X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=8d81f8c49dceb3f114f13aa05e46b267c7b8ccba;hb=0899f9541714086b75987a4ba3d35037a6d6224b;hp=3f49cc49ca923ab2972778efa65f26fc3e9a3c15;hpb=99f3f01792321efb671ac7ad946efffc3a3319a4;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
old mode 100755
new mode 100644
index 3f49cc4..8d81f8c
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,1329 +1,1877 @@
-/*
- * 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 javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SeqPanel extends JPanel implements MouseListener,
-    MouseMotionListener, MouseWheelListener
-
-{
-    /** 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)
-    {
-        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;
-
-        if(!av.isDataset())
-        {
-          addMouseMotionListener(this);
-          addMouseListener(this);
-          addMouseWheelListener(this);
-        }
-    }
-
-    int startWrapBlock=-1;
-    int wrappedBlock=-1;
-    int findRes(MouseEvent evt)
-   {
-     int res = 0;
-     int x = evt.getX();
-
-    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 -= 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)
-      {
-        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++)
-        {
-          int index = av.alignment.findIndex( sg.getSequenceAt(i) );
-          if(index > max)
-            max = index;
-          if(index < min)
-            min = index;
-        }
-
-        max ++;
-
-        if(topLeft)
-        {
-          sg.setStartRes(seqCanvas.cursorX);
-          if(sg.getEndRes()<seqCanvas.cursorX)
-            sg.setEndRes(seqCanvas.cursorX);
-
-          min = seqCanvas.cursorY;
-        }
-        else
-        {
-          sg.setEndRes(seqCanvas.cursorX);
-          if(sg.getStartRes()>seqCanvas.cursorX)
-            sg.setStartRes(seqCanvas.cursorX);
-
-          max = seqCanvas.cursorY+1;
-        }
-
-        if(min>max)
-        {
-          // Only the user can do this
-          av.setSelectionGroup(null);
-        }
-        else
-        {
-          // 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);
-          }
-        }
-      }
-
-      if (av.getSelectionGroup() == null)
-      {
-        SequenceGroup sg = new SequenceGroup();
-        sg.setStartRes(seqCanvas.cursorX);
-        sg.setEndRes(seqCanvas.cursorX);
-        sg.addSequence(sequence, false);
-        av.setSelectionGroup(sg);
-      }
-
-
-      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();
-    }
-
-    void deleteGapAtCursor(boolean group)
-    {
-      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();
-    }
-
-    void numberPressed(char value)
-    {
-      if(keyboardGaps==null)
-        keyboardGaps = new StringBuffer();
-
-      keyboardGaps.append(value);
-    }
-
-    StringBuffer keyboardGaps;
-    int getKeyboardGaps()
-    {
-      if(keyboardGaps==null)
-        return 1;
-      else
-        return Integer.parseInt(keyboardGaps.toString());
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
-    {
-      mouseDragging = false;
-      mouseWheelPressed = false;
-
-      if (!editingSeqs)
-      {
-         doMouseReleasedDefineMode(evt);
-         return;
-      }
-
-       editOccurred();
-
-       endEditing();
-       ap.repaint();
-    }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    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;
-      }
-
-
-
-      int seq = findSeq(evt);
-      int res = findRes(evt);
-
-      if(seq<0 || res<0)
-        return;
-
-      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                                                         av.alignment, HistoryItem.EDIT));
-
-        if ((seq < av.getAlignment().getHeight()) &&
-                (res < av.getAlignment().getSequenceAt(seq).getLength()))
-        {
-            startseq = seq;
-            lastres = res;
-        }
-        else
-        {
-            startseq = -1;
-            lastres = -1;
-        }
-
-        return;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    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);
-
-
-      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
-            return;
-
-      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
-      if (res > sequence.getLength())
-      {
-        return;
-      }
-
-      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
-      {
-        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
-      }
-
-      setStatusMessage(sequence, res, seq);
-
-        // 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>");
-
-              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("");
-        }
-    }
-
-    void setStatusMessage(SequenceI sequence, int res, int seq)
-    {
-      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: ");
-      }
-
-      if (obj != null)
-      {
-
-        if (obj != "")
-        {
-          text.append(obj + " (" + sequence.findPosition(res) +
-                      ")");
-        }
-      }
-      ap.alignFrame.statusBar.setText(text.toString());
-
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
-    {
-      if (!editingSeqs)
-      {
-        doMouseDraggedDefineMode(evt);
-        return;
-      }
-
-        int res = findRes(evt);
-
-        if (res < 0)
-        {
-            res = 0;
-        }
-
-        if ((lastres == -1) || (lastres == res))
-        {
-            return;
-        }
-
-        if ( (res < av.getAlignment().getWidth()) && (res < lastres))
-        {
-          // dragLeft, delete gap
-          editSequence(false, res);
-        }
-        else
-          editSequence(true, res);
-
-        mouseDragging = true;
-        if(scrollThread!=null)
-          scrollThread.setEvent(evt);
-
-    }
-
-    void editSequence(boolean insertGap, int startres)
-    {
-      int fixedLeft = -1;
-      int fixedRight = -1;
-      boolean fixedColumns = false;
-
-       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 (!groupEditing && av.hasHiddenRows)
-        {
-          if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
-          {
-            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;
-          }
-
-          if (fixedLeft > startres)
-          {
-            fixedRight = fixedLeft - 1;
-            fixedLeft = 0;
-          }
-          else if (fixedRight < startres)
-          {
-            fixedLeft = fixedRight;
-            fixedRight = -1;
-          }
-        }
-
-        if (groupEditing)
-        {
-          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 (insertGap)
-          {
-            // Is it valid??
