X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3209960d6f183e9a9901884df259378a40a9f61a;hb=eacce9627f059fc2f9e880c81d8d1bdfbe7fe5b3;hp=5d2a741c35b14859044dc32267e6a50dade548a2;hpb=0e54db5074938de828bc20412dfd59898fafc7db;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 5d2a741..3209960 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,445 +1,1020 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import jalview.datamodel.*;
+
+import java.util.*;
+
 import javax.swing.*;
-import jalview.schemes.*;
-import jalview.analysis.*;
 
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SeqPanel extends JPanel
 {
+    /** DOCUMENT ME!! */
+    public SeqCanvas seqCanvas;
+
+    /** DOCUMENT ME!! */
+    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;
+
+    boolean mouseWheelPressed = false;
+
+    /**
+     * Creates a new SeqPanel object.
+     *
+     * @param avp DOCUMENT ME!
+     * @param p DOCUMENT ME!
+     */
+    public SeqPanel(AlignViewport avp, AlignmentPanel p)
+    {
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+        this.av = avp;
+        setBackground(Color.white);
 
-  public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    parent;
-
-  protected int startres;
-  protected int lastres;
-  protected int endres;
-
-  protected int startseq;
-  protected int padseq;
+        seqCanvas = new SeqCanvas(avp);
+        setLayout(new BorderLayout());
+        add(seqCanvas, BorderLayout.CENTER);
 
-  protected AlignViewport av;
+        ap = p;
 
-  // if character is inserted or deleted, we will need to recalculate the conservation
-  int seqEditOccurred = -1;
 
-  public SeqPanel(AlignViewport avp, AlignmentPanel p) {
-    this.av         = avp;
+        addMouseMotionListener(new MouseMotionAdapter()
+            {
+                public void mouseMoved(MouseEvent evt)
+                {
+                    doMouseMoved(evt);
+                    if (editingSeqs)
+                    {
+                      // This is because MacOSX creates a mouseMoved
+                      // If control is down
+                      if(!av.isDataset())
+                        doMouseDragged(evt);
+                    }
+                }
 
-    seqCanvas  = new SeqCanvas(avp);
-    setLayout(new BorderLayout());
-    add(seqCanvas, BorderLayout.CENTER);
+                public void mouseDragged(MouseEvent evt)
+                {
+                    if (editingSeqs)
+                    {
+                      if(!av.isDataset())
+                        doMouseDragged(evt);
+                    }
+                    else
+                    {
+                      if(!av.isDataset())
+                        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 < 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);
+           }
+
+         }
+       });
+
+
+       if(!av.isDataset())
+       {
+         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);
+           }
+         });
+       }
+    }
 
-    parent = p;
+    int startWrapBlock=-1;
+    int wrappedBlock=-1;
+    int findRes(MouseEvent evt)
+   {
+     int res = 0;
+     int x = evt.getX();
 
-    addMouseMotionListener( new MouseMotionAdapter()
+    if (av.wrapAlignment)
     {
-      public void mouseMoved(MouseEvent evt)
-      {   doMouseMoved(evt);    }
 
-      public void mouseDragged(MouseEvent evt)
-      {
-        if(evt.isShiftDown() || evt.isControlDown())
-          doMouseDragged(evt);
-        else
-          doMouseDraggedDefineMode(evt);
-      }
-    });
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+        hgap += av.charHeight;
 
-    addMouseListener( new MouseAdapter()
-    {
-      public void mouseReleased(MouseEvent evt)
-      {
-        if(evt.isShiftDown() || evt.isControlDown())
-          doMouseReleased(evt);
-        else
-          doMouseReleasedDefineMode(evt);
-      }
-      public void mousePressed(MouseEvent evt)
-      {
-        if(evt.isShiftDown() || evt.isControlDown())
-          doMousePressed(evt);
-        else
-          doMousePressedDefineMode(evt);
-      }
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
-    });
-    repaint();
-  }
+        int y = evt.getY();
+        y -= hgap;
+        x -= seqCanvas.LABEL_WEST;
 
 
-  public void doMouseReleased(MouseEvent evt) {
+        int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
 
-    int x = evt.getX();
-    int res = x/av.getCharWidth() + av.getStartRes();
+        wrappedBlock = y / cHeight;
+        wrappedBlock += av.getStartRes() / cwidth;
 
-    endres = res;
+        res = wrappedBlock * cwidth + x / av.getCharWidth();
 
-    startseq = -1;
-    startres = -1;
-    lastres  = -1;
-    if(seqEditOccurred>-1)
-      updateConservation(seqEditOccurred);
+    }
+    else
+    {
+        res = (x / av.getCharWidth()) + av.getStartRes();
+    }
 
