X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=11ee700584d2865731fab6aa62796e5ddf1c0814;hb=fdf90308b1b24f4063648449c5f316ced24c938b;hp=87e655bc53aa330c0f6ab8079ef28d79b5e33744;hpb=7aa1e482163172b1ea16622eb2195fc8f2039951;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 87e655b..11ee700 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -25,6 +25,7 @@ import jalview.bin.Cache;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
@@ -48,6 +49,7 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -76,6 +78,82 @@ public class SeqPanel extends JPanel
         implements MouseListener, MouseMotionListener, MouseWheelListener,
         SequenceListener, SelectionListener
 {
+  /*
+   * a class that holds computed mouse position
+   * - column of the alignment (0...)
+   * - sequence offset (0...)
+   * - annotation row offset (0...)
+   * where annotation offset is -1 unless the alignment is shown
+   * in wrapped mode, annotations are shown, and the mouse is
+   * over an annnotation row
+   */
+  static class MousePos
+  {
+    /*
+     * alignment column position of cursor (0...)
+     */
+    final int column;
+
+    /*
+     * index in alignment of sequence under cursor,
+     * or nearest above if cursor is not over a sequence
+     */
+    final int seqIndex;
+
+    /*
+     * index in annotations array of annotation under the cursor
+     * (only possible in wrapped mode with annotations shown),
+     * or -1 if cursor is not over an annotation row
+     */
+    final int annotationIndex;
+
+    MousePos(int col, int seq, int ann)
+    {
+      column = col;
+      seqIndex = seq;
+      annotationIndex = ann;
+    }
+
+    boolean isOverAnnotation()
+    {
+      return annotationIndex != -1;
+    }
+
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (obj == null || !(obj instanceof MousePos))
+      {
+        return false;
+      }
+      MousePos o = (MousePos) obj;
+      boolean b = (column == o.column && seqIndex == o.seqIndex
+              && annotationIndex == o.annotationIndex);
+      // System.out.println(obj + (b ? "= " : "!= ") + this);
+      return b;
+    }
+
+    /**
+     * A simple hashCode that ensures that instances that satisfy equals() have
+     * the same hashCode
+     */
+    @Override
+    public int hashCode()
+    {
+      return column + seqIndex + annotationIndex;
+    }
+
+    /**
+     * toString method for debug output purposes only
+     */
+    @Override
+    public String toString()
+    {
+      return String.format("c%d:s%d:a%d", column, seqIndex,
+              annotationIndex);
+    }
+  }
+
   private static final int MAX_TOOLTIP_LENGTH = 300;
 
   public SeqCanvas seqCanvas;
@@ -83,14 +161,9 @@ public class SeqPanel extends JPanel
   public AlignmentPanel ap;
 
   /*
-   * last column position for mouseMoved event
-   */
-  private int lastMouseColumn;
-
-  /*
-   * last sequence offset for mouseMoved event
+   * last position for mouseMoved event
    */
-  private int lastMouseSeq;
+  private MousePos lastMousePosition;
 
   protected int editLastRes;
 
@@ -176,15 +249,91 @@ public class SeqPanel extends JPanel
       ssm.addStructureViewerListener(this);
       ssm.addSelectionListener(this);
     }
-
-    lastMouseColumn = -1;
-    lastMouseSeq = -1;
   }
 
   int startWrapBlock = -1;
 
   int wrappedBlock = -1;
 
