X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1d943f05de7f02ff508207aaf2862fb652da3cf2;hb=2639d90e2b52d49cf586c0b602bc606033c9b8ae;hp=a2c2bd9b8c87a5d7c2dcb7ee5c10dad9a3ca06b4;hpb=04d19d44b27b66c342e35b8933776b0ca7da9f35;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a2c2bd9..1d943f0 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -48,23 +49,28 @@ 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;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JToolTip;
 import javax.swing.SwingUtilities;
+import javax.swing.Timer;
 import javax.swing.ToolTipManager;
 
 /**
@@ -73,17 +79,26 @@ import javax.swing.ToolTipManager;
  * @author $author$
  * @version $Revision: 1.130 $
  */
-public class SeqPanel extends JPanel implements MouseListener,
-        MouseMotionListener, MouseWheelListener, SequenceListener,
-        SelectionListener
-
+public class SeqPanel extends JPanel
+        implements MouseListener, MouseMotionListener, MouseWheelListener,
+        SequenceListener, SelectionListener
 {
-  /** DOCUMENT ME!! */
+  private static final int MAX_TOOLTIP_LENGTH = 300;
+
   public SeqCanvas seqCanvas;
 
-  /** DOCUMENT ME!! */
   public AlignmentPanel ap;
 
+  /*
+   * last column position for mouseMoved event
+   */
+  private int lastMouseColumn;
+
+  /*
+   * last sequence offset for mouseMoved event
+   */
+  private int lastMouseSeq;
+
   protected int lastres;
 
   protected int startseq;
@@ -138,38 +153,41 @@ public class SeqPanel extends JPanel implements MouseListener,
   SearchResultsI lastSearchResults;
 
   /**
-   * Creates a new SeqPanel object.
+   * Creates a new SeqPanel object
    * 
-   * @param avp
-   *          DOCUMENT ME!
-   * @param p
-   *          DOCUMENT ME!
+   * @param viewport
+   * @param alignPanel
    */
-  public SeqPanel(AlignViewport av, AlignmentPanel ap)
+  public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
     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;
+    
+    
+    this.av = viewport;
     setBackground(Color.white);
 
-    seqCanvas = new SeqCanvas(ap);
+    seqCanvas = new SeqCanvas(alignPanel);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    this.ap = ap;
+    this.ap = alignPanel;
 
-    if (!av.isDataset())
+    if (!viewport.isDataset())
     {
       addMouseMotionListener(this);
       addMouseListener(this);
       addMouseWheelListener(this);
-      ssm = av.getStructureSelectionManager();
+      ssm = viewport.getStructureSelectionManager();
       ssm.addStructureViewerListener(this);
       ssm.addSelectionListener(this);
     }
+
+    lastMouseColumn = -1;
+    lastMouseSeq = -1;
   }
 
   int startWrapBlock = -1;
@@ -183,11 +201,12 @@ public class SeqPanel extends JPanel implements MouseListener,
    * @param evt
    * @return
    */
-  int findRes(MouseEvent evt)
+  int findColumn(MouseEvent evt)
   {
     int res = 0;
     int x = evt.getX();
 
+    int startRes = av.getRanges().getStartRes();
     if (av.getWrapAlignment())
     {
 
@@ -201,8 +220,8 @@ public class SeqPanel extends JPanel implements MouseListener,
               + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
-      y -= hgap;
-      x -= seqCanvas.LABEL_WEST;
+      y = Math.max(0, y - hgap);
+      x = Math.max(0, x - seqCanvas.getLabelWidthWest());
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
@@ -211,10 +230,11 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getRanges().getStartRes() / cwidth;
-
-      res = wrappedBlock * cwidth + x / av.getCharWidth();
-
+      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());
     }
     else
     {
@@ -224,7 +244,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
-      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      res = (x / av.getCharWidth()) + startRes;
       if (res > av.getRanges().getEndRes())
       {
         // moused off right
@@ -235,7 +255,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     return res;
@@ -260,15 +280,14 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
-              .getHeight() - 1);
+      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);
+      seq = Math.min(
+              (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+              av.getAlignment().getHeight() - 1);
     }
 
     return seq;
@@ -285,8 +304,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (editCommand != null && editCommand.getSize() > 0)
       {
         ap.alignFrame.addHistoryItem(editCommand);
-        av.firePropertyChange("alignment", null, av.getAlignment()
-                .getSequences());
+        av.firePropertyChange("alignment", null,
+                av.getAlignment().getSequences());
       }
     } finally
     {
@@ -306,13 +325,13 @@ public class SeqPanel extends JPanel implements MouseListener,
   void setCursorRow()
   {
     seqCanvas.cursorY = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorColumn()
   {
     seqCanvas.cursorX = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorRowAndColumn()
@@ -325,7 +344,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       seqCanvas.cursorX = getKeyboardNo1() - 1;
       seqCanvas.cursorY = getKeyboardNo2() - 1;
-      scrollToVisible();
+      scrollToVisible(true);
     }
   }
 