-    seqEditOccurred = -1;
+    return res;
 
-    parent.RefreshPanels();
-    repaint();
+   }
 
-  }
+   int findSeq(MouseEvent evt)
+   {
 
-  public void doMousePressed(MouseEvent evt) {
-    parent.alignFrame.addHistoryItem("sequence edit");
-    int seq;
-    int res;
+     int seq = 0;
+     int y = evt.getY();
 
-    int x = evt.getX();
-    int y = evt.getY();
+     if (av.wrapAlignment)
+     {
+       int hgap = av.charHeight;
+       if (av.scaleAboveWrapped)
+         hgap += av.charHeight;
 
-    res = x/av.getCharWidth() + av.getStartRes();
-    seq = y/av.getCharHeight() + av.getStartSeq();
+       int cHeight = av.getAlignment().getHeight() * av.charHeight
+           + hgap + seqCanvas.getAnnotationHeight();
 
-    if (seq < av.getAlignment().getHeight() &&
-        res < av.getAlignment().getSequenceAt(seq).getLength())
-    {
-      //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
-      // Find the residue's position in the sequence (res is the position
-      // in the alignment
+         y -= hgap;
 
-      startseq = seq;
+       seq = ( (y % cHeight) / av.getCharHeight());
+     }
+     else
+     {
+       seq = (y / av.getCharHeight()) + av.getStartSeq();
+     }
 
-      if (startseq == (av.getAlignment().getHeight() - 1))
-        padseq = 1;
-      else
-        padseq = 1;
+     return seq;
+   }
 
-      startres = res;
-      lastres = res;
 
-    }
-    else
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleased(MouseEvent evt)
     {
-      startseq = -1;
-      startres = -1;
-      lastres = -1;
-    }
+        if (seqEditOccurred > -1)
+        {
+            editOccurred(seqEditOccurred);
+        }
+
+        startseq = -1;
+        lastres = -1;
+        seqEditOccurred = -1;
+        editingSeqs = false;
+        groupEditing = false;
 
-    return;
-  }
+        ap.repaint();
+    }
 
-  public void doMouseMoved(MouseEvent evt)
-  {
-    int res=0, seq=0;
-    int x = evt.getX();
-    int y = evt.getY();
-    if(av.wrapAlignment)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMousePressed(MouseEvent evt)
     {
-      y -= 2*av.charHeight;
-      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                   av.alignment, HistoryItem.EDIT));
 
+      int seq = findSeq(evt);
+      int res = findRes(evt);
 
-      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  x/av.getCharWidth() + av.getStartRes();
+      if(seq<0 || res<0)
+        return;
+
+        if ((seq < av.getAlignment().getHeight()) &&
+                (res < av.getAlignment().getSequenceAt(seq).getLength()))
+        {
+            startseq = seq;
+            lastres = res;
+        }
+        else
+        {
+            startseq = -1;
+            lastres = -1;
+        }
 
-      y %= chunkHeight;
-      seq =     y / av.getCharHeight() + av.getStartSeq();
+        startEdit = lastres;
+        endEdit = lastres;
 
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
-      //  startx += chunkWidth;
+        return;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseMoved(MouseEvent evt)
     {
-      res = x / av.getCharWidth()  + av.getStartRes();
-      seq = y / av.getCharHeight() + av.getStartSeq();
-    }
+      int res = findRes(evt);
+      int seq = findSeq(evt);
 
+      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
+            return;
 
-    if(seq>=av.getAlignment().getHeight())
-      return;
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
-    String aa = "";
-    if(obj!=null)
-         aa = obj.toString();
+      if (res > sequence.getLength())
+      {
+        return;
+      }
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
-    if(aa!="")
-      text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
 
-    parent.alignFrame.statusBar.setText(text.toString());
 
-  }
+        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                sequence.getName());
+
+        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: ");
+        }
 
-  public void doMouseDragged(MouseEvent evt) {
-    // If we're dragging we're editing
+        if (obj != null)
+        {
 
-    int x = evt.getX();
+          if (obj != "")
+          {
+            text.append( obj + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
+        }
 
-    int res = x/av.getCharWidth() + av.getStartRes();
-    if (res < 0)
-      res = 0;
+        ap.alignFrame.statusBar.setText(text.toString());
 
