X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2fe27b381bf84bffe35aac5fb94700b32ef764fa;hb=e25f63a72efddff9e071abdeff0ae5599431e4f8;hp=8146be0314bd1be23d4188153ce7c6111886cd20;hpb=8da7acff9214ddaf0e6d28e76219ab51bd38e62d;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8146be0..2fe27b3 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
@@ -27,8 +25,6 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 
-import java.util.*;
-
 import javax.swing.*;
 
 
@@ -38,7 +34,9 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class SeqPanel extends JPanel
+public class SeqPanel extends JPanel implements MouseListener,
+    MouseMotionListener, MouseWheelListener
+
 {
     /** DOCUMENT ME!! */
     public SeqCanvas seqCanvas;
@@ -52,7 +50,7 @@ public class SeqPanel extends JPanel
     protected AlignViewport av;
 
     // if character is inserted or deleted, we will need to recalculate the conservation
-    int seqEditOccurred = -1;
+    boolean seqEditOccurred = false;
     ScrollThread scrollThread = null;
     boolean mouseDragging = false;
     boolean editingSeqs = false;
@@ -91,116 +89,12 @@ public class SeqPanel extends JPanel
 
         ap = p;
 
-        addMouseMotionListener(new MouseMotionAdapter()
-            {
-                public void mouseMoved(MouseEvent evt)
-                {
-                    doMouseMoved(evt);
-                }
-
-                public void mouseDragged(MouseEvent evt)
-                {
-                    if (editingSeqs)
-                    {
-                        doMouseDragged(evt);
-                    }
-                    else
-                    {
-                        doMouseDraggedDefineMode(evt);
-                    }
-                }
-            });
-
-       addMouseWheelListener(new MouseWheelListener()
-       {
-         public void mouseWheelMoved(MouseWheelEvent e)
-         {
-
-           if (mouseWheelPressed)
-           {
-             Font font = av.getFont();
-             int fontSize = font.getSize();
-             if (e.getWheelRotation() > 0 && fontSize < 30)
-               fontSize++;
-             else if (fontSize > 1)
-               fontSize--;
-
-             av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
-             ap.fontChanged();
-           }
-           else
-           {
-             if (e.getWheelRotation() > 0)
-               ap.scrollUp(false);
-             else
-               ap.scrollUp(true);
-           }
-
-         }
-       });
-
-
-        addMouseListener(new MouseAdapter()
-            {
-                public void mouseReleased(MouseEvent evt)
-                {
-                    mouseWheelPressed = false;
-
-                    if (editingSeqs)
-                    {
-                        doMouseReleased(evt);
-                    }
-                    else
-                    {
-                        doMouseReleasedDefineMode(evt);
-                    }
-                }
-
-                public void mousePressed(MouseEvent evt)
-                {
-                  if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))
-                  {
-                    mouseWheelPressed = true;
-                    return;
-                  }
-
-                    if (evt.isShiftDown() || evt.isAltDown() ||
-                            evt.isControlDown())
-                    {
-                        if (evt.isAltDown() || evt.isControlDown())
-                        {
-                            groupEditing = true;
-                        }
-
-                        editingSeqs = true;
-                        doMousePressed(evt);
-                    }
-                    else
-                    {
-                        doMousePressedDefineMode(evt);
-                    }
-                }
-
-                public void mouseExited(MouseEvent evt)
-                {
-                  if (editingSeqs)
-                  {
-                    return;
-                  }
-
-                  doMouseExitedDefineMode(evt);
-                }
-
-                public void mouseEntered(MouseEvent evt)
-                {
-                  if (editingSeqs)
-                  {
-                    return;
-                  }
-
-                    doMouseEnteredDefineMode(evt);
-                }
-            });
+        if(!av.isDataset())
+        {
+          addMouseMotionListener(this);
+          addMouseListener(this);
+          addMouseWheelListener(this);
+        }
     }
 
     int startWrapBlock=-1;
@@ -212,36 +106,57 @@ public class SeqPanel extends JPanel
 
     if (av.wrapAlignment)
     {
+
+      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 -= (2 * av.charHeight);
+        y -= hgap;
         x -= seqCanvas.LABEL_WEST;
 
