X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=f4f2cfd2bebf7e3aef5ed8ed85b38ed687497335;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=ebde2cfb8cb3b303592fbe0e610ca50d374786c5;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index ebde2cf..f4f2cfd 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -24,11 +24,14 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
 
 public class SeqPanel
-    extends Panel
+    extends Panel implements MouseMotionListener, MouseListener, SequenceListener
 {
 
   public SeqCanvas seqCanvas;
@@ -36,20 +39,35 @@ public class SeqPanel
 
   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;
+  boolean seqEditOccurred = false;
 
   ScrollThread scrollThread = null;
   boolean mouseDragging = false;
-
   boolean editingSeqs = false;
   boolean groupEditing = false;
 
+  int oldSeq = -1;
+  boolean changeEndSeq = false;
+  boolean changeStartSeq = false;
+  boolean changeEndRes = false;
+  boolean changeStartRes = false;
+  SequenceGroup stretchGroup = null;
+
+  StringBuffer keyboardNo1;
+  StringBuffer keyboardNo2;
+
+  boolean mouseWheelPressed = false;
+  Point lastMousePress;
+
+  EditCommand editCommand;
+
+  StructureSelectionManager ssm;
+
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
@@ -60,126 +78,487 @@ public class SeqPanel
 
     ap = p;
 
-    seqCanvas.addMouseMotionListener(new MouseMotionAdapter()
+    seqCanvas.addMouseMotionListener(this);
+    seqCanvas.addMouseListener(this);
+    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm.addStructureViewerListener(this);
+
+    seqCanvas.repaint();
+  }
+
+  void endEditing()
+  {
+    if (editCommand != null && editCommand.getSize() > 0)
     {
-      public void mouseMoved(MouseEvent evt)
+      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 =
+        (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.colSel.isVisible(seqCanvas.cursorX))
+    {
+      int original = seqCanvas.cursorX - dx;
+      int maxWidth = av.alignment.getWidth();
+
+      while (!av.colSel.isVisible(seqCanvas.cursorX)
+             && seqCanvas.cursorX < maxWidth
+             && seqCanvas.cursorX > 0)
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        doMouseMoved(evt);
+        seqCanvas.cursorX += dx;
       }
 
-      public void mouseDragged(MouseEvent evt)
+      if (seqCanvas.cursorX >= maxWidth
+          || !av.colSel.isVisible(seqCanvas.cursorX))
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        if (editingSeqs)
+        seqCanvas.cursorX = original;
+      }
+    }
+    scrollToVisible();
+  }
+
+  void scrollToVisible()
+  {
+    if (seqCanvas.cursorX < 0)
+    {
+      seqCanvas.cursorX = 0;
+    }
+    else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+    {
+      seqCanvas.cursorX = av.alignment.getWidth() - 1;
+    }
+
+    if (seqCanvas.cursorY < 0)
+    {
+      seqCanvas.cursorY = 0;
+    }
+    else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+    {
+      seqCanvas.cursorY = av.alignment.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);
+      }
+      while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+      {
+
+        if (!ap.scrollRight(false))
         {
-          doMouseDragged(evt);
+          break;
         }
-        else
+      }
+      while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+      {
+        if (!ap.scrollRight(true))
         {
-          doMouseDraggedDefineMode(evt);
+          break;
         }
       }
-    });
+    }
+    setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+                     seqCanvas.cursorX, seqCanvas.cursorY);
 
-    seqCanvas.addMouseListener(new MouseAdapter()
+    seqCanvas.repaint();
+  }
+
+  void setSelectionAreaAtCursor(boolean topLeft)
+  {
+    SequenceI sequence =
+        (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+    if (av.getSelectionGroup() != null)
     {
-      public void mouseReleased(MouseEvent evt)
+      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++)
       {
-        if (av.getWrapAlignment())
-        {
-          return;
-        }
-        if (editingSeqs)
+        int index = av.alignment.findIndex(sg.getSequenceAt(i));
+        if (index > max)
         {
-          doMouseReleased(evt);
+          max = index;
         }
-        else
+        if (index < min)
         {
-          doMouseReleasedDefineMode(evt);
+          min = index;
         }
-
       }
 