@@ -334,7 +353,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void moveCursor(int dx, int dy)
@@ -344,16 +363,30 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
-    if (av.hasHiddenColumns()
- && !hidden.isVisible(seqCanvas.cursorX))
+    if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!hidden.isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+      if (!hidden.isVisible(seqCanvas.cursorX))
       {
-        seqCanvas.cursorX += dx;
+        int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
+        int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+        if (region != null) // just in case
+        {
+          if (dx == 1)
+          {
+            // moving right
+            seqCanvas.cursorX = region[1] + 1;
+          }
+          else if (dx == -1)
+          {
+            // moving left
+            seqCanvas.cursorX = region[0] - 1;
+          }
+        }
+        seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
       }
 
       if (seqCanvas.cursorX >= maxWidth
@@ -363,10 +396,16 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    scrollToVisible();
+    scrollToVisible(false);
   }
 
-  void scrollToVisible()
+  /**
+   * Scroll to make the cursor visible in the viewport.
+   * 
+   * @param jump
+   *          just jump to the location rather than scrolling
+   */
+  void scrollToVisible(boolean jump)
   {
     if (seqCanvas.cursorX < 0)
     {
@@ -387,47 +426,44 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     endEditing();
-    if (av.getWrapAlignment())
+
+    boolean repaintNeeded = true;
+    if (jump)
     {
-      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      // only need to repaint if the viewport did not move, as otherwise it will
+      // get a repaint
+      repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
+              seqCanvas.cursorY);
     }
     else
     {
-      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
+      if (av.getWrapAlignment())
       {
-        ap.scrollUp(true);
+        // scrollToWrappedVisible expects x-value to have hidden cols subtracted
+        int x = av.getAlignment().getHiddenColumns()
+                .absoluteToVisibleColumn(seqCanvas.cursorX);
+        av.getRanges().scrollToWrappedVisible(x);
       }
-      while (seqCanvas.cursorY > av.getRanges().getEndSeq())
-      {
-        ap.scrollUp(false);
-      }
-      if (!av.getWrapAlignment())
+      else
       {
-        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
-                .getRanges().getStartRes()))
-        {
-          if (!ap.scrollRight(false))
-          {
-            break;
-          }
-        }
-        while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
-                .getRanges().getEndRes()))
-        {
-          if (!ap.scrollRight(true))
-          {
-            break;
-          }
-        }
+        av.getRanges().scrollToVisible(seqCanvas.cursorX,
+                seqCanvas.cursorY);
       }
     }
-    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+
+    if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
+    {
+      setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
+    }
 
-    seqCanvas.repaint();
+    if (repaintNeeded)
+    {
+      seqCanvas.repaint();
+    }
   }
 
+
   void setSelectionAreaAtCursor(boolean topLeft)
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
@@ -498,7 +534,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       av.setSelectionGroup(sg);
     }
 
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -590,6 +626,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    boolean didDrag = mouseDragging; // did we come here after a drag
     mouseDragging = false;
     mouseWheelPressed = false;
 
@@ -600,13 +637,14 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (!editingSeqs)
+    if (editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
-      return;
+      endEditing();
+    }
+    else
+    {
+      doMouseReleasedDefineMode(evt, didDrag);
     }
-
-    endEditing();
   }
 
   /**
@@ -642,7 +680,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < 0 || res < 0)
     {
@@ -666,6 +704,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   String lastMessage;
 
+  private String formattedTooltipText;
+
   @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
@@ -694,22 +734,28 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     lastSearchResults = results;
 