+  MousePos findMousePosition(MouseEvent evt)
+  {
+    return findMousePosition(evt, null);
+  }
+
+  /**
+   * Computes the column and sequence row (and possibly annotation row when in
+   * wrapped mode) for the given mouse position
+   * 
+   * @param evt
+   * @return
+   */
+  MousePos findMousePosition(MouseEvent evt, String debug)
+  {
+    int col = findColumn(evt, debug);
+    int seqIndex = -1;
+    int annIndex = -1;
+    int y = evt.getY();
+
+    int charHeight = av.getCharHeight();
+    int alignmentHeight = av.getAlignment().getHeight();
+    if (debug != null)
+    {
+      System.out.println(String.format(
+              "%s: charHeight %d alHeight %d canvasWidth %d canvasHeight %d",
+              debug, charHeight, alignmentHeight, seqCanvas.getWidth(),
+              seqCanvas.getHeight()));
+    }
+    if (av.getWrapAlignment())
+    {
+      seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(),
+              seqCanvas.getHeight());
+
+      /*
+       * yPos modulo height of repeating width
+       */
+      int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx;
+
+      /*
+       * height of sequences plus space / scale above,
+       * plus gap between sequences and annotations
+       */
+      int alignmentHeightPixels = seqCanvas.wrappedSpaceAboveAlignment
+              + alignmentHeight * charHeight
+              + SeqCanvas.SEQS_ANNOTATION_GAP;
+      if (yOffsetPx >= alignmentHeightPixels)
+      {
+        /*
+         * mouse is over annotations; find annotation index, also set
+         * last sequence above (for backwards compatible behaviour)
+         */
+        AlignmentAnnotation[] anns = av.getAlignment()
+                .getAlignmentAnnotation();
+        int rowOffsetPx = yOffsetPx - alignmentHeightPixels;
+        annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns);
+        seqIndex = alignmentHeight - 1;
+      }
+      else
+      {
+        /*
+         * mouse is over sequence (or the space above sequences)
+         */
+        yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment;
+        if (yOffsetPx >= 0)
+        {
+          seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1);
+        }
+      }
+    }
+    else
+    {
+      ViewportRanges ranges = av.getRanges();
+      seqIndex = Math.min((y / charHeight) + ranges.getStartSeq(),
+              alignmentHeight - 1);
+      seqIndex = Math.min(seqIndex, ranges.getEndSeq());
+    }
+
+    return new MousePos(col, seqIndex, annIndex);
+  }
   /**
    * Returns the aligned sequence position (base 0) at the mouse position, or
    * the closest visible one
@@ -194,13 +343,19 @@ public class SeqPanel extends JPanel
    */
   int findColumn(MouseEvent evt)
   {
+    return findColumn(evt, null);
+  }
+
+  int findColumn(MouseEvent evt, String debug)
+  {
     int res = 0;
     int x = evt.getX();
 
-    int startRes = av.getRanges().getStartRes();
+    final int startRes = av.getRanges().getStartRes();
+    final int charWidth = av.getCharWidth();
+
     if (av.getWrapAlignment())
     {
-
       int hgap = av.getCharHeight();
       if (av.getScaleAboveWrapped())
       {
@@ -212,35 +367,50 @@ public class SeqPanel extends JPanel
 
       int y = evt.getY();
       y = Math.max(0, y - hgap);
-      x = Math.max(0, x - seqCanvas.getLabelWidthWest());
+      x -= seqCanvas.getLabelWidthWest();
+      if (debug != null)
+      {
+        System.out.println(
+                String.format("%s: x %d labelWest %d charWidth %d ", debug,
+                x, seqCanvas.getLabelWidthWest(), charWidth));
+      }
+      if (x < 0)
+      {
+        // mouse is over left scale
+        return -1;
+      }
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
       {
         return 0;
       }
+      if (x >= cwidth * charWidth)
+      {
+        if (debug != null)
+        {
+          System.out.println(debug + ": cwidth = " + cwidth);
+        }
+        // mouse is over right scale
+        return -1;
+      }
 
       wrappedBlock = y / cHeight;
       wrappedBlock += startRes / cwidth;
       // allow for wrapped view scrolled right (possible from Overview)
       int startOffset = startRes % cwidth;
       res = wrappedBlock * cwidth + startOffset
-              + +Math.min(cwidth - 1, x / av.getCharWidth());
+              + Math.min(cwidth - 1, x / charWidth);
     }
     else
     {
-      if (x > seqCanvas.getX() + seqCanvas.getWidth())
-      {
-        // make sure we calculate relative to visible alignment, rather than
-        // right-hand gutter
-        x = seqCanvas.getX() + seqCanvas.getWidth();
-      }
-      res = (x / av.getCharWidth()) + startRes;
-      if (res > av.getRanges().getEndRes())
-      {
-        // moused off right
-        res = av.getRanges().getEndRes();
-      }
+      /*
+       * make sure we calculate relative to visible alignment, 
+       * rather than right-hand gutter
+       */
+      x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth());
+      res = (x / charWidth) + startRes;
+      res = Math.min(res, av.getRanges().getEndRes());
     }
 
