)
+        public ScrollThread()
         {
-          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);
-          }
+            start();
+        }
 
-          if (mouseDragging && (evt.getX() < 0))
-          {
-            running = ap.scrollRight(true);
-          }
-          else if (mouseDragging && (evt.getX() >= getWidth()))
-          {
-            running = ap.scrollRight(false);
-          }
+        public void setEvent(MouseEvent e)
+        {
+            evt = e;
         }
 
-        try
+        public void stopScrolling()
         {
-          Thread.sleep(75);
+            running = false;
         }
-        catch (Exception ex)
+
+        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(false);
+                    }
+                    else if (mouseDragging && (evt.getX() >= getWidth()))
+                    {
+                        running = ap.scrollRight(true);
+                    }
+                }
+
+                try
+                {
+                    Thread.sleep(20);
+                }
+                catch (Exception ex)
+                {
+                }
+            }
         }
-      }
     }
-  }
 }