-            // Find the next gap before the end
-            // of the visible region boundary
-            if (av.hasHiddenColumns)
-            {
-             // 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
-          {
-            /// Are we able to delete?
-            // ie are all columns blank?
-
-            for (int s = 0; s < sg.getSize(); s++)
-            {
-              seq = sg.getSequenceAt(s);
-
-              for (int j = startres; 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
-                  endEditing();
-                  return;
-                }
-              }
-            }
-          }
-
-
-          for (int i = 0; i < sg.getSize(); i++)
-          {
-            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 /////Editing a single sequence///////////
-        {
-
-          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);
-              }
-            }
-          }
-        }
-
-        lastres = startres;
-        seqCanvas.repaint();
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param j DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     */
-    void insertChar(int j, SequenceI seq)
-    {
-        seq.insertCharAt(j, av.getGapCharacter());
-        seqEditOccurred = true;
-    }
-
-    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)))
-    {
-          //Theres a space, so break and insert the gap
-          break;
-        }
-      }
-
-      if (blankColumn <= j)
-      {
-        endEditing();
-        return;
-      }
-
-      if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
-      {
-        //Just Checking
-        System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
-        return;
-      }
-
-      seq.deleteCharAt(blankColumn);
-      seq.insertCharAt(j, av.getGapCharacter());
-      seqEditOccurred = true;
-    }
-
-    void deleteChar(int j, SequenceI seq, int fixedColumn)
-    {
-      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;
-    }
-
-    /**
-     * 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;
-      }
-
-        seq.deleteCharAt(j);
-        seqEditOccurred = true;
-        seqCanvas.repaint();
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent e)
-    {
-        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)
-    {
-      e.consume();
-      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 i DOCUMENT ME!
-     */
-    void editOccurred()
-    {
-      if (!seqEditOccurred)
-      {
-        ap.alignFrame.historyList.pop();
-        ap.alignFrame.updateEditMenuBar();
-      }
-
-      endEditing();
-
-      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
-
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMousePressedDefineMode(MouseEvent evt)
-    {
-      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 (av.cursorMode)
-        {
-          seqCanvas.cursorX = findRes(evt);
-          seqCanvas.cursorY = findSeq(evt);
-          seqCanvas.repaint();
-          return;
-        }
-
-
-        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();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseReleasedDefineMode(MouseEvent evt)
-    {
-        if (stretchGroup == null)
-        {
-            return;
-        }
-
-
-        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);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void doMouseDraggedDefineMode(MouseEvent evt)
-    {
-      int res = findRes(evt);
-      int y = findSeq(evt);
-
-      if(wrappedBlock!=startWrapBlock)
-        return;
-
-       if (stretchGroup == null)
-       {
-            return;
-       }
-
-
-        if(y > av.alignment.getHeight())
-        {
-          y = av.alignment.getHeight() -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();
-        }
-
-        if (changeEndRes)
-        {
-            if (res > (stretchGroup.getStartRes() - 1))
-            {
-                stretchGroup.setEndRes(res);
-            }
-        }
-        else if (changeStartRes)
-        {
-            if (res < (stretchGroup.getEndRes() + 1))
-            {
-                stretchGroup.setStartRes(res);
-            }
-        }
-
-        int dragDirection = 0;
-
-        if (y > oldSeq)
-        {
-            dragDirection = 1;
-        }
-        else if (y < oldSeq)
-        {
-            dragDirection = -1;
-        }
-
-
-        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);
-
-            oldSeq += dragDirection;
-
-            if(oldSeq<0)
-              break;
-
-            Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
-            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();
-    }
-
-
-
-    // this class allows scrolling off the bottom of the visible alignment
-    class ScrollThread extends Thread
-    {
-        MouseEvent evt;
-        boolean running = false;
-
-        public ScrollThread()
-        {
-            start();
-        }
-
-        public void setEvent(MouseEvent e)
-        {
-            evt = e;
-        }
-
-        public void stopScrolling()
-        {
-            running = false;
-        }
-
-        public void run()
-        {
-            running = true;
-
-            while (running)
-            {
-                if (evt != null)
-                {
-                    if (mouseDragging && (evt.getY() < 0) &&
-                            (av.getStartSeq() > 0))
-                    {
-                        running = ap.scrollUp(true);
-                    }
-
-                    if (mouseDragging && (evt.getY() >= getHeight()) &&
-                            (av.alignment.getHeight() > av.getEndSeq()))
-                    {
-                        running = ap.scrollUp(false);
-                    }
-
-                    if (mouseDragging && (evt.getX() < 0))
-                    {
-                        running = ap.scrollRight(false);
-                    }
-                    else if (mouseDragging && (evt.getX() >= getWidth()))
-                    {
-                        running = ap.scrollRight(true);
-                    }
-                }
-
-                try
-                {
-                    Thread.sleep(20);
-                }
-                catch (Exception ex)
-                {
-                }
-            }
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+import java.util.List;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.*;
+import jalview.structure.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.130 $
+ */
+public class SeqPanel extends JPanel implements MouseListener,
+        MouseMotionListener, MouseWheelListener, SequenceListener,
+        SelectionListener
+
+{
+  /** DOCUMENT ME!! */
+  public SeqCanvas seqCanvas;
+
+  /** DOCUMENT ME!! */
+  public AlignmentPanel ap;
+
+  protected int lastres;
+
+  protected int startseq;
+
+  protected AlignViewport av;
+
+  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;
+
+  Point lastMousePress;
+
+  boolean mouseWheelPressed = false;
+
+  StringBuffer keyboardNo1;
+
+  StringBuffer keyboardNo2;
+
+  java.net.URL linkImageURL;
+  private final SequenceAnnotationReport seqARep;
+  StringBuffer tooltipText = new StringBuffer("<html>");
+
+  String tmpString;
+
+  EditCommand editCommand;
+
+  StructureSelectionManager ssm;
+
+  /**
+   * Creates a new SeqPanel object.