-        int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+
         int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
-        wrappedBlock = y/chunkHeight;
-        wrappedBlock += av.getStartRes()/cwidth;
 
-        res = wrappedBlock*cwidth   +   x / av.getCharWidth();
+        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)
      {
-       y -= (2 * av.charHeight);
-       int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-       seq = ( (y % chunkHeight) / av.getCharHeight());
+       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
      {
@@ -251,35 +166,70 @@ public class SeqPanel extends JPanel
      return seq;
    }
 
+   void endEditing()
+   {
+     startseq = -1;
+     lastres = -1;
+     seqEditOccurred = false;
+     editingSeqs = false;
+     groupEditing = false;
+    }
 
     /**
      * DOCUMENT ME!
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMouseReleased(MouseEvent evt)
+    public void mouseReleased(MouseEvent evt)
     {
-        if (seqEditOccurred > -1)
+      mouseDragging = false;
+
+      if (!editingSeqs)
+      {
+         doMouseReleasedDefineMode(evt);
+         return;
+      }
+
+        if (seqEditOccurred)
         {
-            editOccurred(seqEditOccurred);
+            editOccurred();
         }
 
-        startseq = -1;
-        lastres = -1;
-        seqEditOccurred = -1;
-        editingSeqs = false;
-        groupEditing = false;
-
+        endEditing();
         ap.repaint();
     }
 
+
+
     /**
      * DOCUMENT ME!
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMousePressed(MouseEvent evt)
+    public void mousePressed(MouseEvent evt)
     {
+      if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+      {
+        mouseWheelPressed = true;
+        return;
+      }
+
+      if (evt.isShiftDown() || evt.isAltDown() ||
+          evt.isControlDown())
+      {
+        if (evt.isAltDown() || evt.isControlDown())
+        {
+          groupEditing = true;
+        }
+        editingSeqs = true;
+      }
+      else
+      {
+        doMousePressedDefineMode(evt);
+        return;
+      }
+
+
       ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
                                                    av.alignment, HistoryItem.EDIT));
 
@@ -312,8 +262,15 @@ public class SeqPanel extends JPanel
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMouseMoved(MouseEvent evt)
+    public void mouseMoved(MouseEvent evt)
     {
+      if (editingSeqs)
+      {
+       // This is because MacOSX creates a mouseMoved
+       // If control is down, other platforms will not.
+       mouseDragged(evt);
+      }
+
       int res = findRes(evt);
       int seq = findSeq(evt);
 
@@ -324,25 +281,41 @@ public class SeqPanel extends JPanel
 
       if (res > sequence.getLength())
       {
-          return;
-        }
+        return;
+      }
 
-        Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                "");
-        String aa = "";
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
 
-        if (obj != null)
-        {
-            aa = obj.toString();
-        }
 
         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
                 sequence.getName());
 
-        if (aa != "")
+        Object obj = null;
+        if (av.alignment.isNucleotide())
         {
-            text.append("  Residue: " + aa + " (" +
-                av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          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 + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
         }
 
         ap.alignFrame.statusBar.setText(text.toString());
@@ -350,32 +323,62 @@ public class SeqPanel extends JPanel
         // 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 [] features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
             {
-                SequenceFeature sf = (SequenceFeature) e.nextElement();
+              StringBuffer sbuffer = new StringBuffer("<html>");
 
-                if ((sf.getStart() <= sequence.findPosition(res)) &&
-                        (sf.getEnd() >= sequence.findPosition(res)))
+              for (int i = 0; i < features.length; i++)
+              {
+
+                if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
+                    (features[i].getEnd() >= sequence.findPosition(res)))
                 {
-                    if (sbuffer.length() > 0)
+                  if(!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))
                     {
-                        sbuffer.append("; ");
+                      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(sf.getType() + " " + sf.getDescription());
+                    sbuffer.append(features[i].getType());
 
-                    if (sf.getStatus().length() > 0)
+                    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(" (" + sf.getStatus() + ")");
+                      sbuffer.append("; (" + features[i].getStatus() + ")");
                     }
+                  }
                 }
-            }
 
-            this.setToolTipText(sbuffer.toString());
+              }
+
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
+            }
+            else
+              setToolTipText("");
         }
     }
 