+    boolean wasScrolled = false;
+
     if (av.isFollowHighlight())
     {
-      /*
-       * if scrollToPosition requires a scroll adjustment, this flag prevents
-       * another scroll event being propagated back to the originator
-       * 
-       * @see AlignmentPanel#adjustmentValueChanged
-       */
-      ap.setDontScrollComplement(true);
-      if (ap.scrollToPosition(results, false))
+      // don't allow highlight of protein/cDNA to also scroll a complementary
+      // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+      // 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);
+      if (wasScrolled)
       {
         seqCanvas.revalidate();
       }
+      ap.setToScrollComplementPanel(true);
+    }
+
+    boolean fastPaint = !(wasScrolled && av.getWrapAlignment());
+    if (seqCanvas.highlightSearchResults(results, fastPaint))
+    {
+      setStatusMessage(results);
     }
-    setStatusMessage(results);
-    seqCanvas.highlightSearchResults(results);
   }
 
   @Override
@@ -726,10 +772,12 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on mouse movement is to update the status bar to show the current
+   * sequence position, and (if features are shown) to show any features at the
+   * position in a tooltip. Does nothing if the mouse move does not change
+   * residue position.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent evt)
@@ -741,25 +789,39 @@ public class SeqPanel extends JPanel implements MouseListener,
       mouseDragged(evt);
     }
 
-    int res = findRes(evt);
-    int seq = findSeq(evt);
-    int pos;
-    if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+    final int column = findColumn(evt);
+    final int seq = findSeq(evt);
+
+    if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
     {
+      lastMouseSeq = -1;
       return;
     }
+    if (column == lastMouseColumn && seq == lastMouseSeq)
+    {
+      /*
+       * just a pixel move without change of residue
+       */
+      return;
+    }
+    lastMouseColumn = column;
+    lastMouseSeq = seq;
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if (res >= sequence.getLength())
+    if (column >= sequence.getLength())
     {
       return;
     }
 
-    pos = setStatusMessage(sequence, res, seq);
-    if (ssm != null && pos > -1)
+    /*
+     * set status bar message, returning residue position in sequence
+     */
+    boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+    final int pos = setStatusMessage(sequence, column, seq);
+    if (ssm != null && !isGapped)
     {
-      mouseOverSequence(sequence, res, pos);
+      mouseOverSequence(sequence, column, pos);
     }
 
     tooltipText.setLength(6); // Cuts the buffer back to <html>
@@ -769,7 +831,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       for (int g = 0; g < groups.length; g++)
       {
-        if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+        if (groups[g].getStartRes() <= column
+                && groups[g].getEndRes() >= column)
         {
           if (!groups[g].getName().startsWith("JTreeGroup")
                   && !groups[g].getName().startsWith("JGroup"))
@@ -785,15 +848,17 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    // use aa to see if the mouse pointer is on a
+    /*
+     * add any features at the position to the tooltip; if over a gap, only
+     * add features that straddle the gap (pos may be the residue before or
+     * after the gap)
+     */
     if (av.isShowSequenceFeatures())
     {
-      int rpos;
       List<SequenceFeature> features = ap.getFeatureRenderer()
-              .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      rpos = sequence.findPosition(res));
-      seqARep.appendFeatures(tooltipText, rpos, features,
-              this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
+              .findFeaturesAtColumn(sequence, column + 1);
+      seqARep.appendFeatures(tooltipText, pos, features,
+              this.ap.getSeqPanel().seqCanvas.fr);
     }
     if (tooltipText.length() == 6) // <html>
     {
@@ -802,22 +867,28 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      if (lastTooltip == null
-              || !lastTooltip.equals(tooltipText.toString()))
+      if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
       {
-        String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
-                tooltipText.toString());
-        // String formatedTooltipText = tooltipText.toString();
-        setToolTipText(formatedTooltipText);
-        lastTooltip = tooltipText.toString();
+        tooltipText.setLength(MAX_TOOLTIP_LENGTH);
+        tooltipText.append("...");
+      }
+      String textString = tooltipText.toString();
+      if (lastTooltip == null || !lastTooltip.equals(textString))
+      {
+        formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+                textString);
+        setToolTipText(formattedTooltipText);
+        
+        lastTooltip = textString;
       }
-
     }
-
   }
 
+  
   private Point lastp = null;
 