+   *
+   * @param avp
+   *          DOCUMENT ME!
+   * @param p
+   *          DOCUMENT ME!
+   */
+  public SeqPanel(AlignViewport av, AlignmentPanel ap)
+  {
+    linkImageURL = getClass().getResource("/images/link.gif");
+    seqARep=new SequenceAnnotationReport(linkImageURL.toString());
+    ToolTipManager.sharedInstance().registerComponent(this);
+    ToolTipManager.sharedInstance().setInitialDelay(0);
+    ToolTipManager.sharedInstance().setDismissDelay(10000);
+    this.av = av;
+    setBackground(Color.white);
+
+    seqCanvas = new SeqCanvas(ap);
+    setLayout(new BorderLayout());
+    add(seqCanvas, BorderLayout.CENTER);
+
+    this.ap = ap;
+
+    if (!av.isDataset())
+    {
+      addMouseMotionListener(this);
+      addMouseListener(this);
+      addMouseWheelListener(this);
+      ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+      ssm.addStructureViewerListener(this);
+      ssm.addSelectionListener(this);
+    }
+  }
+
+  int startWrapBlock = -1;
+
+  int wrappedBlock = -1;
+
+  int findRes(MouseEvent evt)
+  {
+    int res = 0;
+    int x = evt.getX();
+
+    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 -= hgap;
+      x -= seqCanvas.LABEL_WEST;
+
+      int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+      if (cwidth < 1)
+      {
+        return 0;
+      }
+
+      wrappedBlock = y / cHeight;
+      wrappedBlock += av.getStartRes() / cwidth;
+
+      res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+    }
+    else
+    {
+      if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+      {
+        // make sure we calculate relative to visible alignment, rather than right-hand gutter
+        x = seqCanvas.getX()+seqCanvas.getWidth();
+      }
+      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 = Math.min((y % cHeight) / av.getCharHeight(),
+              av.getAlignment().getHeight() - 1);
+    }
+    else
+    {
+      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
+              av.getAlignment().getHeight() - 1);
+    }
+
+    return seq;
+  }
+
+  SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+  {
+    Vector tmp = new Vector();
+    SequenceFeature[] features = sequence.getSequenceFeatures();
+    if (features != null)
+    {
+      for (int i = 0; i < features.length; i++)
+      {
+        if (av.featuresDisplayed == null
+                || !av.featuresDisplayed.containsKey(features[i].getType()))
+        {
+          continue;
+        }
+
+        if (features[i].featureGroup != null
+                && seqCanvas.fr.featureGroups != null
+                && seqCanvas.fr.featureGroups
+                        .containsKey(features[i].featureGroup)
+                && !((Boolean) seqCanvas.fr.featureGroups
+                        .get(features[i].featureGroup)).booleanValue())
+          continue;
+
+        if ((features[i].getBegin() <= res)
+                && (features[i].getEnd() >= res))
+        {
+          tmp.addElement(features[i]);
+        }
+      }
+    }
+
+    features = new SequenceFeature[tmp.size()];
+    tmp.copyInto(features);
+
+    return features;
+  }
+
+  void endEditing()
+  {
+    if (editCommand != null && editCommand.getSize() > 0)
+    {
+      ap.alignFrame.addHistoryItem(editCommand);
+      av.firePropertyChange("alignment", null, av.getAlignment()
+              .getSequences());
+    }
+
+    startseq = -1;
+    lastres = -1;
+    editingSeqs = false;
+    groupEditing = false;
+    keyboardNo1 = null;
+    keyboardNo2 = null;
+    editCommand = null;
+  }
+
+  void setCursorRow()
+  {
+    seqCanvas.cursorY = getKeyboardNo1() - 1;
+    scrollToVisible();
+  }
+
+  void setCursorColumn()
+  {
+    seqCanvas.cursorX = getKeyboardNo1() - 1;
+    scrollToVisible();
+  }
+
+  void setCursorRowAndColumn()
+  {
+    if (keyboardNo2 == null)
+    {
+      keyboardNo2 = new StringBuffer();
+    }
+    else
+    {
+      seqCanvas.cursorX = getKeyboardNo1() - 1;
+      seqCanvas.cursorY = getKeyboardNo2() - 1;
+      scrollToVisible();
+    }
+  }
+
+  void setCursorPosition()
+  {
+    SequenceI sequence = av.getAlignment().getSequenceAt(
+            seqCanvas.cursorY);
+
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+    scrollToVisible();
+  }
+
+  void moveCursor(int dx, int dy)
+  {
+    seqCanvas.cursorX += dx;
+    seqCanvas.cursorY += dy;
+    if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+    {
+      int original = seqCanvas.cursorX - dx;
+      int maxWidth = av.getAlignment().getWidth();
+
+      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+      {
+        seqCanvas.cursorX += dx;
+      }
+
+      if (seqCanvas.cursorX >= maxWidth
+              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+      {
+        seqCanvas.cursorX = original;
+      }
+    }
+
+    scrollToVisible();
+  }
+
+  void scrollToVisible()
+  {
+    if (seqCanvas.cursorX < 0)
+    {
+      seqCanvas.cursorX = 0;
+    }
+    else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
+    {
+      seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
+    }
+
+    if (seqCanvas.cursorY < 0)
+    {
+      seqCanvas.cursorY = 0;
+    }
+    else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
+    {
+      seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
+    }
+
+    endEditing();
+    if (av.wrapAlignment)
+    {