@@ -384,9 +387,14 @@ public class SeqPanel extends JPanel
      *
      * @param evt DOCUMENT ME!
      */
-    public void doMouseDragged(MouseEvent evt)
+    public void mouseDragged(MouseEvent evt)
     {
-        // If we're dragging we're editing
+      if (!editingSeqs)
+      {
+        doMouseDraggedDefineMode(evt);
+        return;
+      }
+
         int res = findRes(evt);
 
         if (res < 0)
@@ -405,25 +413,131 @@ public class SeqPanel extends JPanel
         {
             dragRight = false;
         }
+        else if(av.hasHiddenColumns)
+        {
+          //Stop editing if the user has dragged beyond hiddenBoundary
+          int lastCol = av.getColumnSelection().getHiddenRegionBoundary(lastres);
+          if( lastCol < res)
+          {
+            if(lastres!=lastCol)
+            {
+              endEditing();
+              return;
+            }
+          }
+        }
+
+        if(!groupEditing && av.hasHiddenRows)
+        {
+          if(av.alignment.getSequenceAt(startseq).getHiddenSequences()!=null)
+          {
+            groupEditing = true;
+          }
+        }
+
 
         if (res != lastres)
         {
+            SequenceI seq;
             // Group editing
             if (groupEditing)
             {
                 SequenceGroup sg = av.getSelectionGroup();
 
-                if (sg == null)
+                if (av.hasHiddenRows)
                 {
-                    lastres = -1;
+                  //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)
                 {
-                    sg.setEndRes(sg.getEndRes() + (res - lastres));
+
+                  // Is it valid??
+                  // Find the next gap before the end
+                  // of the visible region boundary
+                  if (av.hasHiddenColumns)
+                  {
+                    if(res-lastres > 1)
+                    {
+                      res = lastres+1;
+                    }
+
+
+                    int lastCol = av.getColumnSelection().
+                          getHiddenRegionBoundary(res);
+
+                    if(lastCol!=res)
+                    {
+                      for (blankColumn = lastCol;
+                           blankColumn > lastres;
+                           blankColumn--)
+                      {
+                        boolean blank = true;
+                        for (int s = 0; s < sg.getSize(); s++)
+                        {
+                          seq = sg.getSequenceAt(s);
+
+                          if (seq.getSequence().length() <= blankColumn)
+                          {
+                            continue;
+                          }
+
+                          if (!jalview.util.Comparison.isGap(
+                              seq.getSequence().charAt(blankColumn)))
+                          {
+                            blank = false;
+                            continue;
+                          }
+                        }
+                        if (blank)
+                          break;
+                      }
+
+
+                      if (blankColumn <= lastres)
+                      {
+                        endEditing();
+                        return;
+                      }
+                    }
+                    else
+                      blankColumn = -1;
+
+                  }
+
+                  sg.setEndRes(sg.getEndRes() + (res - lastres));
                 }
 
                 // drag to left
@@ -431,11 +545,10 @@ public class SeqPanel extends JPanel
                 {
                     /// Are we able to delete?
                     // ie are all columns blank?
-                    boolean deleteAllowed = false;
 
                     for (int s = 0; s < sg.getSize(); s++)
                     {
-                        SequenceI seq = sg.getSequenceAt(s);
+                        seq = sg.getSequenceAt(s);
 
                         for (int j = res; j < lastres; j++)
                         {
@@ -448,37 +561,29 @@ public class SeqPanel extends JPanel
                                         seq.getSequence().charAt(j)))
                             {
                                 // Not a gap, block edit not valid
-                                res = j + 1;
-                                deleteAllowed = false;
-
-                                continue;
+                                endEditing();
+                                return;
                             }
-
-                            deleteAllowed = true;
                         }
                     }
 
-                    if (!deleteAllowed)
+                    if(res<sg.getStartRes())
                     {
-                        lastres = -1;
-
-                        return;
+                      sg.setStartRes(sg.getStartRes() - 1);
                     }
-
                     sg.setEndRes(sg.getEndRes() - (lastres - res));
                 }
 
                 for (int i = 0; i < sg.getSize(); i++)
                 {
-                    SequenceI s = sg.getSequenceAt(i);
-                    int k = av.alignment.findIndex(s);
+                    seq = sg.getSequenceAt(i);
 