-    if (res != lastres)
-    {
-	// Group editing
-	if (evt.isControlDown())
+        // use aa to see if the mouse pointer is on a
+        if (av.showSequenceFeatures)
         {
-	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
-          if (sg != null)
-          {
-            boolean deleteAllowed = false;
-            if (res < av.getAlignment().getWidth() && res < lastres)
+            Vector features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
             {
-              /// Are we able to delete?
-              boolean allGaps = true;
-              for (int i = 0; i < sg.getSize(); i++)
+              StringBuffer sbuffer = new StringBuffer("<html>");
+
+              for (int i = 0; i < features.size(); i++)
               {
-                SequenceI s = sg.getSequenceAt(i);
-                for (int j = lastres-1; j >= res && allGaps; j--)
+                SequenceFeature sf = (SequenceFeature) features.elementAt(i);
+
+                if ( (sf.getBegin() <= sequence.findPosition(res)) &&
+                    (sf.getEnd() >= sequence.findPosition(res)))
                 {
-                    if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))
+                  if (sf.getType().equals("disulfide bond"))
+                  {
+                    if (sf.getBegin() == sequence.findPosition(res)
+                        || sf.getEnd() == sequence.findPosition(res))
+                    {
+                      if (sbuffer.length() > 6)
+                        sbuffer.append("<br>");
+                      sbuffer.append("disulfide bond " + sf.getBegin() + ":" +
+                                     sf.getEnd());
+                    }
+                  }
+                  else
+                  {
+                    if (sbuffer.length() > 6)
+                      sbuffer.append("<br>");
+                    sbuffer.append(sf.getType());
+                    if (sf.getDescription() != null)
+                      sbuffer.append(" " + sf.getDescription());
+
+                    if (sf.getStatus() != null)
                     {
-                      res = j + 1;
-                      allGaps = false;
+                      sbuffer.append(" (" + sf.getStatus() + ")");
                     }
+                  }
                 }
 
-                if(!deleteAllowed && allGaps)
-                  deleteAllowed = true;
-
               }
+
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
             }
+            else
+              setToolTipText("");
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDragged(MouseEvent evt)
+    {
+        // If we're dragging we're editing
+        int res = findRes(evt);
+
+        if (res < 0)
+        {
+            res = 0;
+        }
+
+        if ((lastres == -1) || (lastres == res))
+        {
+            return;
+        }
+
+        boolean dragRight = true;
 
+        if ((res < av.getAlignment().getWidth()) && (res < lastres))
+        {
+            dragRight = false;
+        }
 
-            for (int i = 0; i < sg.getSize(); i++)
+        if (res != lastres)
+        {
+            // Group editing
+            if (groupEditing)
             {
-              SequenceI s = sg.getSequenceAt(i);
-              int k = av.alignment.findIndex(s);
+                SequenceGroup sg = av.getSelectionGroup();
 
-              // drag to right
-              if (res < av.getAlignment().getWidth() && res > lastres)
-                for (int j = lastres; j < res; j++)
-                  insertChar(j, k);
+                if (sg == null)
+                {
+                    lastres = -1;
 
-              // drag to left
-              else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)
-              {
-                for (int j = res; j < lastres; j++)
+                    return;
+                }
+
+                // drag to right
+                if (dragRight)
                 {
-                  deleteChar(j, k);
-                  startres = res;
+                    sg.setEndRes(sg.getEndRes() + (res - lastres));
+                }
+
+                // drag to left
+                else
+                {
+                    /// 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);
+
+                        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;
+                            }
+
+                            deleteAllowed = true;
+                        }
+                    }
+
+                    if (!deleteAllowed)
+                    {
+                        lastres = -1;
+
+                        return;
+                    }
+
+                    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);
+
+                    // drag to right
+                    if (dragRight)
+                    {
+                        for (int j = lastres; j < res; j++)
+                        {
+                            insertChar(j, k);
+                        }
+                    }
+
+                    // drag to left
+                    else
+                    {
+                        for (int j = res; j < lastres; j++)
+                        {
+                            if (s.getLength() > j)
+                            {
+                                deleteChar(res, k);
+                            }
+                        }
+                    }
                 }
-              }
             }
-          }
-        }
-        else /////Editing a single sequence///////////
-        {
-          if (res < av.getAlignment().getWidth() && res > lastres)
-          {
-            // dragging to the right
-            for (int j = lastres; j < res; j++)
-              insertChar(j, startseq);
-          }
-          else if (res < av.getAlignment().getWidth() && res < lastres)
-          {
-            // dragging to the left
-            for (int j = res; j < lastres; j++)
+            else /////Editing a single sequence///////////
             {
-              deleteChar(j, startseq);
-              startres = res;
+                if ((res < av.getAlignment().getWidth()) && (res > lastres))
+                {
+                    // dragging to the right
+                    for (int j = lastres; j < res; j++)
+                    {
+                        insertChar(j, startseq);
+                    }
+                }
+                else if ((res < av.getAlignment().getWidth()) &&
+                        (res < lastres))
+                {
+                    // dragging to the left
+                    for (int j = lastres; j > res; j--)
+                    {
+                        if (jalview.util.Comparison.isGap(
+                                    av.alignment.getSequenceAt(startseq)
+                                                    .getSequence().charAt(res)))
+                        {
+                            deleteChar(res, startseq);
+                        }
+                        else
+                        {
+                            break;
+                        }
+                    }
+                }
             }
-	  }
+        }
 