+      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+    }
+    else
+    {
+      while (seqCanvas.cursorY < av.startSeq)
+      {
+        ap.scrollUp(true);
+      }
+      while (seqCanvas.cursorY + 1 > av.endSeq)
+      {
+        ap.scrollUp(false);
+      }
+      if (!av.wrapAlignment)
+      {
+        while (seqCanvas.cursorX < av.getColumnSelection()
+                .adjustForHiddenColumns(av.startRes))
+        {
+          if (!ap.scrollRight(false))
+          {
+            break;
+          }
+        }
+        while (seqCanvas.cursorX > av.getColumnSelection()
+                .adjustForHiddenColumns(av.endRes))
+        {
+          if (!ap.scrollRight(true))
+          {
+            break;
+          }
+        }
+      }
+    }
+    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+            seqCanvas.cursorX, seqCanvas.cursorY);
+
+    seqCanvas.repaint();
+  }
+
+  void setSelectionAreaAtCursor(boolean topLeft)
+  {
+    SequenceI sequence = av.getAlignment().getSequenceAt(
+            seqCanvas.cursorY);
+
+    if (av.getSelectionGroup() != null)
+    {
+      SequenceGroup sg = av.getSelectionGroup();
+      // Find the top and bottom of this group
+      int min = av.getAlignment().getHeight(), max = 0;
+      for (int i = 0; i < sg.getSize(); i++)
+      {
+        int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
+        if (index > max)
+        {
+          max = index;
+        }
+        if (index < min)
+        {
+          min = index;
+        }
+      }
+
+      max++;
+
+      if (topLeft)
+      {
+        sg.setStartRes(seqCanvas.cursorX);
+        if (sg.getEndRes() < seqCanvas.cursorX)
+        {
+          sg.setEndRes(seqCanvas.cursorX);
+        }
+
+        min = seqCanvas.cursorY;
+      }
+      else
+      {
+        sg.setEndRes(seqCanvas.cursorX);
+        if (sg.getStartRes() > seqCanvas.cursorX)
+        {
+          sg.setStartRes(seqCanvas.cursorX);
+        }
+
+        max = seqCanvas.cursorY + 1;
+      }
+
+      if (min > max)
+      {
+        // Only the user can do this
+        av.setSelectionGroup(null);
+      }
+      else
+      {
+        // Now add any sequences between min and max
+        sg.getSequences(null).clear();
+        for (int i = min; i < max; i++)
+        {
+          sg.addSequence(av.getAlignment().getSequenceAt(i), false);
+        }
+      }
+    }
+
+    if (av.getSelectionGroup() == null)
+    {
+      SequenceGroup sg = new SequenceGroup();
+      sg.setStartRes(seqCanvas.cursorX);
+      sg.setEndRes(seqCanvas.cursorX);
+      sg.addSequence(sequence, false);
+      av.setSelectionGroup(sg);
+    }
+
+    ap.paintAlignment(false);
+    av.sendSelection();
+  }
+
+  void insertGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX;
+    editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
+    endEditing();
+  }
+
+  void deleteGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX + getKeyboardNo1();
+    editSequence(false, false, seqCanvas.cursorX);
+    endEditing();
+  }
+
+  void insertNucAtCursor(boolean group,String nuc){
+	  groupEditing = group;
+	    startseq = seqCanvas.cursorY;
+	    lastres = seqCanvas.cursorX;
+	    editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+	    endEditing();
+  }
+
+  void numberPressed(char value)
+  {
+    if (keyboardNo1 == null)
+    {
+      keyboardNo1 = new StringBuffer();
+    }
+
+    if (keyboardNo2 != null)
+    {
+      keyboardNo2.append(value);
+    }
+    else
+    {
+      keyboardNo1.append(value);
+    }
+  }
+
+  int getKeyboardNo1()
+  {
+    if (keyboardNo1 == null)
+      return 1;
+    else
+    {
+      int value = Integer.parseInt(keyboardNo1.toString());
+      keyboardNo1 = null;
+      return value;
+    }
+  }
+
+  int getKeyboardNo2()
+  {
+    if (keyboardNo2 == null)
+      return 1;
+    else
+    {
+      int value = Integer.parseInt(keyboardNo2.toString());
+      keyboardNo2 = null;
+      return value;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseReleased(MouseEvent evt)
+  {
+    mouseDragging = false;
+    mouseWheelPressed = false;
+
+    if (!editingSeqs)
+    {
+      doMouseReleasedDefineMode(evt);
+      return;
+    }
+
+    endEditing();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mousePressed(MouseEvent evt)
+  {
+    lastMousePress = evt.getPoint();
+
+    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;
+    }
+
+    int seq = findSeq(evt);
+    int res = findRes(evt);
+
+    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;
+    }
+
+    return;
+  }
+
+  String lastMessage;
+
+  @Override
+  public void mouseOverSequence(SequenceI sequence, int index, int pos)
+  {
+    String tmp = sequence.hashCode() + " " + index + " " + pos;
+
+    if (lastMessage == null || !lastMessage.equals(tmp))
+    {
+      // System.err.println("mouseOver Sequence: "+tmp);
+      ssm.mouseOverSequence(sequence, index, pos, av);
+    }
+    lastMessage = tmp;
+  }
+
+  @Override
+  public void highlightSequence(SearchResults results)
+  {
+    if (av.followHighlight)
+    {
+      if (ap.scrollToPosition(results, false))
+      {
+      seqCanvas.revalidate();
+      }
+    }
+    seqCanvas.highlightSearchResults(results);
+  }
+
+  @Override
+  public void updateColours(SequenceI seq, int index)
+  {
+    System.out.println("update the seqPanel colours");