     if (av.hasHiddenColumns())
@@ -250,38 +420,6 @@ public class SeqPanel extends JPanel
     }
 
     return res;
-
-  }
-
-  int findSeq(MouseEvent evt)
-  {
-    int seq = 0;
-    int y = evt.getY();
-
-    if (av.getWrapAlignment())
-    {
-      int hgap = av.getCharHeight();
-      if (av.getScaleAboveWrapped())
-      {
-        hgap += av.getCharHeight();
-      }
-
-      int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
-              + hgap + seqCanvas.getAnnotationHeight();
-
-      y -= hgap;
-
-      seq = Math.min((y % cHeight) / av.getCharHeight(),
-              av.getAlignment().getHeight() - 1);
-    }
-    else
-    {
-      seq = Math.min(
-              (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
-              av.getAlignment().getHeight() - 1);
-    }
-
-    return seq;
   }
 
   /**
@@ -617,24 +755,31 @@ public class SeqPanel extends JPanel
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    MousePos pos = findMousePosition(evt);
+    if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+    {
+      return;
+    }
+
     boolean didDrag = mouseDragging; // did we come here after a drag
     mouseDragging = false;
     mouseWheelPressed = false;
 
     if (evt.isPopupTrigger()) // Windows: mouseReleased
     {
-      showPopupMenu(evt);
+      showPopupMenu(evt, pos);
       evt.consume();
       return;
     }
 
-    if (!editingSeqs)
+    if (editingSeqs)
+    {
+      endEditing();
+    }
+    else
     {
       doMouseReleasedDefineMode(evt, didDrag);
-      return;
     }
-
-    endEditing();
   }
 
   /**
@@ -647,6 +792,11 @@ public class SeqPanel extends JPanel
   public void mousePressed(MouseEvent evt)
   {
     lastMousePress = evt.getPoint();
+    MousePos pos = findMousePosition(evt);
+    if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+    {
+      return;
+    }
 
     if (SwingUtilities.isMiddleMouseButton(evt))
     {
@@ -665,17 +815,12 @@ public class SeqPanel extends JPanel
     }
     else
     {
-      doMousePressedDefineMode(evt);
+      doMousePressedDefineMode(evt, pos);
       return;
     }
 
-    int seq = findSeq(evt);
-    int res = findColumn(evt);
-
-    if (seq < 0 || res < 0)
-    {
-      return;
-    }
+    int seq = pos.seqIndex;
+    int res = pos.column;
 
     if ((seq < av.getAlignment().getHeight())
             && (res < av.getAlignment().getSequenceAt(seq).getLength()))
@@ -731,7 +876,7 @@ public class SeqPanel extends JPanel
       // over residue to change abruptly, causing highlighted residue in panel 2
       // to change, causing a scroll in panel 1 etc)
       ap.setToScrollComplementPanel(false);
-      wasScrolled = ap.scrollToPosition(results, false);
+      wasScrolled = ap.scrollToPosition(results);
       if (wasScrolled)
       {
         seqCanvas.revalidate();
@@ -777,23 +922,32 @@ public class SeqPanel extends JPanel
       mouseDragged(evt);
     }
 
-    final int column = findColumn(evt);
-    final int seq = findSeq(evt);
+    final MousePos mousePos = findMousePosition(evt);
+    if (mousePos.equals(lastMousePosition))
+    {
+      /*
+       * just a pixel move without change of 'cell'
+       */
+      return;
+    }
+    lastMousePosition = mousePos;
 