+  private JToolTip tempTip = new JLabel().createToolTip();
+
   /*
    * (non-Javadoc)
    * 
@@ -826,18 +897,31 @@ public class SeqPanel extends JPanel implements MouseListener,
   @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
+    // BH 2018
+
+    if (tooltipText == null || tooltipText.length() == 6)
+      return null;
+
+    if (lastp != null && event.isShiftDown())
+      return lastp;
+
     Point p = lastp;
-    if (!event.isShiftDown() || p == null)
-    {
-      p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
-              event.getX() + wdth, event.getY() - 20) : null;
-    }
+    int x = event.getX();
+    int y = event.getY();
+    int w = getWidth();
+
+    tempTip.setTipText(formattedTooltipText);
+    int tipWidth = (int) tempTip.getPreferredSize().getWidth();
+    
+    // was      x += (w - x < 200) ? -(w / 2) : 5;
+    x = (x + tipWidth < w ? x + 10 : w - tipWidth);
+    p = new Point(x, y + 20); // BH 2018 was - 20?
     /*
      * TODO: try to modify position region is not obcured by tooltip
+     * 
+     * Done? 
      */
+
     return lastp = p;
   }
 
@@ -845,11 +929,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   /**
    * set when the current UI interaction has resulted in a change that requires
-   * overview shading to be recalculated. this could be changed to something
-   * more expressive that indicates what actually has changed, so selective
-   * redraws can be applied
+   * shading in overviews and structures to be recalculated. this could be
+   * changed to a something more expressive that indicates what actually has
+   * changed, so selective redraws can be applied (ie. only structures, only
+   * overview, etc)
    */
-  private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
+  private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
 
   /**
    * set if av.getSelectionGroup() refers to a group that is defined on the
@@ -859,59 +944,88 @@ public class SeqPanel extends JPanel implements MouseListener,
   // avcontroller or viewModel
 
   /**
-   * Set status message in alignment panel
+   * Sets the status message in alignment panel, showing the sequence number
+   * (index) and id, and residue and residue position if not at a gap, for the
+   * given sequence and column position. Returns the residue position returned
+   * by Sequence.findPosition. Note this may be for the nearest adjacent residue
+   * if at a gapped position.
    * 
    * @param sequence
    *          aligned sequence object
-   * @param res
+   * @param column
    *          alignment column
-   * @param seq
+   * @param seqIndex
    *          index of sequence in alignment
-   * @return position of res in sequence
+   * @return sequence position of residue at column, or adjacent residue if at a
+   *         gap
    */
-  int setStatusMessage(SequenceI sequence, int res, int seq)
+  int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
+  {
+    char sequenceChar = sequence.getCharAt(column);
+    int pos = sequence.findPosition(column);
+    setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+
+    return pos;
+  }
+
+  /**
+   * Builds the status message for the current cursor location and writes it to
+   * the status bar, for example
+   * 
+   * <pre>
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   * </pre>
+   * 
+   * @param sequence
+   * @param seqIndex
+   *          sequence position in the alignment (1..)
+   * @param sequenceChar
+   *          the character under the cursor
+   * @param residuePos
+   *          the sequence residue position (if not over a gap)
+   */
+  protected void setStatusMessage(SequenceI sequence, int seqIndex,
+          char sequenceChar, int residuePos)
   {
     StringBuilder text = new StringBuilder(32);
 
     /*
      * Sequence number (if known), and sequence name.
      */
-    String seqno = seq == -1 ? "" : " " + (seq + 1);
+    String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
     text.append("Sequence").append(seqno).append(" ID: ")
             .append(sequence.getName());
 
     String residue = null;
+
     /*
      * Try to translate the display character to residue name (null for gap).
      */
-    final String displayChar = String.valueOf(sequence.getCharAt(res));
-    if (av.getAlignment().isNucleotide())
+    boolean isGapped = Comparison.isGap(sequenceChar);
+
+    if (!isGapped)
     {
-      residue = ResidueProperties.nucleotideName.get(displayChar);
-      if (residue != null)
+      boolean nucleotide = av.getAlignment().isNucleotide();
+      String displayChar = String.valueOf(sequenceChar);
+      if (nucleotide)
       {
-        text.append(" Nucleotide: ").append(residue);
+        residue = ResidueProperties.nucleotideName.get(displayChar);
       }
-    }
-    else
-    {
-      residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
-              .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
-              .get(displayChar));
-      if (residue != null)
+      else
       {
-        text.append(" Residue: ").append(residue);
+        residue = "X".equalsIgnoreCase(displayChar) ? "X"
+                : ("*".equals(displayChar) ? "STOP"
+                        : ResidueProperties.aa2Triplet.get(displayChar));
       }
-    }
+      text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
+              .append(": ").append(residue == null ? displayChar : residue);
 