-      public void mousePressed(MouseEvent evt)
+      max++;
+
+      if (topLeft)
       {
-        if (av.getWrapAlignment())
+        sg.setStartRes(seqCanvas.cursorX);
+        if (sg.getEndRes() < seqCanvas.cursorX)
         {
-          return;
+          sg.setEndRes(seqCanvas.cursorX);
         }
-        if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
-        {
-          if (evt.isAltDown() || evt.isControlDown())
-          {
-            groupEditing = true;
-          }
 
-          editingSeqs = true;
-          doMousePressed(evt);
-        }
-        else
+        min = seqCanvas.cursorY;
+      }
+      else
+      {
+        sg.setEndRes(seqCanvas.cursorX);
+        if (sg.getStartRes() > seqCanvas.cursorX)
         {
-          doMousePressedDefineMode(evt);
+          sg.setStartRes(seqCanvas.cursorX);
         }
+
+        max = seqCanvas.cursorY + 1;
       }
 
-      public void mouseExited(MouseEvent evt)
+      if (min > max)
       {
-        if (av.getWrapAlignment() || editingSeqs)
+        // Only the user can do this
+        av.setSelectionGroup(null);
+      }
+      else
+      {
+        // Now add any sequences between min and max
+        sg.getSequences(null).removeAllElements();
+        for (int i = min; i < max; i++)
         {
-          return;
+          sg.addSequence(av.alignment.getSequenceAt(i), false);
         }
-        doMouseExitedDefineMode(evt);
+      }
+    }
+
+    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);
+  }
+
+  void insertGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX;
+    editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+    endEditing();
+  }
+
+  void deleteGapAtCursor(boolean group)
+  {
+    groupEditing = group;
+    startseq = seqCanvas.cursorY;
+    lastres = seqCanvas.cursorX + getKeyboardNo1();
+    editSequence(false, seqCanvas.cursorX);
+    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;
+    }
+  }
+
+
+  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)
+    {
 
-      public void mouseEntered(MouseEvent evt)
+      if (obj != "")
       {
-        if (av.getWrapAlignment() || editingSeqs)
-        {
-          return;
-        }
-        doMouseEnteredDefineMode(evt);
+        text.append(obj + " (" + sequence.findPosition(res) +
+                    ")");
       }
+    }
+
+    ap.alignFrame.statusBar.setText(text.toString());
 
-    });
-    seqCanvas.repaint();
   }
 
-  public void doMouseReleased(MouseEvent evt)
+  public void mousePressed(MouseEvent evt)
   {
+    lastMousePress = evt.getPoint();
 
-    if (seqEditOccurred > -1)
+    //For now, ignore the mouseWheel font resizing on Macs
+    //As the Button2_mask always seems to be true
+    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
+        InputEvent.BUTTON2_MASK && !av.MAC)
     {
-      editOccurred(seqEditOccurred);
+      mouseWheelPressed = true;
+      return;
     }
 
-    startseq = -1;
-    lastres = -1;
-    seqEditOccurred = -1;
-    editingSeqs = false;
-    groupEditing = false;
-    ap.repaint();
+    if (evt.isShiftDown()
+        || evt.isControlDown()
+        || evt.isAltDown())
+    {
+      if (evt.isControlDown() || evt.isAltDown())
+      {
+        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;
   }
 
-  public void doMousePressed(MouseEvent evt)
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseReleased(MouseEvent evt)
   {
-    ap.alignFrame.addHistoryItem(new HistoryItem(
-        "Edit Sequence", av.alignment, HistoryItem.EDIT));
-    int seq;
-    int res;
+    mouseDragging = false;
+    mouseWheelPressed = false;
+    ap.paintAlignment(true);
 
+    if (!editingSeqs)
+    {
+      doMouseReleasedDefineMode(evt);
+      return;
+    }
+
+    endEditing();
+
+  }
+
+  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(getSize().width);
+      if (cwidth < 1)
+      {
+        return 0;
+      }
+
+      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();
 