-    if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+    if (mousePos.isOverAnnotation())
     {
-      lastMouseSeq = -1;
+      mouseMovedOverAnnotation(mousePos);
       return;
     }
-    if (column == lastMouseColumn && seq == lastMouseSeq)
+    final int seq = mousePos.seqIndex;
+
+    final int column = mousePos.column;
+    if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
     {
-      /*
-       * just a pixel move without change of residue
-       */
+      lastMousePosition = null;
+      setToolTipText(null);
+      lastTooltip = null;
+      ap.alignFrame.setStatus("");
       return;
     }
-    lastMouseColumn = column;
-    lastMouseSeq = seq;
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
@@ -871,6 +1025,35 @@ public class SeqPanel extends JPanel
     }
   }
 
+  /**
+   * When the view is in wrapped mode, and the mouse is over an annotation row,
+   * shows the corresponding tooltip and status message (if any)
+   * 
+   * @param pos
+   * @param column
+   */
+  protected void mouseMovedOverAnnotation(MousePos pos)
+  {
+    final int column = pos.column;
+    final int rowIndex = pos.annotationIndex;
+
+    if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation()
+            || rowIndex < 0)
+    {
+      return;
+    }
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+
+    String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
+            anns);
+    setToolTipText(tooltip);
+    lastTooltip = tooltip;
+
+    String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
+            anns[rowIndex]);
+    ap.alignFrame.setStatus(msg);
+  }
+
   private Point lastp = null;
 
   /*
@@ -881,20 +1064,26 @@ public class SeqPanel extends JPanel
   @Override
   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
+    if (tooltipText == null || tooltipText.length() <= 6)
+    {
+      lastp = null;
+      return null;
+    }
+
+    int x = event.getX();
+    int w = getWidth();
+    // switch sides when tooltip is too close to edge
+    int wdth = (w - x < 200) ? -(w / 2) : 5;
     Point p = lastp;
     if (!event.isShiftDown() || p == null)
     {
-      p = (tooltipText != null && tooltipText.length() > 6)
-              ? new Point(event.getX() + wdth, event.getY() - 20)
-              : null;
+      p = new Point(event.getX() + wdth, event.getY() - 20);
+      lastp = p;
     }
     /*
-     * TODO: try to modify position region is not obcured by tooltip
+     * TODO: try to set position so region is not obscured by tooltip
      */
-    return lastp = p;
+    return p;
   }
 
   String lastTooltip;
@@ -997,7 +1186,7 @@ public class SeqPanel extends JPanel
 
       text.append(" (").append(Integer.toString(residuePos)).append(")");
     }
-    ap.alignFrame.statusBar.setText(text.toString());
+    ap.alignFrame.setStatus(text.toString());
   }
 
   /**
@@ -1039,6 +1228,12 @@ public class SeqPanel extends JPanel
   @Override
   public void mouseDragged(MouseEvent evt)
   {
+    MousePos pos = findMousePosition(evt);
+    if (pos.isOverAnnotation() || pos.column == -1)
+    {
+      return;
+    }
+
     if (mouseWheelPressed)
     {
       boolean inSplitFrame = ap.av.getCodingComplement() != null;
@@ -1134,11 +1329,11 @@ public class SeqPanel extends JPanel
 
     if (!editingSeqs)
     {
-      doMouseDraggedDefineMode(evt);
+      dragStretchGroup(evt);
       return;
     }
 
-    int res = findColumn(evt);
+    int res = pos.column;
 
     if (res < 0)
     {
@@ -1161,9 +1356,9 @@ public class SeqPanel extends JPanel
     }
 
     mouseDragging = true;
-    if ((scrollThread != null) && (scrollThread.isRunning()))
+    if (scrollThread != null)
     {
-      scrollThread.setEvent(evt);
+      scrollThread.setMousePosition(evt.getPoint());
     }
   }
 
@@ -1212,6 +1407,8 @@ public class SeqPanel extends JPanel
       }
     }
 
+    StringBuilder message = new StringBuilder(64); // for status bar
+
     /*
      * make a name for the edit action, for
      * status bar message and Undo/Redo menu
@@ -1219,10 +1416,12 @@ public class SeqPanel extends JPanel
     String label = null;
     if (groupEditing)
     {
+        message.append("Edit group:");
       label = MessageManager.getString("action.edit_group");
     }
     else
     {
+        message.append("Edit sequence: " + seq.getName());
       label = seq.getName();
       if (label.length() > 10)
       {
@@ -1242,6 +1441,18 @@ public class SeqPanel extends JPanel
       editCommand = new EditCommand(label);
     }
 