+    // repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  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);
+    int pos;
+    if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+    {
+      return;
+    }
+
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+    if (res >= sequence.getLength())
+    {
+      return;
+    }
+
+    pos = setStatusMessage(sequence, res, seq);
+    if (ssm != null && pos > -1)
+      mouseOverSequence(sequence, res, pos);
+
+    tooltipText.setLength(6); // Cuts the buffer back to <html>
+
+    SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
+    if (groups != null)
+    {
+      for (int g = 0; g < groups.length; g++)
+      {
+        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+        {
+          if (tooltipText.length() > 6)
+          {
+            tooltipText.append("<br>");
+          }
+
+          if (!groups[g].getName().startsWith("JTreeGroup")
+                  && !groups[g].getName().startsWith("JGroup"))
+          {
+            tooltipText.append(groups[g].getName());
+          }
+
+          if (groups[g].getDescription() != null)
+          {
+            tooltipText.append(": " + groups[g].getDescription());
+          }
+        }
+      }
+    }
+
+    // use aa to see if the mouse pointer is on a
+    if (av.showSequenceFeatures)
+    {
+      int rpos;
+      SequenceFeature[] features = findFeaturesAtRes(
+              sequence.getDatasetSequence(),
+              rpos = sequence.findPosition(res));
+      seqARep.appendFeatures(tooltipText,  rpos, features,
+              this.ap.seqPanel.seqCanvas.fr.minmax);
+    }
+    if (tooltipText.length() == 6) // <html></html>
+    {
+      setToolTipText(null);
+      lastTooltip = null;
+    }
+    else
+    {
+      tooltipText.append("</html>");
+      if (lastTooltip == null
+              || !lastTooltip.equals(tooltipText.toString()))
+      {
+        setToolTipText(tooltipText.toString());
+        lastTooltip = tooltipText.toString();
+      }
+
+    }
+
+  }
+
+  private Point lastp = null;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+   */
+  public Point getToolTipLocation(MouseEvent event)
+  {
+    int x = event.getX(), w = getWidth();
+    int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
+    // close to edge
+    Point p = lastp;
+    if (!event.isShiftDown() || p == null)
+    {
+      p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
+              event.getX() + wdth, event.getY() - 20) : null;
+    }
+    /*
+     * TODO: try to modify position region is not obcured by tooltip
+     */
+    return lastp = p;
+  }
+
+
+  String lastTooltip;
+
+  /**
+   * Set status message in alignment panel
+   *
+   * @param sequence
+   *          aligned sequence object
+   * @param res
+   *          alignment column
+   * @param seq
+   *          index of sequence in alignment
+   * @return position of res in sequence
+   */
+  int setStatusMessage(SequenceI sequence, int res, int seq)
+  {
+    int pos = -1;
+    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+            + sequence.getName());
+
+    Object obj = null;
+    if (av.getAlignment().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)
+    {
+      pos = sequence.findPosition(res);
+      if (obj != "")
+      {
+        text.append(obj + " (" + pos + ")");
+      }
+    }
+    ap.alignFrame.statusBar.setText(text.toString());
+    return pos;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseDragged(MouseEvent evt)
+  {
+    if (mouseWheelPressed)
+    {
+      int oldWidth = av.charWidth;
+
+      // Which is bigger, left-right or up-down?
+      if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
+              .getX() - lastMousePress.getX()))
+      {
+        int fontSize = av.font.getSize();
+
+        if (evt.getY() < lastMousePress.getY())
+        {
+          fontSize--;
+        }
+        else if (evt.getY() > lastMousePress.getY())
+        {
+          fontSize++;
+        }
+
+        if (fontSize < 1)
+        {
+          fontSize = 1;
+        }
+
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.charWidth = oldWidth;
+        ap.fontChanged();
+      }
+      else
+      {
+        if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+        {
+          av.charWidth--;
+        }
+        else if (evt.getX() > lastMousePress.getX())
+        {
+          av.charWidth++;
+        }
+
+        ap.paintAlignment(false);
+      }
+
+      FontMetrics fm = getFontMetrics(av.getFont());
+      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+      lastMousePress = evt.getPoint();
+
+      return;
+    }
+
+    if (!editingSeqs)
+    {
+      doMouseDraggedDefineMode(evt);
+      return;
+    }
+
+    int res = findRes(evt);
+
+    if (res < 0)
+    {
+      res = 0;
+    }
+
+    if ((lastres == -1) || (lastres == res))
+    {
+      return;
+    }
+
+    if ((res < av.getAlignment().getWidth()) && (res < lastres))
+    {
+      // dragLeft, delete gap
+      editSequence(false, false,res);
+    }
+    else
+    {
+      editSequence(true, false,res);
+    }
+
+    mouseDragging = true;
+    if (scrollThread != null)
+    {
+      scrollThread.setEvent(evt);
+    }
+  }
+
+  //TODO: Make it more clever than many booleans
+  synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
+  {
+    int fixedLeft = -1;