-	}
+        endEdit = res;
+        lastres = res;
+        seqCanvas.repaint();
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seqstart DOCUMENT ME!
+     * @param seqend DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     */
+    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();
     }
 
-    lastres = res;
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public void insertChar(int j, int seq)
+    {
+        av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
+        seqEditOccurred = seq;
+    }
 
-  public void drawChars(int seqstart, int seqend, int start) {
-    seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
-    repaint();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param j DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     */
+    public void deleteChar(int j, int seq)
+    {
+        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+        seqEditOccurred = seq;
 
-  public void insertChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred=seq;
-  }
+        av.alignment.getWidth();
+        seqCanvas.repaint();
+    }
 
-  public void deleteChar(int j, int seq)
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    void editOccurred(int i)
+    {
+      if (endEdit == startEdit)
+      {
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
+      }
 
-    if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
 
-    av.alignment.getWidth();
-    repaint();
-    seqEditOccurred=seq;
-  }
-
-
-  void updateConservation(int i)
-  {
-  /*  Alignment al = (Alignment) av.getAlignment();
-    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
-    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
-      return;
-
-    Conservation c = sg.getConservation();
-
-    c = new Conservation("All", al.cons,
-                         ResidueProperties.propHash, 3, sg.sequences, 0,
-                         al.getWidth());
-    c.calculate();
-    c.verdict(false, 100);
-    sg.setConservation(c);
-    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;*/
-  }
-
-//////////////////////////////////////////
-/////Everything below this is for defining the boundary of the rubberband
-//////////////////////////////////////////
-  int oldSeq = -1;
-  public void doMousePressedDefineMode(MouseEvent evt)
-  {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
-    oldSeq = seq;
-
-    stretchGroup = av.getRubberbandGroup();
-
-    if(stretchGroup == null)
-        stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
-
-    else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
-            || stretchGroup.getStartRes()>res
-            || stretchGroup.getEndRes()<res)
-     {
-       stretchGroup = null;
-     }
+    }
 
-    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)av.getAlignment().getSequenceAt(seq) );
-      av.setRubberbandGroup( sg );
-      stretchGroup = sg;
+      int res = findRes(evt);
+      int seq = findSeq(evt);
+      oldSeq = seq;
+
+      startWrapBlock=wrappedBlock;
+
+      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);
+
+        if ((sequence == null) || (res > sequence.getLength()))
+        {
+            return;
+        }
+
+        stretchGroup = av.getSelectionGroup();
+
+        if (stretchGroup == null)
+        {
+            stretchGroup = av.alignment.findGroup(sequence);
+
+            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;
+
+            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;
+                    }
+                }
+            }
+        }
+
+        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 (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());
+
+            // edit the properties of existing group
+        }
+
+        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;
+        }
+
+        stretchGroup.getWidth();
+
+        seqCanvas.repaint();
     }
-    else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseReleasedDefineMode(MouseEvent evt)
     {
-        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);
-        pop.show(this, evt.getX(), evt.getY());
+        if (mouseDragging)
+        {
+            stretchGroup.recalcConservation();
+            mouseDragging = false;
+        }
+
+        if (stretchGroup == null)
+        {
+            return;
+        }
 
-    // edit the properties of existing group
+        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());
+          }
+          else
+          {
+            SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                                           stretchGroup.getName());
+          }
+        }
+        changeEndRes = false;
+        changeStartRes = false;
+        stretchGroup = null;
+        PaintRefresher.Refresh(av.alignment);
     }
 
-    if(stretchGroup!=null && stretchGroup.getEndRes()==res)
-      // Edit end res position of selected group
-      changeEndRes = true;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void doMouseDraggedDefineMode(MouseEvent evt)
+    {
+      int res = findRes(evt);
+      int y = findSeq(evt);
 