-    res = x / av.getCharWidth() + av.getStartRes();
-    seq = y / av.getCharHeight() + av.getStartSeq();
+    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.alignment.getHeight() - 1);
+      if (seq < 0)
+      {
+        seq = 0;
+      }
+    }
+    else
+    {
+      seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                     av.alignment.getHeight() - 1);
+      if (seq < 0)
+      {
+        seq = 0;
+      }
+    }
+
+    return seq;
+  }
+
+  public void doMousePressed(MouseEvent evt)
+  {
+
+    int seq = findSeq(evt);
+    int res = findRes(evt);
 
     if (seq < av.getAlignment().getHeight() &&
         res < av.getAlignment().getSequenceAt(seq).getLength())
@@ -200,296 +579,696 @@ public class SeqPanel
     return;
   }
 
-  public void doMouseMoved(MouseEvent evt)
+
+  String lastMessage;
+  public void mouseOverSequence(SequenceI sequence, int index)
   {
-    int res = 0, seq = 0;
-    int x = evt.getX();
-    int y = evt.getY();
-    if (av.wrapAlignment)
+    String tmp = sequence.hashCode()+index+"";
+    if (lastMessage == null || !lastMessage.equals(tmp))
+      ssm.mouseOverSequence(sequence, index);
+
+    lastMessage = tmp;
+  }
+
+
+  public void highlightSequence(jalview.datamodel.SequenceI seq, int index)
+  {
+    if(av.alignment.findIndex(seq)>-1)
+    {
+      SearchResults highlight = new SearchResults();
+      highlight.addResult(seq,index,index);
+      seqCanvas.highlightSearchResults(highlight);
+    }
+  }
+
+  public void updateColours(SequenceI seq, int index)
+  {
+    System.out.println("update the seqPanel colours");
+    //repaint();
+  }
+
+  public void mouseMoved(MouseEvent evt)
+  {
+    int res = findRes(evt);
+    int seq = findSeq(evt);
+
+    if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+    {
+      if (tooltip != null)
+      {
+        tooltip.setTip("");
+      }
+      return;
+    }
+
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    if (res > sequence.getLength())
+    {
+      if (tooltip != null)
+      {
+        tooltip.setTip("");
+      }
+      return;
+    }
+
+
+    if (ssm != null)
+      mouseOverSequence(sequence, sequence.findPosition(res));
+
+
+    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());
+
+    StringBuffer tooltipText = new StringBuffer();
+    SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+    if (groups != null)
+    {
+      for (int g = 0; g < groups.length; g++)
+      {
+        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+        {
+          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());
+          }
+          tooltipText.append("\n");
+        }
+      }
+    }
+
+    // use aa to see if the mouse pointer is on a
+    if (av.showSequenceFeatures
+        && sequence.getSequenceFeatures() != null
+        && av.featuresDisplayed != null)
     {
-      y -= 2 * av.charHeight;
-      int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
 
-      res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +
-          x / av.getCharWidth() + av.getStartRes();
+      Vector allFeatures = getAllFeaturesAtRes(sequence,
+                                               sequence.findPosition(res));
 
-      y %= chunkHeight;
-      seq = y / av.getCharHeight() + av.getStartSeq();
+      int index = 0;
+      while (index < allFeatures.size())
+      {
+        SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
 
+        tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+
+        if (sf.getDescription() != null)
+        {
+          tooltipText.append(" " + sf.getDescription());
+        }
+
+        if (sf.getValue("status") != null)
+        {
+          String status = sf.getValue("status").toString();
+          if (status.length() > 0)
+          {
+            tooltipText.append(" (" + sf.getValue("status") + ")");
+          }
+        }
+        tooltipText.append("\n");
+
+        index++;
+      }
+    }
+
+    if (tooltip == null)
+    {
+      tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
     }
     else
     {
-      res = x / av.getCharWidth() + av.getStartRes();
-      seq = y / av.getCharHeight() + av.getStartSeq();
+      tooltip.setTip(tooltipText.toString());
     }
+  }
 