+    int fixedRight = -1;
+    boolean fixedColumns = false;
+    SequenceGroup sg = av.getSelectionGroup();
+
+    SequenceI seq = av.getAlignment().getSequenceAt(startseq);
+
+    // No group, but the sequence may represent a group
+    if (!groupEditing && av.hasHiddenRows())
+    {
+      if (av.isHiddenRepSequence(seq))
+      {
+        sg = av.getRepresentedSequences(seq);
+        groupEditing = true;
+      }
+    }
+
+    StringBuffer message = new StringBuffer();
+    if (groupEditing)
+    {
+      message.append("Edit group:");
+      if (editCommand == null)
+      {
+        editCommand = new EditCommand("Edit Group");
+      }
+    }
+    else
+    {
+      message.append("Edit sequence: " + seq.getName());
+      String label = seq.getName();
+      if (label.length() > 10)
+      {
+        label = label.substring(0, 10);
+      }
+      if (editCommand == null)
+      {
+        editCommand = new EditCommand("Edit " + label);
+      }
+    }
+
+    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
+            || (sg != null && sg.getSequences(av.getHiddenRepSequences())
+                    .contains(seq)))
+    {
+      fixedColumns = true;
+
+      // sg might be null as the user may only see 1 sequence,
+      // but the sequence represents a group
+      if (sg == null)
+      {
+        if (!av.isHiddenRepSequence(seq))
+        {
+          endEditing();
+          return;
+        }
+        sg = av.getRepresentedSequences(seq);
+      }
+
+      fixedLeft = sg.getStartRes();
+      fixedRight = sg.getEndRes();
+
+      if ((startres < fixedLeft && lastres >= fixedLeft)
+              || (startres >= fixedLeft && lastres < fixedLeft)
+              || (startres > fixedRight && lastres <= fixedRight)
+              || (startres <= fixedRight && lastres > fixedRight))
+      {
+        endEditing();
+        return;
+      }
+
+      if (fixedLeft > startres)
+      {
+        fixedRight = fixedLeft - 1;
+        fixedLeft = 0;
+      }
+      else if (fixedRight < startres)
+      {
+        fixedLeft = fixedRight;
+        fixedRight = -1;
+      }
+    }
+
+    if (av.hasHiddenColumns())
+    {
+      fixedColumns = true;
+      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+
+      if ((insertGap && startres > y1 && lastres < y1)
+              || (!insertGap && startres < y2 && lastres > y2))
+      {
+        endEditing();
+        return;
+      }
+
+      // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      // Selection spans a hidden region
+      if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+      {
+        if (startres >= y2)
+        {
+          fixedLeft = y2;
+        }
+        else
+        {
+          fixedRight = y2 - 1;
+        }
+      }
+    }
+
+    if (groupEditing)
+    {
+      List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
+      int g, groupSize = vseqs.size();
+      SequenceI[] groupSeqs = new SequenceI[groupSize];
+      for (g = 0; g < groupSeqs.length; g++)
+      {
+        groupSeqs[g] = vseqs.get(g);
+      }
+
+      // drag to right
+      if (insertGap)
+      {
+        // If the user has selected the whole sequence, and is dragging to
+        // the right, we can still extend the alignment and selectionGroup
+        if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
+                && sg.getEndRes() == av.getAlignment().getWidth() - 1)
+        {
+          sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
+          fixedRight = sg.getEndRes();
+        }
+
+        // Is it valid with fixed columns??
+        // Find the next gap before the end
+        // of the visible region boundary
+        boolean blank = false;
+        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
+        {
+          blank = true;
+
+          for (g = 0; g < groupSize; g++)
+          {
+            for (int j = 0; j < startres - lastres; j++)
+            {
+              if (!jalview.util.Comparison.isGap(groupSeqs[g]
+                      .getCharAt(fixedRight - j)))
+              {
+                blank = false;
+                break;
+              }
+            }
+          }
+          if (blank)
+          {
+            break;
+          }
+        }
+
+        if (!blank)
+        {
+          if (sg.getSize() == av.getAlignment().getHeight())
+          {
+            if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
+                    .getHiddenBoundaryRight(startres)))
+            {
+              endEditing();
+              return;
+            }
+
+            int alWidth = av.getAlignment().getWidth();
+            if (av.hasHiddenRows())
+            {
+              int hwidth = av.getAlignment().getHiddenSequences().getWidth();
+              if (hwidth > alWidth)
+              {
+                alWidth = hwidth;
+              }
+            }
+            // We can still insert gaps if the selectionGroup
+            // contains all the sequences
+            sg.setEndRes(sg.getEndRes() + startres - lastres);
+            fixedRight = alWidth + startres - lastres;
+          }
+          else
+          {
+            endEditing();
+            return;
+          }
+        }
+      }
+
+      // drag to left
+      else if (!insertGap)
+      {
+        // / Are we able to delete?
+        // ie are all columns blank?