-    int pos = -1;
-    if (residue != null)
-    {
-      pos = sequence.findPosition(res);
-      text.append(" (").append(Integer.toString(pos)).append(")");
+      text.append(" (").append(Integer.toString(residuePos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
-    return pos;
   }
 
   /**
@@ -939,12 +1053,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (seq == ds)
       {
-        /*
-         * Convert position in sequence (base 1) to sequence character array
-         * index (base 0)
-         */
-        int start = m.getStart() - m.getSequence().getStart();
-        setStatusMessage(seq, start, sequenceIndex);
+        int start = m.getStart();
+        setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+                start);
         return;
       }
     }
@@ -964,8 +1075,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       int oldWidth = av.getCharWidth();
 
       // Which is bigger, left-right or up-down?
-      if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
-              .getX() - lastMousePress.getX()))
+      if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
+              .abs(evt.getX() - lastMousePress.getX()))
       {
         /*
          * on drag up or down, decrement or increment font size
@@ -1024,7 +1135,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         if (newWidth > 0)
         {
-          ap.paintAlignment(false);
+          ap.paintAlignment(false, false);
           if (copyChanges)
           {
             /*
@@ -1055,7 +1166,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (res < 0)
     {
@@ -1080,7 +1191,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     mouseDragging = true;
     if (scrollThread != null)
     {
-      scrollThread.setEvent(evt);
+      scrollThread.setMousePosition(evt.getPoint());
     }
   }
 
@@ -1125,8 +1236,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.formatMessage(
-                "label.edit_params", new String[] { label }));
+        editCommand = new EditCommand(MessageManager
+                .formatMessage("label.edit_params", new String[]
+                { label }));
       }
     }
 
@@ -1143,9 +1255,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     ap.alignFrame.statusBar.setText(message.toString());
 
     // Are we editing within a selection group?
-    if (groupEditing
-            || (sg != null && sg.getSequences(av.getHiddenRepSequences())
-                    .contains(seq)))
+    if (groupEditing || (sg != null
+            && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
     {
       fixedColumns = true;
 
@@ -1189,9 +1300,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       fixedColumns = true;
       int y1 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryLeft(startres);
+              .getNextHiddenBoundary(true, startres);
       int y2 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryRight(startres);
+              .getNextHiddenBoundary(false, startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1241,7 +1352,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         // Find the next gap before the end
         // of the visible region boundary
         boolean blank = false;
-        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
+        for (; fixedRight > lastres; fixedRight--)
         {
           blank = true;
 
@@ -1267,7 +1378,8 @@ public class SeqPanel extends JPanel implements MouseListener,
           if (sg.getSize() == av.getAlignment().getHeight())
           {
             if ((av.hasHiddenColumns() && startres < av.getAlignment()
-                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
+                    .getHiddenColumns()
+                    .getNextHiddenBoundary(false, startres)))
             {
               endEditing();
               return;
@@ -1333,8 +1445,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
-                  - lastres);
+          appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+                  startres - lastres);
         }
       }
       else
@@ -1349,8 +1461,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
-                  - startres);
+          appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+                  lastres - startres);
         }
 
       }
@@ -1491,10 +1603,10 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * 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)
@@ -1503,31 +1615,21 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       oldSeq = 0;
     }
-
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-      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)
   {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
-
     if (mouseDragging)
     {
-      scrollThread = new ScrollThread();
+      startScrolling(e.getPoint());
     }
   }
 
@@ -1550,9 +1652,14 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
+      int column = findColumn(evt);
+
+      /*
+       * find features at the position (if not gapped), or straddling
+       * the position (if at a gap)
+       */
       List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
-              .findFeaturesAtRes(sequence.getDatasetSequence(),
-                      sequence.findPosition(findRes(evt)));
+              .findFeaturesAtColumn(sequence, column + 1);
 
       if (!features.isEmpty())
       {
@@ -1562,16 +1669,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         SearchResultsI highlight = new SearchResults();
         highlight.addResult(sequence, features.get(0).getBegin(), features
                 .get(0).getEnd());
-        seqCanvas.highlightSearchResults(highlight);
+        seqCanvas.highlightSearchResults(highlight, true);
 