+    if (insertGap)
+    {
+      message.append(" insert ");
+    }
+    else
+    {
+      message.append(" delete ");
+    }
+
+    message.append(Math.abs(startres - editLastRes) + " gaps.");
+    ap.alignFrame.setStatus(message.toString());
+
     /*
      * is there a selection group containing the sequence being edited?
      * if so the boundary of the group is the limit of the edit
@@ -1327,7 +1538,7 @@ public class SeqPanel extends JPanel
      * what was requested), by inspecting the edit commands added
      */
     String msg = getEditStatusMessage(editCommand);
-    ap.alignFrame.statusBar.setText(msg == null ? " " : msg);
+    ap.alignFrame.setStatus(msg == null ? " " : msg);
     if (!success)
     {
       endEditing();
@@ -1718,10 +1929,10 @@ public class SeqPanel extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * On reentering the panel, stops any scrolling that was started on dragging
+   * out of the panel
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseEntered(MouseEvent e)
@@ -1730,23 +1941,20 @@ public class SeqPanel extends JPanel
     {
       oldSeq = 0;
     }
-
-    if ((scrollThread != null) && (scrollThread.isRunning()))
-    {
-      scrollThread.stopScrolling();
-      scrollThread = null;
-    }
+    stopScrolling();
   }
 
   /**
-   * DOCUMENT ME!
+   * On leaving the panel, if the mouse is being dragged, starts a thread to
+   * scroll it until the mouse is released (in unwrapped mode only)
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseExited(MouseEvent e)
   {
+    lastMousePosition = null;
+    ap.alignFrame.setStatus(" ");
     if (av.getWrapAlignment())
     {
       return;
@@ -1767,7 +1975,12 @@ public class SeqPanel extends JPanel
   public void mouseClicked(MouseEvent evt)
   {
     SequenceGroup sg = null;
-    SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
+    MousePos pos = findMousePosition(evt);
+    if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
+    {
+      return;
+    }
+
     if (evt.getClickCount() > 1)
     {
       sg = av.getSelectionGroup();
@@ -1777,12 +1990,13 @@ public class SeqPanel extends JPanel
         av.setSelectionGroup(null);
       }
 
-      int column = findColumn(evt);
+      int column = pos.column;
 
       /*
        * find features at the position (if not gapped), or straddling
        * the position (if at a gap)
        */
+      SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex);
       List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
 
@@ -1849,32 +2063,22 @@ public class SeqPanel extends JPanel
   /**
    * DOCUMENT ME!
    * 
-   * @param evt
+   * @param pos
    *          DOCUMENT ME!
    */
-  public void doMousePressedDefineMode(MouseEvent evt)
+  protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos)
   {
-    final int res = findColumn(evt);
-    final int seq = findSeq(evt);
-    oldSeq = seq;
-    updateOverviewAndStructs = false;
-
-    startWrapBlock = wrappedBlock;
-
-    if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
+    if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-              MessageManager.getString(
-                      "label.cannot_edit_annotations_in_wrapped_view"),
-              MessageManager.getString("label.wrapped_view_no_edit"),
-              JvOptionPane.WARNING_MESSAGE);
       return;
     }
 
-    if (seq < 0 || res < 0)
-    {
-      return;
-    }
+    final int res = pos.column;
+    final int seq = pos.seqIndex;
+    oldSeq = seq;
+    updateOverviewAndStructs = false;
+
+    startWrapBlock = wrappedBlock;
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
@@ -1898,7 +2102,7 @@ public class SeqPanel extends JPanel
 
     if (evt.isPopupTrigger()) // Mac: mousePressed
     {
-      showPopupMenu(evt);
+      showPopupMenu(evt, pos);
       return;
     }
 