+
+        for (g = 0; g < groupSize; g++)
+        {
+          for (int j = startres; j < lastres; j++)
+          {
+            if (groupSeqs[g].getLength() <= j)
+            {
+              continue;
+            }
+
+            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+            {
+              // Not a gap, block edit not valid
+              endEditing();
+              return;
+            }
+          }
+        }
+      }
+
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
+          {
+            insertChar(j, groupSeqs, fixedRight);
+          }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+                  startres, startres - lastres, av.getAlignment(), true);
+        }
+      }
+      else
+      {
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j > startres; j--)
+          {
+            deleteChar(startres, groupSeqs, fixedRight);
+          }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+                  startres, lastres - startres, av.getAlignment(), true);
+        }
+
+      }
+    }
+    else
+    // ///Editing a single sequence///////////
+    {
+      if (insertGap)
+      {
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j < startres; j++)
+          {
+            insertChar(j, new SequenceI[]
+            { seq }, fixedRight);
+          }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+          { seq }, lastres, startres - lastres, av.getAlignment(), true);
+         }
+      }
+      else
+      {
+    	if(!editSeq){
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
+        {
+          for (int j = lastres; j > startres; j--)
+          {
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+            {
+              endEditing();
+              break;
+            }
+            deleteChar(startres, new SequenceI[]
+            { seq }, fixedRight);
+          }
+        }
+        else
+        {
+          // could be a keyboard edit trying to delete none gaps
+          int max = 0;
+          for (int m = startres; m < lastres; m++)
+          {
+            if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+            {
+              break;
+            }
+            max++;
+          }
+
+          if (max > 0)
+          {
+            editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+            { seq }, startres, max, av.getAlignment(), true);
+          }
+        }
+    	}else{//insertGap==false AND editSeq==TRUE;
+    		if (fixedColumns && fixedRight != -1)
+            {
+              for (int j = lastres; j < startres; j++)
+              {
+                insertChar(j, new SequenceI[]
+                { seq }, fixedRight);
+              }
+              }
+            else
+            {
+              editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+              { seq }, lastres, startres - lastres, av.getAlignment(), true);
+             }
+    	}
+      }
+    }
+
+    lastres = startres;
+    seqCanvas.repaint();
+  }
+
+  void insertChar(int j, SequenceI[] seq, int fixedColumn)
+  {
+    int blankColumn = fixedColumn;
+    for (int s = 0; s < seq.length; s++)
+    {
+      // Find the next gap before the end of the visible region boundary
+      // If lastCol > j, theres a boundary after the gap insertion
+
+      for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+      {
+        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        {
+          // Theres a space, so break and insert the gap
+          break;
+        }
+      }
+
+      if (blankColumn <= j)
+      {
+        blankColumn = fixedColumn;
+        endEditing();
+        return;
+      }
+    }
+
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+            av.getAlignment(), true);
+
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
+            true);
+
+  }
+
+  void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+  {
+
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
+            true);
+
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+            av.getAlignment(), true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseEntered(MouseEvent e)
+  {
+    if (oldSeq < 0)
+    {
+      oldSeq = 0;
+    }
+
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseExited(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+    {
+      return;
+    }
+
+    if (mouseDragging)
+    {
+      scrollThread = new ScrollThread();
+    }
+  }
+
+  @Override
+  public void mouseClicked(MouseEvent evt)
+  {
+    SequenceGroup sg = null;
+    SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
+    if (evt.getClickCount() > 1)
+    {
+      sg = av.getSelectionGroup();
+      if (sg != null && sg.getSize() == 1
+              && sg.getEndRes() - sg.getStartRes() < 2)
+      {
+        av.setSelectionGroup(null);
+      }
+
+      SequenceFeature[] features = findFeaturesAtRes(
+              sequence.getDatasetSequence(),
+              sequence.findPosition(findRes(evt)));
+
+      if (features != null && features.length > 0)
+      {
+        SearchResults highlight = new SearchResults();
+        highlight.addResult(sequence, features[0].getBegin(),
+                features[0].getEnd());
+        seqCanvas.highlightSearchResults(highlight);
+      }
+      if (features != null && features.length > 0)
+      {
+        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
+        { sequence }, features, false, ap);
+
+        seqCanvas.highlightSearchResults(null);
+      }
+    }
+  }
+
+  @Override
+  public void mouseWheelMoved(MouseWheelEvent e)
+  {
+    e.consume();
+    if (e.getWheelRotation() > 0)
+    {
+      if (e.isShiftDown())
+      {
+        ap.scrollRight(true);
+        
+      } else {
+        ap.scrollUp(false);
+      }
+    }
+    else
+    {
+      if (e.isShiftDown())
+      {
+        ap.scrollRight(false);
+      } else {
+        ap.scrollUp(true);
+      }
+    }
+    // TODO Update tooltip for new position.
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void doMousePressedDefineMode(MouseEvent evt)
+  {
+    int res = findRes(evt);
+    int seq = findSeq(evt);
+    oldSeq = seq;
+
+    startWrapBlock = wrappedBlock;
+
+    if (av.wrapAlignment && seq > av.getAlignment().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 = av.getAlignment().getSequenceAt(seq);
+
+    if ((sequence == null) || (res > sequence.getLength()))
+    {
+      return;
+    }
+
+    stretchGroup = av.getSelectionGroup();
+
+    if (stretchGroup == null)
+    {
+      stretchGroup = av.getAlignment().findGroup(sequence);
+
+      if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
+              && (res < stretchGroup.getEndRes()))
+      {
+        av.setSelectionGroup(stretchGroup);
+      }
+      else
+      {
+        stretchGroup = null;
+      }
+    }
+    else if (!stretchGroup.getSequences(null).contains(sequence)
+            || (stretchGroup.getStartRes() > res)
+            || (stretchGroup.getEndRes() < res))
+    {
+      stretchGroup = null;
+
+      SequenceGroup[] allGroups = av.getAlignment().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];
+            break;
+          }
+        }
+      }
+
+      av.setSelectionGroup(stretchGroup);
+
+    }
+
+    if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+    {