         /*
-         * open the Amend Features dialog; clear highlighting afterwards,
-         * whether changes were made or not
+         * open the Amend Features dialog
          */
-        List<SequenceI> seqs = Collections.singletonList(sequence);
-        seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
-                ap, null);
-        seqCanvas.highlightSearchResults(null);
+        new FeatureEditor(ap, Collections.singletonList(sequence), features,
+                false).showDialog();
       }
     }
   }
@@ -1580,30 +1684,37 @@ public class SeqPanel extends JPanel implements MouseListener,
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    if (e.getWheelRotation() > 0)
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
     {
       if (e.isShiftDown())
       {
-        ap.scrollRight(true);
+        av.getRanges().scrollRight(true);
 
       }
       else
       {
-        ap.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
-        ap.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
       else
       {
-        ap.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
-    // TODO Update tooltip for new position.
+
+    /*
+     * update status bar and tooltip for new position
+     * (need to synthesize a mouse movement to refresh tooltip)
+     */
+    mouseMoved(e);
+    ToolTipManager.sharedInstance().mouseMoved(e);
   }
 
   /**
@@ -1614,17 +1725,18 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   public void doMousePressedDefineMode(MouseEvent evt)
   {
-    final int res = findRes(evt);
+    final int res = findColumn(evt);
     final int seq = findSeq(evt);
     oldSeq = seq;
-    needOverviewUpdate = false;
+    updateOverviewAndStructs = false;
 
     startWrapBlock = wrappedBlock;
 
     if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
-              .getString("label.cannot_edit_annotations_in_wrapped_view"),
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString(
+                      "label.cannot_edit_annotations_in_wrapped_view"),
               MessageManager.getString("label.wrapped_view_no_edit"),
               JvOptionPane.WARNING_MESSAGE);
       return;
@@ -1673,7 +1785,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.cursorMode)
     {
-      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorX = findColumn(evt);
       seqCanvas.cursorY = findSeq(evt);
       seqCanvas.repaint();
       return;
@@ -1681,43 +1793,53 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (stretchGroup == null)
     {
-      // Only if left mouse button do we want to change group sizes
+      createStretchGroup(res, sequence);
+    }
 
-      // 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 (stretchGroup != null)
+    {
+      stretchGroup.addPropertyChangeListener(seqCanvas);
+    }
 
-      if (av.getConservationSelected())
-      {
-        SliderPanel.setConservationSlider(ap, av.getResidueShading(),
-                ap.getViewName());
-      }
+    seqCanvas.repaint();
+  }
 
-      if (av.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
-                ap.getViewName());
-      }
-      // TODO: stretchGroup will always be not null. Is this a merge error ?
-      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();
+  private void createStretchGroup(int res, SequenceI sequence)
+  {
+    // 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.getResidueShading(),
+              ap.getViewName());
     }
 
-    seqCanvas.repaint();
+    if (av.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+              ap.getViewName());
+    }
+    // TODO: stretchGroup will always be not null. Is this a merge error ?
+    // or is there a threading issue here?
+    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();
+
   }
 
   /**
@@ -1729,50 +1851,46 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   void showPopupMenu(MouseEvent evt)
   {
-    final int res = findRes(evt);
+    final int column = findColumn(evt);
     final int seq = findSeq(evt);
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
-            .findFeaturesAtRes(sequence.getDatasetSequence(),
-                    sequence.findPosition(res));
-    List<String> links = new ArrayList<String>();
-    for (SequenceFeature sf : allFeatures)
-    {
-      if (sf.links != null)
-      {
-        for (String link : sf.links)
-        {
-          links.add(link);
-        }
-      }
-    }
+    List<SequenceFeature> features = ap.getFeatureRenderer()
+            .findFeaturesAtColumn(sequence, column + 1);
 
-    PopupMenu pop = new PopupMenu(ap, null, links);
+    PopupMenu pop = new PopupMenu(ap, null, features);
     pop.show(this, evt.getX(), evt.getY());
   }
 
   /**
-   * DOCUMENT ME!
+   * Update the display after mouse up on a selection or group
    * 
    * @param evt
-   *          DOCUMENT ME!
+   *          mouse released event details
+   * @param afterDrag
+   *          true if this event is happening after a mouse drag (rather than a
+   *          mouse down)
    */
-  public void doMouseReleasedDefineMode(MouseEvent evt)
+  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
   {
     if (stretchGroup == null)
     {
       return;
     }
+
+    stretchGroup.removePropertyChangeListener(seqCanvas);
+
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+    updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
+            && afterDrag;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
               av.getHiddenRepSequences());
 