-    if (seq >= av.getAlignment().getHeight())
+  Vector getAllFeaturesAtRes(SequenceI seq, int res)
+  {
+    Vector allFeatures = new Vector();
+    int index = 0;
+    if (seq.getSequenceFeatures() != null)
     {
+      while (index < seq.getSequenceFeatures().length)
+      {
+        SequenceFeature sf = seq.getSequenceFeatures()[index];
+        if (sf.getBegin() <= res &&
+            sf.getEnd() >= res)
+        {
+          if (av.featuresDisplayed.containsKey(sf.getType()))
+          {
+            allFeatures.addElement(sf);
+          }
+        }
+        index++;
+      }
+    }
+    return allFeatures;
+  }
+
+  Tooltip tooltip;
+
+  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.y)
+          > Math.abs(evt.getX() - lastMousePress.x))
+      {
+        int fontSize = av.font.getSize();
+
+        if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+        {
+          fontSize--;
+        }
+        else if (evt.getY() > lastMousePress.y)
+        {
+          fontSize++;
+        }
+
+        if (fontSize < 1)
+        {
+          fontSize = 1;
+        }
+
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.charWidth = oldWidth;
+      }
+      else
+      {
+        if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+        {
+          av.charWidth--;
+        }
+        else if (evt.getX() > lastMousePress.x)
+        {
+          av.charWidth++;
+        }
+
+        if (av.charWidth < 1)
+        {
+          av.charWidth = 1;
+        }
+      }
+
+      ap.fontChanged();
+
+      FontMetrics fm = getFontMetrics(av.getFont());
+      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+      lastMousePress = evt.getPoint();
+
+      ap.paintAlignment(false);
+      ap.annotationPanel.image = null;
+      return;
+    }
+
+    if (!editingSeqs)
+    {
+      doMouseDraggedDefineMode(evt);
       return;
     }
-
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    if (res > sequence.getLength())
+
+    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);
+    }
+
+  }
+
+  synchronized void editSequence(boolean insertGap, int startres)
+  {
+    int fixedLeft = -1;
+    int fixedRight = -1;
+    boolean fixedColumns = false;
+    SequenceGroup sg = av.getSelectionGroup();
+
+    SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+    if (!groupEditing && av.hasHiddenRows)
+    {
+      if (av.hiddenRepSequences != null
+          && av.hiddenRepSequences.containsKey(seq))
+      {
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        groupEditing = true;
+      }
+    }
+
+    StringBuffer message = new StringBuffer();
+    if (groupEditing)
+    {
+      message.append("Edit group:");
+      if (editCommand == null)
+      {
+        editCommand = new EditCommand("Edit Group");
+      }
+    }
+    else
     {
-      return;
+      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);
+      }
     }
 
-    Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-    String aa = "";
-    if (obj != null)
+    if (insertGap)
     {
-      aa = obj.toString();
+      message.append(" insert ");
     }
-
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                                         sequence.getName());
-    if (aa != "")
+    else
     {
-      text.append("  Residue: " + aa + " (" +
-                  av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+      message.append(" delete ");
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+    message.append(Math.abs(startres - lastres) + " gaps.");
+    ap.alignFrame.statusBar.setText(message.toString());
 
-    // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    //Are we editing within a selection group?
+    if (groupEditing
+        || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
     {
-      Vector features = sequence.getSequenceFeatures();
-      Enumeration e = features.elements();
-      StringBuffer sbuffer = new StringBuffer();
+      fixedColumns = true;
 
-      while (e.hasMoreElements())
+      //sg might be null as the user may only see 1 sequence,
+      //but the sequence represents a group
+      if (sg == null)
       {
-        SequenceFeature sf = (SequenceFeature) e.nextElement();
-        if (sf.getStart() <= sequence.findPosition(res) &&
-            sf.getEnd() >= sequence.findPosition(res))
+        if (av.hiddenRepSequences == null
+            || !av.hiddenRepSequences.containsKey(seq))
         {
-          if (sbuffer.length() > 0)
-          {
-            sbuffer.append("; ");
-          }
-          sbuffer.append(sf.getType() + " " + sf.getDescription());
-          if (sf.getStatus().length() > 0)
-          {
-            sbuffer.append(" (" + sf.getStatus() + ")");
-          }
+          endEditing();
+          return;
         }
 