@@ -1914,8 +2118,8 @@ public class SeqPanel extends JPanel
 
     if (av.cursorMode)
     {
-      seqCanvas.cursorX = findColumn(evt);
-      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.cursorX = res;
+      seqCanvas.cursorY = seq;
       seqCanvas.repaint();
       return;
     }
@@ -1973,15 +2177,14 @@ public class SeqPanel extends JPanel
 
   /**
    * Build and show a pop-up menu at the right-click mouse position
-   * 
+   *
    * @param evt
-   * @param res
-   * @param sequences
+   * @param pos
    */
-  void showPopupMenu(MouseEvent evt)
+  void showPopupMenu(MouseEvent evt, MousePos pos)
   {
-    final int column = findColumn(evt);
-    final int seq = findSeq(evt);
+    final int column = pos.column;
+    final int seq = pos.seqIndex;
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
     List<SequenceFeature> features = ap.getFeatureRenderer()
             .findFeaturesAtColumn(sequence, column + 1);
@@ -1999,7 +2202,8 @@ public class SeqPanel extends JPanel
    *          true if this event is happening after a mouse drag (rather than a
    *          mouse down)
    */
-  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
+  protected void doMouseReleasedDefineMode(MouseEvent evt,
+          boolean afterDrag)
   {
     if (stretchGroup == null)
     {
@@ -2015,8 +2219,11 @@ public class SeqPanel extends JPanel
             && afterDrag;
     if (stretchGroup.cs != null)
     {
-      stretchGroup.cs.alignmentChanged(stretchGroup,
-              av.getHiddenRepSequences());
+      if (afterDrag)
+      {
+        stretchGroup.cs.alignmentChanged(stretchGroup,
+                av.getHiddenRepSequences());
+      }
 
       ResidueShaderI groupColourScheme = stretchGroup
               .getGroupColourScheme();
@@ -2042,31 +2249,34 @@ public class SeqPanel extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Resizes the borders of a selection group depending on the direction of
+   * mouse drag
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
-  public void doMouseDraggedDefineMode(MouseEvent evt)
+  protected void dragStretchGroup(MouseEvent evt)
   {
-    int res = findColumn(evt);
-    int y = findSeq(evt);
-
-    if (wrappedBlock != startWrapBlock)
+    if (stretchGroup == null)
     {
       return;
     }
 
-    if (stretchGroup == null)
+    MousePos pos = findMousePosition(evt);
+    if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1)
     {
       return;
     }
 
-    if (res >= av.getAlignment().getWidth())
+    int res = pos.column;
+    int y = pos.seqIndex;
+
+    if (wrappedBlock != startWrapBlock)
     {
-      res = av.getAlignment().getWidth() - 1;
+      return;
     }
 
+    res = Math.min(res, av.getAlignment().getWidth()-1);
+
     if (stretchGroup.getEndRes() == res)
     {
       // Edit end res position of selected group
@@ -2151,9 +2361,9 @@ public class SeqPanel extends JPanel
 
     mouseDragging = true;
 
-    if ((scrollThread != null) && (scrollThread.isRunning()))
+    if (scrollThread != null)
     {
-      scrollThread.setEvent(evt);
+      scrollThread.setMousePosition(evt.getPoint());
     }
 
     /*
@@ -2183,83 +2393,120 @@ public class SeqPanel extends JPanel
     ap.alignFrame.setStatus(status.toString());
   }
 
-  void scrollCanvas(MouseEvent evt)
+  /**
+   * Stops the scroll thread if it is running
+   */
+  void stopScrolling()
   {
-    if (evt == null)
+    if (scrollThread != null)
     {
-      if ((scrollThread != null) && (scrollThread.isRunning()))
-      {
-        scrollThread.stopScrolling();
-        scrollThread = null;
-      }
-      mouseDragging = false;
+      scrollThread.stopScrolling();
+      scrollThread = null;
     }
-    else
-    {
-      if (scrollThread == null)
-      {
-        scrollThread = new ScrollThread();
-      }
+    mouseDragging = false;
+  }
 