-      ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
+      ResidueShaderI groupColourScheme = stretchGroup
+              .getGroupColourScheme();
       String name = stretchGroup.getName();
       if (stretchGroup.cs.conservationApplied())
       {
@@ -1784,8 +1902,10 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
-    needOverviewUpdate = false;
+    // TODO: structure colours only need updating if stretchGroup used to or now
+    // does contain sequences with structure views
+    ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+    updateOverviewAndStructs = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1800,7 +1920,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = findRes(evt);
+    int res = findColumn(evt);
     int y = findSeq(evt);
 
     if (wrappedBlock != startWrapBlock)
@@ -1813,10 +1933,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (res >= av.getAlignment().getWidth())
-    {
-      res = av.getAlignment().getWidth() - 1;
-    }
+    res = Math.min(res, av.getAlignment().getWidth()-1);
 
     if (stretchGroup.getEndRes() == res)
     {
@@ -1839,7 +1956,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1847,7 +1964,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1881,7 +1998,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1891,7 +2008,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1904,90 +2021,151 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (scrollThread != null)
     {
-      scrollThread.setEvent(evt);
+      scrollThread.setMousePosition(evt.getPoint());
     }
+  }
 
-    seqCanvas.repaint();
+  /**
+   * Stops the scroll thread if it is running
+   */
+  void stopScrolling()
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.stopScrolling();
+      scrollThread = null;
+    }
+    mouseDragging = false;
   }
 
-  void scrollCanvas(MouseEvent evt)
+  /**
+   * Starts a thread to scroll the alignment, towards a given mouse position
+   * outside the panel bounds, unless the alignment is in wrapped mode
+   * 
+   * @param mousePos
+   */
+  void startScrolling(Point mousePos)
   {
-    if (evt == null)
+    /*
+     * set this.mouseDragging in case this was called from 
+     * a drag in ScalePanel or AnnotationPanel
+     */
+    mouseDragging = true;
+    if (!av.getWrapAlignment() && scrollThread == null)
     {
-      if (scrollThread != null)
+      scrollThread = new ScrollThread();
+      scrollThread.setMousePosition(mousePos);
+      if (!Jalview.isJS())
       {
-        scrollThread.running = false;
-        scrollThread = null;
+        /*
+         * Java - run in a new thread
+         */
+        scrollThread.start();
       }
-      mouseDragging = false;
-    }
-    else
-    {
-      if (scrollThread == null)
+      else
       {
-        scrollThread = new ScrollThread();
+        /*
+         * Javascript - run every 20ms until scrolling stopped
+         * or reaches the limit of scrollable alignment
+         */
+        // java.util.Timer version:
+        // Timer t = new Timer("ScrollThreadTimer", true);
+        // TimerTask task = new TimerTask()
+        // {
+        // @Override
+        // public void run()
+        // {
+        // if (!scrollThread.scrollOnce())
+        // {
+        // cancel();
+        // }
+        // }
+        // };
+        // t.schedule(task, 20, 20);
+        Timer t = new Timer(20, new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            if (scrollThread != null)
+            {
+              // if (!scrollOnce() {t.stop();}) gives compiler error :-(
+              scrollThread.scrollOnce();
+            }
+          }
+        });
+        t.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            if (scrollThread == null)
+            {
+              // finished and nulled itself
+              t.stop();
+            }
+          }
+        });
+        t.start();
       }
-
-      mouseDragging = true;
-      scrollThread.setEvent(evt);
     }
-
   }
 
-  // this class allows scrolling off the bottom of the visible alignment
+  /**
+   * Performs scrolling of the visible alignment left, right, up or down, until
+   * scrolling is stopped by calling stopScrolling, mouse drag is ended, or the
+   * limit of the alignment is reached
+   */
   class ScrollThread extends Thread
   {
-    MouseEvent evt;
+    private Point mousePos;
 
-    boolean running = false;
+    private volatile boolean keepRunning = true;
 
+    /**
+     * Constructor
+     */
     public ScrollThread()
     {
-      start();
+      setName("SeqPanel$ScrollThread");
     }
 
-    public void setEvent(MouseEvent e)
+    /**
+     * Sets the position of the mouse that determines the direction of the
+     * scroll to perform. If this is called as the mouse moves, scrolling should
+     * respond accordingly. For example, if the mouse is dragged right, scroll
+     * right should start; if the drag continues down, scroll down should also
+     * happen.
+     * 
+     * @param p
+     */
+    public void setMousePosition(Point p)
     {
-      evt = e;
+      mousePos = p;
     }
 