+        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
       }
-    }
 
-  }
+      fixedLeft = sg.getStartRes();
+      fixedRight = sg.getEndRes();
 
-  public void doMouseDragged(MouseEvent evt)
-  {
+      if ( (startres < fixedLeft && lastres >= fixedLeft)
+          || (startres >= fixedLeft && lastres < fixedLeft)
+          || (startres > fixedRight && lastres <= fixedRight)
+          || (startres <= fixedRight && lastres > fixedRight))
+      {
+        endEditing();
+        return;
+      }
 
-    // If we're dragging we're editing
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    if (res < 0)
-    {
-      res = 0;
+      if (fixedLeft > startres)
+      {
+        fixedRight = fixedLeft - 1;
+        fixedLeft = 0;
+      }
+      else if (fixedRight < startres)
+      {
+        fixedLeft = fixedRight;
+        fixedRight = -1;
+      }
     }
 
-    if (lastres == -1 || lastres == res)
+    if (av.hasHiddenColumns)
     {
-      return;
-    }
+      fixedColumns = true;
+      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-    boolean dragRight = true;
-    if (res < av.getAlignment().getWidth() && res < lastres)
-    {
-      dragRight = false;
-    }
+      if ( (insertGap && startres > y1 && lastres < y1)
+          || (!insertGap && startres < y2 && lastres > y2))
+      {
+        endEditing();
+        return;
+      }
 
-    if (res != lastres)
-    {
-      // Group editing
-      if (groupEditing)
+      //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+      //Selection spans a hidden region
+      if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
       {
-        SequenceGroup sg = av.getSelectionGroup();
-        if (sg == null)
+        if (startres >= y2)
         {
-          lastres = -1;
-          return;
+          fixedLeft = y2;
+        }
+        else
+        {
+          fixedRight = y2 - 1;
         }
+      }
+    }
+
+    if (groupEditing)
+    {
+      Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+      int g, groupSize = vseqs.size();
+      SequenceI[] groupSeqs = new SequenceI[groupSize];
+      for (g = 0; g < groupSeqs.length; g++)
+      {
+        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+      }
 
-        // drag to right
-        if (dragRight)
+      // 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.alignment.getWidth() - 1
+            )
         {
-          sg.setEndRes(sg.getEndRes() + (res - lastres));
+          sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+          fixedRight = sg.getEndRes();
         }
 
-        // drag to left
-        else
+        // 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--)
         {
-          /// Are we able to delete?
-          // ie are all columns blank?
-          boolean deleteAllowed = false;
-          for (int s = 0; s < sg.getSize(); s++)
+          blank = true;
+
+          for (g = 0; g < groupSize; g++)
           {
-            SequenceI seq = sg.getSequenceAt(s);
-            for (int j = res; j < lastres; j++)
+            for (int j = 0; j < startres - lastres; j++)
             {
-              if (seq.getSequence().length() <= j)
+              if (!jalview.util.Comparison.isGap(
+                  groupSeqs[g].getCharAt(fixedRight - j)))
               {
-                continue;
+                blank = false;
+                break;
               }
+            }
+          }
+          if (blank)
+          {
+            break;
+          }
+        }
+
+        if (!blank)
+        {
+          if (sg.getSize() == av.alignment.getHeight())
+          {
+            if ( (av.hasHiddenColumns
+                  &&
+                  startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
+            {
+              endEditing();
+              return;
+            }
 
-              if (!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))
+            int alWidth = av.alignment.getWidth();
+            if (av.hasHiddenRows)
+            {
+              int hwidth = av.alignment.getHiddenSequences().getWidth();
+              if (hwidth > alWidth)
               {
-                // Not a gap, block edit not valid
-                res = j + 1;
-                deleteAllowed = false;
-                continue;
+                alWidth = hwidth;
               }
-              deleteAllowed = true;
             }
+            //We can still insert gaps if the selectionGroup
+            //contains all the sequences
+            sg.setEndRes(sg.getEndRes() + startres - lastres);
+            fixedRight = alWidth + startres - lastres;
           }
-
-          if (!deleteAllowed)
+          else
           {
-            lastres = -1;
+            endEditing();
             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 left
+      else if (!insertGap)
+      {
+        /// Are we able to delete?
+        // ie are all columns blank?
 