-      mouseDragging = true;
-      scrollThread.setEvent(evt);
+  /**
+   * Starts a thread to scroll the alignment, towards a given mouse position
+   * outside the panel bounds
+   * 
+   * @param mousePos
+   */
+  void startScrolling(Point mousePos)
+  {
+    if (scrollThread == null)
+    {
+      scrollThread = new ScrollThread();
     }
 
+    mouseDragging = true;
+    scrollThread.setMousePosition(mousePos);
   }
 
-  // this class allows scrolling off the bottom of the visible alignment
+  /**
+   * Performs scrolling of the visible alignment left, right, up or down
+   */
   class ScrollThread extends Thread
   {
-    MouseEvent evt;
+    private Point mousePos;
 
     private volatile boolean threadRunning = true;
 
+    /**
+     * Constructor
+     */
     public ScrollThread()
     {
+      setName("SeqPanel$ScrollThread");
       start();
     }
 
-    public void setEvent(MouseEvent e)
+    /**
+     * Sets the position of the mouse that determines the direction of the
+     * scroll to perform
+     * 
+     * @param p
+     */
+    public void setMousePosition(Point p)
     {
-      evt = e;
+      mousePos = p;
     }
 
+    /**
+     * Sets a flag that will cause the thread to exit
+     */
     public void stopScrolling()
     {
       threadRunning = false;
     }
 
-    public boolean isRunning()
-    {
-      return threadRunning;
-    }
-
+    /**
+     * Scrolls the alignment left or right, and/or up or down, depending on the
+     * last notified mouse position, until the limit of the alignment is
+     * reached, or a flag is set to stop the scroll
+     */
     @Override
     public void run()
     {
-      while (threadRunning)
+      while (threadRunning && mouseDragging)
       {
-        if (evt != null)
+        if (mousePos != null)
         {
-          if (mouseDragging && (evt.getY() < 0)
-                  && (av.getRanges().getStartSeq() > 0))
+          boolean scrolled = false;
+          ViewportRanges ranges = SeqPanel.this.av.getRanges();
+
+          /*
+           * scroll up or down
+           */
+          if (mousePos.y < 0)
           {
-            av.getRanges().scrollUp(true);
+            // mouse is above this panel - try scroll up
+            scrolled = ranges.scrollUp(true);
           }
-
-          if (mouseDragging && (evt.getY() >= getHeight()) && (av
-                  .getAlignment().getHeight() > av.getRanges().getEndSeq()))
+          else if (mousePos.y >= getHeight())
           {
-            av.getRanges().scrollUp(false);
+            // mouse is below this panel - try scroll down
+            scrolled = ranges.scrollUp(false);
           }
 
-          if (mouseDragging && (evt.getX() < 0))
+          /*
+           * scroll left or right
+           */
+          if (mousePos.x < 0)
+          {
+            scrolled |= ranges.scrollRight(false);
+          }
+          else if (mousePos.x >= getWidth())
           {
-            av.getRanges().scrollRight(false);
+            scrolled |= ranges.scrollRight(true);
           }
-          else if (mouseDragging && (evt.getX() >= getWidth()))
+          if (!scrolled)
           {
-            av.getRanges().scrollRight(true);
+            /*
+             * we have reached the limit of the visible alignment - quit
+             */
+            threadRunning = false;
+            SeqPanel.this.ap.repaint();
           }
         }
 
@@ -2449,7 +2696,7 @@ public class SeqPanel extends JPanel
     HiddenColumns hs = new HiddenColumns();
     MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
-    av.getAlignment().setHiddenColumns(hs);
+    boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs);
 
     // lastly, update any dependent dialogs
     if (ap.getCalculationDialog() != null)
@@ -2457,7 +2704,11 @@ public class SeqPanel extends JPanel
       ap.getCalculationDialog().validateCalcTypes();
     }
 
-    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    /*
+     * repaint alignment, and also Overview or Structure
+     * if hidden column selection has changed
+     */
+    ap.paintAlignment(hiddenChanged, hiddenChanged);
 
     return true;
   }