+      SequenceFeature[] allFeatures = findFeaturesAtRes(
+              sequence.getDatasetSequence(), sequence.findPosition(res));
+      Vector links = new Vector();
+      for (int i = 0; i < allFeatures.length; i++)
+      {
+        if (allFeatures[i].links != null)
+        {
+          for (int j = 0; j < allFeatures[i].links.size(); j++)
+          {
+            links.addElement(allFeatures[i].links.elementAt(j));
+          }
+        }
+      }
+
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+      pop.show(this, evt.getX(), evt.getY());
+      return;
+    }
+
+    if (av.cursorMode)
+    {
+      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.repaint();
+      return;
+    }
+
+    if (stretchGroup == null)
+    {
+      // Only if left mouse button do we want to change group sizes
+
+      // 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");
+      }
+      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();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void doMouseReleasedDefineMode(MouseEvent evt)
+  {
+    if (stretchGroup == null)
+    {
+      return;
+    }
+
+    stretchGroup.recalcConservation(); // always do this - annotation has own
+                                       // state
+    if (stretchGroup.cs != null)
+    {
+      stretchGroup.cs.alignmentChanged(
+                stretchGroup,av.getHiddenRepSequences());
+
+      if (stretchGroup.cs.conservationApplied())
+      {
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                stretchGroup.getName());
+      }
+      else
+      {
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                stretchGroup.getName());
+      }
+    }
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    ap.paintAlignment(true);
+
+    changeEndRes = false;
+    changeStartRes = false;
+    stretchGroup = null;
+    av.sendSelection();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void doMouseDraggedDefineMode(MouseEvent evt)
+  {
+    int res = findRes(evt);
+    int y = findSeq(evt);
+
+    if (wrappedBlock != startWrapBlock)
+    {
+      return;
+    }
+
+    if (stretchGroup == null)
+    {
+      return;
+    }
+
+    if (res >= av.getAlignment().getWidth())
+    {
+      res = av.getAlignment().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();
+    }
+
+    if (changeEndRes)
+    {
+      if (res > (stretchGroup.getStartRes() - 1))
+      {
+        stretchGroup.setEndRes(res);
+      }
+    }
+    else if (changeStartRes)
+    {
+      if (res < (stretchGroup.getEndRes() + 1))
+      {
+        stretchGroup.setStartRes(res);
+      }
+    }
+
+    int dragDirection = 0;
+
+    if (y > oldSeq)
+    {
+      dragDirection = 1;
+    }
+    else if (y < oldSeq)
+    {
+      dragDirection = -1;
+    }
+
+    while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
+    {
+      // This routine ensures we don't skip any sequences, as the
+      // selection is quite slow.
+      Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      oldSeq += dragDirection;
+
+      if (oldSeq < 0)
+      {
+        break;
+      }
+
+      Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+      if (stretchGroup.getSequences(null).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();
+  }
+
+  void scrollCanvas(MouseEvent evt)
+  {
+    if (evt == null)
+    {
+      if (scrollThread != null)
+      {
+        scrollThread.running = false;
+        scrollThread = null;
+      }
+      mouseDragging = false;
+    }
+    else
+    {
+      if (scrollThread == null)
+      {
+        scrollThread = new ScrollThread();
+      }
+
+      mouseDragging = true;
+      scrollThread.setEvent(evt);
+    }
+
+  }
+
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread extends Thread
+  {
+    MouseEvent evt;
+
+    boolean running = false;
+
+    public ScrollThread()
+    {
+      start();
+    }
+
+    public void setEvent(MouseEvent e)
+    {
+      evt = e;
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    @Override
+    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.getAlignment().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)
+        {
+        }
+      }
+    }
+  }
+
+  /**
+   * modify current selection according to a received message.
+   */
+  @Override
+  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+          SelectionSource source)
+  {
+    // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+    // handles selection messages...
+    // TODO: extend config options to allow user to control if selections may be
+    // shared between viewports.
+    if (av == source
+            || !av.followSelection
+            || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+            || (source instanceof AlignViewport && ((AlignViewport) source)
+                    .getSequenceSetId().equals(av.getSequenceSetId())))
+    {
+      return;
+    }
+    // do we want to thread this ? (contention with seqsel and colsel locks, I
+    // suspect)
+    // rules are: colsel is copied if there is a real intersection between
+    // sequence selection
+    boolean repaint = false, copycolsel = true;
+    // if (!av.isSelectionGroupChanged(false))
+    {
+      SequenceGroup sgroup = null;
+      if (seqsel != null && seqsel.getSize()>0)
+      {
+        if (av.getAlignment() == null)
+        {
+          jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+                  + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+                  + " 's alignment is NULL! returning immediatly.");
+          return;
+        }
+        sgroup = seqsel.intersect(av.getAlignment(),
+                (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+        if ((sgroup == null || sgroup.getSize() == 0)
+                || (colsel == null || colsel.size() == 0))
+        {
+          // don't copy columns if the region didn't intersect.
+          copycolsel = false;
+        }
+      }
+      if (sgroup != null && sgroup.getSize() > 0)
+      {
+        av.setSelectionGroup(sgroup);
+      }
+      else
+      {
+        av.setSelectionGroup(null);
+      }
+      av.isSelectionGroupChanged(true);
+      repaint = true;
+    }
+    if (copycolsel)
+    {
+      // the current selection is unset or from a previous message
+      // so import the new colsel.
+      if (colsel == null || colsel.size() == 0)
+      {
+        if (av.getColumnSelection() != null)
+        {
+          av.getColumnSelection().clear();
+          repaint=true;
+        }
+      }
+      else
+      {
+        // TODO: shift colSel according to the intersecting sequences
+        if (av.getColumnSelection() == null)
+        {
+          av.setColumnSelection(new ColumnSelection(colsel));
+        }
+        else
+        {
+          av.getColumnSelection().setElementsFrom(colsel);
+        }
+      }
+      av.isColSelChanged(true);
+      repaint = true;
+    }
+    if (copycolsel && av.hasHiddenColumns()
+            && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
+    {
+      System.err.println("Bad things");
+    }
+    if (repaint)
+    {
+      // probably finessing with multiple redraws here
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+      // ap.paintAlignment(false);
+    }
+  }
+}