-          // drag to right
-          if (dragRight)
+        for (g = 0; g < groupSize; g++)
+        {
+          for (int j = startres; j < lastres; j++)
           {
-            for (int j = lastres; j < res; j++)
+            if (groupSeqs[g].getLength() <= j)
             {
-              insertChar(j, k);
+              continue;
             }
-          }
 
-          // drag to left
-          else
-          {
-            for (int j = res; j < lastres; j++)
+            if (!jalview.util.Comparison.isGap(
+                groupSeqs[g].getCharAt(j)))
             {
-              if (s.getLength() > j)
-              {
-                deleteChar(res, k);
-              }
+              // Not a gap, block edit not valid
+              endEditing();
+              return;
             }
           }
         }
       }
-      else /////Editing a single sequence///////////
+
+      if (insertGap)
       {
-        if (res < av.getAlignment().getWidth() && res > lastres)
+        // dragging to the right
+        if (fixedColumns && fixedRight != -1)
         {
-          // dragging to the right
-          for (int j = lastres; j < res; j++)
+          for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, startseq);
+            insertChar(j, groupSeqs, fixedRight);
           }
         }
-        else if (res < av.getAlignment().getWidth() && res < lastres)
+        else
+        {
+          editCommand.appendEdit(EditCommand.INSERT_GAP,
+                                 groupSeqs,
+                                 startres, startres - lastres,
+                                 av.alignment,
+                                 true);
+        }
+      }
+      else
+      {
+        // dragging to the left
+        if (fixedColumns && fixedRight != -1)
         {
-          // dragging to the left
-          for (int j = lastres; j > res; j--)
+          for (int j = lastres; j > startres; j--)
           {
-            if (jalview.util.Comparison.isGap(
-                av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))
-            {
+            deleteChar(startres, groupSeqs, fixedRight);
+          }
+        }
+        else
+        {
+          editCommand.appendEdit(EditCommand.DELETE_GAP,
+                                 groupSeqs,
+                                 startres, lastres - startres,
+                                 av.alignment,
+                                 true);
+        }
 
-              deleteChar(res, startseq);
-            }
-            else
+      }
+    }
+    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.alignment,
+                                 true);
+        }
+      }
+      else
+      {
+        // 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.alignment,
+                                   true);
+          }
+        }
       }
     }
 
-    endEdit = res;
-    lastres = res;
-    seqCanvas.repaint();
-  }
-
-  public void drawChars(int seqstart, int seqend, int start)
-  {
-    seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,
-                        av.getStartRes(), av.getStartSeq(), 0);
+    lastres = startres;
     seqCanvas.repaint();
   }
 
-  public void insertChar(int j, int seq)
-  {
-    av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
-    seqEditOccurred = seq;
-  }
-
-  public void deleteChar(int j, int seq)
-  {
-
-    av.alignment.getSequenceAt(seq).deleteCharAt(j);
-    seqEditOccurred = seq;
-    av.alignment.getWidth();
-    repaint();
-  }
-
-  void editOccurred(int i)
+  void insertChar(int j, SequenceI[] seq, int fixedColumn)
   {
-    if (endEdit == startEdit)
+    int blankColumn = fixedColumn;
+    for (int s = 0; s < seq.length; s++)
     {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
-    }
+      //Find the next gap before the end of the visible region boundary
+      //If lastCol > j, theres a boundary after the gap insertion
 