                     // drag to right
                     if (dragRight)
                     {
                         for (int j = lastres; j < res; j++)
                         {
-                            insertChar(j, k);
+                            insertChar(j, seq, blankColumn);
                         }
                     }
 
@@ -487,9 +592,9 @@ public class SeqPanel extends JPanel
                     {
                         for (int j = res; j < lastres; j++)
                         {
-                            if (s.getLength() > j)
+                            if (seq.getLength()-1 > res)
                             {
-                                deleteChar(res, k);
+                                deleteChar(res, seq);
                             }
                         }
                     }
@@ -497,12 +602,13 @@ public class SeqPanel extends JPanel
             }
             else /////Editing a single sequence///////////
             {
+                seq = av.alignment.getSequenceAt(startseq);
                 if ((res < av.getAlignment().getWidth()) && (res > lastres))
                 {
                     // dragging to the right
                     for (int j = lastres; j < res; j++)
                     {
-                        insertChar(j, startseq);
+                        insertChar(j, seq, j);
                     }
                 }
                 else if ((res < av.getAlignment().getWidth()) &&
@@ -515,7 +621,7 @@ public class SeqPanel extends JPanel
                                     av.alignment.getSequenceAt(startseq)
                                                     .getSequence().charAt(res)))
                         {
-                            deleteChar(res, startseq);
+                            deleteChar(res, seq);
                         }
                         else
                         {
@@ -526,6 +632,10 @@ public class SeqPanel extends JPanel
             }
         }
 
+        mouseDragging = true;
+        if(scrollThread!=null)
+          scrollThread.setEvent(evt);
+
         endEdit = res;
         lastres = res;
         seqCanvas.repaint();
@@ -534,27 +644,111 @@ public class SeqPanel extends JPanel
     /**
      * DOCUMENT ME!
      *
-     * @param seqstart DOCUMENT ME!
-     * @param seqend DOCUMENT ME!
-     * @param start DOCUMENT ME!
+     * @param e DOCUMENT ME!
      */
-    public void drawChars(int seqstart, int seqend, int start)
+    public void mouseEntered(MouseEvent e)
     {
-        seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
-            seqend, av.getStartRes(), av.getStartSeq(), 0);
-        seqCanvas.repaint();
+        if(oldSeq < 0)
+          oldSeq = 0;
+
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+            scrollThread = null;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent e)
+    {
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
+
+        if (mouseDragging)
+        {
+            scrollThread = new ScrollThread();
+        }
+    }
+
+    public void mouseClicked(MouseEvent evt)
+    {}
+
+    public void mouseWheelMoved(MouseWheelEvent e)
+    {
+      if (mouseWheelPressed)
+      {
+        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
+      {
+        if (e.getWheelRotation() > 0)
+          ap.scrollUp(false);
+        else
+          ap.scrollUp(true);
+      }
+
     }
 
+
     /**
      * DOCUMENT ME!
      *
      * @param j DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public void insertChar(int j, int seq)
+    void insertChar(int j, SequenceI seq, int blankColumn)
     {
-        av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-        seqEditOccurred = seq;
+        if(av.hasHiddenColumns)
+        {
+          //Find the next gap before the end of the visible region boundary
+          int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);
+          if(lastCol != j)
+          {
+            if (!groupEditing || lastCol <= j)
+            {
+              blankColumn = lastCol;
+              //If lastCol > j, theres a boundary after the gap insertion
+              if (lastCol > j)
+              {
+                for (blankColumn = lastCol; blankColumn > j; blankColumn--)
+                {
+                  if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
+                  {
+                    //Theres a space, so break and insert the gap
+                    break;
+                  }
+                }
+
+                if (blankColumn <= j)
+                {
+                  endEditing();
+                  return;
+                }
+              }
+
+            }
+
+            // Editing with hidden regions only!!
+            seq.deleteCharAt(blankColumn);
+          }
+      }
+
+        seq.insertCharAt(j, av.getGapCharacter());
+        seqEditOccurred = true;
     }
 