+    /**
+     * Sets a flag that will cause the thread to exit
+     */
     public void stopScrolling()
     {
-      running = false;
+      keepRunning = false;
     }
 
+    /**
+     * 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()
     {
-      running = true;
-
-      while (running)
+      while (keepRunning)
       {
-        if (evt != null)
+        if (mousePos != null)
         {
-          if (mouseDragging && (evt.getY() < 0)
-                  && (av.getRanges().getStartSeq() > 0))
-          {
-            running = ap.scrollUp(true);
-          }
-
-          if (mouseDragging && (evt.getY() >= getHeight())
-                  && (av.getAlignment().getHeight() > av.getRanges()
-                          .getEndSeq()))
-          {
-            running = ap.scrollUp(false);
-          }
-
-          if (mouseDragging && (evt.getX() < 0))
-          {
-            running = ap.scrollRight(false);
-          }
-          else if (mouseDragging && (evt.getX() >= getWidth()))
-          {
-            running = ap.scrollRight(true);
-          }
+          keepRunning = scrollOnce();
         }
-
         try
         {
           Thread.sleep(20);
@@ -1995,6 +2173,60 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
         }
       }
+      SeqPanel.this.scrollThread = null;
+    }
+
+    /**
+     * Scrolls
+     * <ul>
+     * <li>one row up, if the mouse is above the panel</li>
+     * <li>one row down, if the mouse is below the panel</li>
+     * <li>one column left, if the mouse is left of the panel</li>
+     * <li>one column right, if the mouse is right of the panel</li>
+     * </ul>
+     * Answers true if a scroll was performed, false if not - meaning either
+     * that the mouse position is within the panel, or the edge of the alignment
+     * has been reached.
+     */
+    boolean scrollOnce()
+    {
+      /*
+       * quit after mouseUp ensures interrupt in JalviewJS
+       */
+      if (!mouseDragging)
+      {
+        return false;
+      }
+
+      boolean scrolled = false;
+      ViewportRanges ranges = SeqPanel.this.av.getRanges();
+
+      /*
+       * scroll up or down
+       */
+      if (mousePos.y < 0)
+      {
+        // mouse is above this panel - try scroll up
+        scrolled = ranges.scrollUp(true);
+      }
+      else if (mousePos.y >= getHeight())
+      {
+        // mouse is below this panel - try scroll down
+        scrolled = ranges.scrollUp(false);
+      }
+
+      /*
+       * scroll left or right
+       */
+      if (mousePos.x < 0)
+      {
+        scrolled |= ranges.scrollRight(false);
+      }
+      else if (mousePos.x >= getWidth())
+      {
+        scrolled |= ranges.scrollRight(true);
+      }
+      return scrolled;
     }
   }
 
@@ -2009,8 +2241,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     // handles selection messages...
     // TODO: extend config options to allow user to control if selections may be
     // shared between viewports.
-    boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
-            .getSequenceSetId().equals(av.getSequenceSetId())));
+    boolean iSentTheSelection = (av == source
+            || (source instanceof AlignViewport
+                    && ((AlignmentViewport) source).getSequenceSetId()
+                            .equals(av.getSequenceSetId())));
 
     if (iSentTheSelection)
     {
@@ -2020,11 +2254,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         ap.getCalculationDialog().validateCalcTypes();
       }
 
-      // process further ?
-      if (!av.followSelection)
-      {
-        return;
-      }
+      return;
+    }
+
+    // process further ?
+    if (!av.followSelection)
+    {
+      return;
     }
 
     /*
@@ -2110,10 +2346,8 @@ public class SeqPanel extends JPanel implements MouseListener,
       repaint = true;
     }
 
-    if (copycolsel
-            && av.hasHiddenColumns()
-            && (av.getAlignment().getHiddenColumns() == null || av
-                    .getAlignment().getHiddenColumns().getHiddenRegions() == null))
+    if (copycolsel && av.hasHiddenColumns()
+            && (av.getAlignment().getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }
@@ -2184,4 +2418,13 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     return true;
   }
+
+  /**
+   * 
+   * @return null or last search results handled by this panel
+   */
+  public SearchResultsI getLastSearchResults()
+  {
+    return lastSearchResults;
+  }
 }