-    av.updateConservation();
-    av.updateConsensus();
-
-    // Y O Y CLUSTALX
-    ColourSchemeI cs = av.getGlobalColourScheme();
-    if (cs.conservationApplied())
-    {
-      if (cs instanceof ClustalxColourScheme)
+      for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
-        jalview.analysis.Conservation c = new jalview.analysis.Conservation
-            ("All",
-             ResidueProperties.propHash, 3,
-             av.alignment.getSequences(), 0,
-             av.alignment.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, av.ConsPercGaps);
+        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        {
+          //Theres a space, so break and insert the gap
+          break;
+        }
+      }
 
-        ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
-        cs.setConservation(c);
-        av.setGlobalColourScheme(cs);
+      if (blankColumn <= j)
+      {
+        blankColumn = fixedColumn;
+        endEditing();
+        return;
       }
     }
 
-    if (cs instanceof ClustalxColourScheme)
-    {
-      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                 av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
-    }
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           blankColumn, 1, av.alignment, true);
+
+    editCommand.appendEdit(EditCommand.INSERT_GAP,
+                           seq,
+                           j, 1, av.alignment,
+                           true);
+
+  }
+
+  void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+  {
+
+    editCommand.appendEdit(EditCommand.DELETE_GAP,
+                           seq,
+                           j, 1, av.alignment, true);
 
+    editCommand.appendEdit(EditCommand.INSERT_GAP,
+                           seq,
+                           fixedColumn, 1, av.alignment, true);
   }
 
 //////////////////////////////////////////
 /////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();
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+      scrollThread = null;
+    }
+
+    int res = findRes(evt);
+    int seq = findSeq(evt);
     oldSeq = seq;
+    startWrapBlock = wrappedBlock;
+
+    if (seq == -1)
+    {
+      return;
+    }
 
     SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -514,7 +1293,7 @@ public class SeqPanel
       }
     }
 
-    else if (!stretchGroup.sequences.contains(sequence)
+    else if (!stretchGroup.getSequences(null).contains(sequence)
              || stretchGroup.getStartRes() > res
              || stretchGroup.getEndRes() < res)
     {
@@ -530,13 +1309,52 @@ public class SeqPanel
               allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
-            av.setSelectionGroup(stretchGroup);
             break;
           }
         }
       }
+      av.setSelectionGroup(stretchGroup);
+    }
+
+    // DETECT RIGHT MOUSE BUTTON IN AWT
+    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+        InputEvent.BUTTON3_MASK)
+    {
+      Vector allFeatures = getAllFeaturesAtRes(sequence,
+                                               sequence.findPosition(res));
+
+      Vector links = null;
+      if (allFeatures != null)
+      {
+        for (int i = 0; i < allFeatures.size(); i++)
+        {
+          SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+          if (sf.links != null)
+          {
+            links = new Vector();
+            for (int j = 0; j < sf.links.size(); j++)
+            {
+              links.addElement(sf.links.elementAt(j));
+            }
+          }
+        }
+      }
+      APopupMenu popup = new APopupMenu(ap, null, links);
+      this.add(popup);
+      popup.show(this, evt.getX(), evt.getY());
+      return;
+    }
+
+    if (av.cursorMode)
+    {
+      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.repaint();
+      return;
     }
 
+    //Only if left mouse button do we want to change group sizes
+
     if (stretchGroup == null)
     {
       // define a new group here
@@ -559,55 +1377,37 @@ public class SeqPanel
       }
 
     }
-
-    // DETECT RIGHT MOUSE BUTTON IN AWT
-    else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
-             InputEvent.BUTTON3_MASK)
-    {
-      APopupMenu popup = new APopupMenu(ap, null, null);
-      this.add(popup);
-      popup.show(this, evt.getX(), evt.getY());
-    }
-
-    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;
-    }
-
   }
 
-  boolean changeEndSeq = false;
-  boolean changeStartSeq = false;
-  boolean changeEndRes = false;
-  boolean changeStartRes = false;
-  SequenceGroup stretchGroup = null;
-
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
-    if(mouseDragging)
-     {
-       stretchGroup.recalcConservation();
-       mouseDragging = false;
-     }
-
     if (stretchGroup == null)
     {
       return;
     }
 