     /**
@@ -563,12 +757,23 @@ public class SeqPanel extends JPanel
      * @param j DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public void deleteChar(int j, int seq)
+    public void deleteChar(int j, SequenceI seq)
     {
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
-        seqEditOccurred = seq;
+      if (av.hasHiddenColumns)
+      {
+        //Find the next gap before the end of the visible region boundary
+        int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);
+
+        //If lastCol > j, theres a boundary after the gap insertion
+        if (lastCol > j)
+        {
+          seq.insertCharAt(lastCol, av.getGapCharacter());
+        }
+      }
+
+        seq.deleteCharAt(j);
+        seqEditOccurred = true;
 
-        av.alignment.getWidth();
         seqCanvas.repaint();
     }
 
@@ -577,7 +782,7 @@ public class SeqPanel extends JPanel
      *
      * @param i DOCUMENT ME!
      */
-    void editOccurred(int i)
+    void editOccurred()
     {
       if (endEdit == startEdit)
       {
@@ -602,8 +807,18 @@ public class SeqPanel extends JPanel
 
       startWrapBlock=wrappedBlock;
 
-      if(seq<0 || res<0)
+      if(av.wrapAlignment && seq>av.alignment.getHeight())
+      {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Cannot edit annotations in wrapped view.",
+              "Wrapped view - no edit",
+              JOptionPane.WARNING_MESSAGE);
         return;
+      }
+
+      if(seq<0 || res<0)
+            return;
+
 
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -705,17 +920,12 @@ public class SeqPanel extends JPanel
      */
     public void doMouseReleasedDefineMode(MouseEvent evt)
     {
-        if (mouseDragging)
-        {
-            stretchGroup.recalcConservation();
-            mouseDragging = false;
-        }
-
         if (stretchGroup == null)
         {
             return;
         }
 
+
         if(stretchGroup.cs!=null)
         {
           if (stretchGroup.cs instanceof ClustalxColourScheme)
@@ -729,6 +939,7 @@ public class SeqPanel extends JPanel
           {
             SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                               stretchGroup.getName());
+            stretchGroup.recalcConservation();
           }
           else
           {
@@ -755,14 +966,15 @@ public class SeqPanel extends JPanel
       if(wrappedBlock!=startWrapBlock)
         return;
 
-      if (stretchGroup == null)
-      {
+       if (stretchGroup == null)
+       {
             return;
-        }
+       }
+
 
-        if (res > av.alignment.getWidth())
+        if(y > av.alignment.getHeight())
         {
-            res = av.alignment.getWidth() - 1;
+          y = av.alignment.getHeight() -1;
         }
 
         if (stretchGroup.getEndRes() == res)
@@ -780,10 +992,6 @@ public class SeqPanel extends JPanel
         {
             res = av.getStartRes();
         }
-        else if (res > av.getEndRes() && !av.getWrapAlignment())
-        {
-            res = av.getEndRes();
-        }
 
         if (changeEndRes)
         {
@@ -811,7 +1019,8 @@ public class SeqPanel extends JPanel
             dragDirection = -1;
         }
 
-        while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
+
+        while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
         {
             // This routine ensures we don't skip any sequences, as the
             // selection is quite slow.
@@ -819,6 +1028,9 @@ public class SeqPanel extends JPanel
 
             oldSeq += dragDirection;
 
+            if(oldSeq<0)
+              break;
+
             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
             if (stretchGroup.sequences.contains(nextSeq))
@@ -836,7 +1048,9 @@ public class SeqPanel extends JPanel
             }
         }
 
-        oldSeq = y;
+        if(oldSeq < 0)
+          oldSeq = -1;
+
         mouseDragging = true;
 
         if (scrollThread != null)
@@ -847,36 +1061,7 @@ public class SeqPanel extends JPanel
         seqCanvas.repaint();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void doMouseEnteredDefineMode(MouseEvent e)
-    {
-        if (scrollThread != null)
-        {
-            scrollThread.running = false;
-        }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    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
@@ -931,7 +1116,7 @@ public class SeqPanel extends JPanel
 
                 try
                 {
-                    Thread.sleep(75);
+                    Thread.sleep(20);
                 }
                 catch (Exception ex)
                 {