-   else if(stretchGroup!=null && stretchGroup.getStartRes()==res)
-      // Edit end res position of selected group
-      changeStartRes = true;
+      if(wrappedBlock!=startWrapBlock)
+        return;
 
+      if (stretchGroup == null)
+      {
+            return;
+        }
 
-    seqCanvas.paintFlag = true;
-    repaint();
+        if (res > av.alignment.getWidth())
+        {
+            res = av.alignment.getWidth() - 1;
+        }
 
+        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 (res < av.getStartRes())
+        {
+            res = av.getStartRes();
+        }
+        else if (res > av.getEndRes() && !av.getWrapAlignment())
+        {
+            res = av.getEndRes();
+        }
+
+        if (changeEndRes)
+        {
+            if (res > (stretchGroup.getStartRes() - 1))
+            {
+                stretchGroup.setEndRes(res);
+            }
+        }
+        else if (changeStartRes)
+        {
+            if (res < (stretchGroup.getEndRes() + 1))
+            {
+                stretchGroup.setStartRes(res);
+            }
+        }
 
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
+        int dragDirection = 0;
 
-  public void doMouseReleasedDefineMode(MouseEvent evt)
-  {
-    changeEndRes = false;
-    changeStartRes = false;
-    stretchGroup = null;
-  }
+        if (y > oldSeq)
+        {
+            dragDirection = 1;
+        }
+        else if (y < oldSeq)
+        {
+            dragDirection = -1;
+        }
 
+        while ((y != oldSeq) && (oldSeq > 0) && (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);
 
-  boolean remove = false;
-  public void doMouseDraggedDefineMode(MouseEvent evt)
-  {
-    int res = evt.getX()/av.getCharWidth() + av.getStartRes();
-    int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
+            oldSeq += dragDirection;
 
+            Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-    if(stretchGroup.getEndRes()==res)
-      // Edit end res position of selected group
-      changeEndRes = true;
+            if (stretchGroup.sequences.contains(nextSeq))
+            {
+                stretchGroup.deleteSequence(seq, false);
+            }
+            else
+            {
+                if (seq != null)
+                {
+                    stretchGroup.addSequence(seq, false);
+                }
 
-    else if(stretchGroup.getStartRes()==res)
-      // Edit end res position of selected group
-      changeStartRes = true;
+                stretchGroup.addSequence(nextSeq, false);
+            }
+        }
 
+        oldSeq = y;
+        mouseDragging = true;
 
-    if(res<av.getStartRes())
-      res = av.getStartRes();
-    else if(res>av.getEndRes())
-      res = av.getEndRes();
+        if (scrollThread != null)
+        {
+            scrollThread.setEvent(evt);
+        }
 
-    if(changeEndRes)
-    {
-      if(res>stretchGroup.getStartRes()-1)
-        stretchGroup.setEndRes( res );
+        seqCanvas.repaint();
     }
-    else if(changeStartRes)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void doMouseEnteredDefineMode(MouseEvent e)
     {
-      if(res<stretchGroup.getEndRes()+1)
-        stretchGroup.setStartRes( res );
+        if (scrollThread != null)
+        {
+            scrollThread.running = false;
+        }
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void doMouseExitedDefineMode(MouseEvent e)
+    {
+        if (av.getWrapAlignment())
+        {
+            return;
+        }
 
-    int dragDirection = 0;
-    if (y > oldSeq)
-      dragDirection = 1;
-    else if (y < oldSeq)
-      dragDirection = -1;
+        if (mouseDragging)
+        {
+            scrollThread = new ScrollThread();
+        }
+    }
 
-    while (y != oldSeq)
+    // this class allows scrolling off the bottom of the visible alignment
+    class ScrollThread extends Thread
     {
-      // This routine ensures we don't skip any sequences, as the
-      // selection is quite slow.
-      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+        MouseEvent evt;
+        boolean running = false;
 
-      oldSeq += dragDirection;
-      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-      if (stretchGroup.sequences.contains(nextSeq))
-      {
-        stretchGroup.deleteSequence(seq);
-        stretchGroup.deleteSequence(nextSeq);
-      }
-      else
-      {
-        stretchGroup.addSequence(seq);
-        stretchGroup.addSequence(nextSeq);
-      }
-    }
-    oldSeq = y;
+        public ScrollThread()
+        {
+            start();
+        }
 
-    seqCanvas.paintFlag = true;
-    repaint();
-  }
+        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);
+                    }
+                }
 
+                try
+                {
+                    Thread.sleep(20);
+                }
+                catch (Exception ex)
+                {
+                }
+            }
+        }
+    }
+}