-    if(stretchGroup.cs!=null)
+    if (stretchGroup.cs != null)
     {
+      if (stretchGroup.cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+            stretchGroup.getSequences(av.hiddenRepSequences),
+            stretchGroup.getWidth());
+      }
+
+      if (stretchGroup.cs instanceof Blosum62ColourScheme
+          || stretchGroup.cs instanceof PIDColourScheme
+          || stretchGroup.cs.conservationApplied()
+          || stretchGroup.cs.getThreshold() > 0)
+      {
+        stretchGroup.recalcConservation();
+      }
+
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
                                           stretchGroup.getName());
+        stretchGroup.recalcConservation();
       }
       else
       {
@@ -618,22 +1418,33 @@ public class SeqPanel
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-    seqCanvas.repaint();
-    ap.repaint();
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    ap.paintAlignment(true);
   }
 
-  boolean remove = false;
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    int y = evt.getY() / av.getCharHeight() + av.getStartSeq();
+    int res = findRes(evt);
+    int y = findSeq(evt);
+
+    if (wrappedBlock != startWrapBlock)
+    {
+      return;
+    }
 
     if (stretchGroup == null)
     {
       return;
     }
 
-    if (res > av.alignment.getWidth())
+    mouseDragging = true;
+
+    if (y > av.alignment.getHeight())
+    {
+      y = av.alignment.getHeight() - 1;
+    }
+
+    if (res >= av.alignment.getWidth())
     {
       res = av.alignment.getWidth() - 1;
     }
@@ -643,38 +1454,34 @@ public class SeqPanel
       // 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())
+    if (res < 0)
     {
-      res = av.getEndRes();
+      res = 0;
     }
 
     if (changeEndRes)
     {
-      if (res > stretchGroup.getStartRes() - 1)
+      if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
       }
     }
     else if (changeStartRes)
     {
-      if (res < stretchGroup.getEndRes() + 1)
+      if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
       }
     }
 
     int dragDirection = 0;
+
     if (y > oldSeq)
     {
       dragDirection = 1;
@@ -684,16 +1491,22 @@ public class SeqPanel
       dragDirection = -1;
     }
 
-    while (y != oldSeq && oldSeq > 0 && y < av.alignment.getHeight())
+    while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
       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))
+      if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
       }
@@ -703,11 +1516,22 @@ public class SeqPanel
         {
           stretchGroup.addSequence(seq, false);
         }
+
         stretchGroup.addSequence(nextSeq, false);
       }
     }
-    oldSeq = y;
-    mouseDragging = true;
+
+    if (oldSeq < 0)
+    {
+      oldSeq = -1;
+    }
+
+    if (res > av.endRes || res < av.startRes
+        || y < av.startSeq || y > av.endSeq)
+    {
+      mouseExited(evt);
+    }
+
     if (scrollThread != null)
     {
       scrollThread.setEvent(evt);
@@ -716,25 +1540,54 @@ public class SeqPanel
     seqCanvas.repaint();
   }
 
-  public void doMouseEnteredDefineMode(MouseEvent e)
+  public void mouseEntered(MouseEvent e)
   {
+    if (oldSeq < 0)
+    {
+      oldSeq = 0;
+    }
+
     if (scrollThread != null)
     {
       scrollThread.running = false;
+      scrollThread = null;
     }
   }
 
-  public void doMouseExitedDefineMode(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
     {
       return;
     }
 
-    if (mouseDragging)
+    if (mouseDragging && scrollThread == null)
     {
       scrollThread = new ScrollThread();
     }
+  }
+
+  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);
+    }
 
   }
 
@@ -764,6 +1617,7 @@ public class SeqPanel
       running = true;
       while (running)
       {
+
         if (evt != null)
         {
 
@@ -780,12 +1634,12 @@ public class SeqPanel
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = ap.scrollRight(true);
+            running = ap.scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = ap.scrollRight(false);
+            running = ap.scrollRight(true);
           }
         }