X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1903294140283cfedd325160b1cd6cd3462a2a0c;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=bdfcef466942d8965fa6b621416cf999f9745c77;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
old mode 100755
new mode 100644
index bdfcef4..1903294
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -22,6 +21,7 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
 import jalview.commands.*;
@@ -33,10 +33,11 @@ import jalview.structure.*;
  * DOCUMENT ME!
  * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
  */
 public class SeqPanel extends JPanel implements MouseListener,
-        MouseMotionListener, MouseWheelListener, SequenceListener
+        MouseMotionListener, MouseWheelListener, SequenceListener,
+        SelectionListener
 
 {
   /** DOCUMENT ME!! */
@@ -98,9 +99,9 @@ public class SeqPanel extends JPanel implements MouseListener,
    * Creates a new SeqPanel object.
    * 
    * @param avp
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param p
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public SeqPanel(AlignViewport av, AlignmentPanel ap)
   {
@@ -122,8 +123,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       addMouseMotionListener(this);
       addMouseListener(this);
       addMouseWheelListener(this);
-      ssm = StructureSelectionManager.getStructureSelectionManager();
+      ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
       ssm.addStructureViewerListener(this);
+      ssm.addSelectionListener(this);
     }
   }
 
@@ -166,6 +168,11 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
+      if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+      {
+        // make sure we calculate relative to visible alignment, rather than right-hand gutter
+        x = seqCanvas.getX()+seqCanvas.getWidth();
+      }
       res = (x / av.getCharWidth()) + av.getStartRes();
     }
 
@@ -196,8 +203,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
-              .getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(),
+              av.alignment.getHeight() - 1);
     }
     else
     {
@@ -455,6 +462,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     ap.paintAlignment(false);
+    av.sendSelection();
   }
 
   void insertGapAtCursor(boolean group)
@@ -462,7 +470,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX;
-    editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+    editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
     endEditing();
   }
 
@@ -471,9 +479,17 @@ public class SeqPanel extends JPanel implements MouseListener,
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX + getKeyboardNo1();
-    editSequence(false, seqCanvas.cursorX);
+    editSequence(false, false, seqCanvas.cursorX);
     endEditing();
   }
+  
+  void insertNucAtCursor(boolean group,String nuc){
+	  groupEditing = group;
+	    startseq = seqCanvas.cursorY;
+	    lastres = seqCanvas.cursorX;
+	    editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+	    endEditing();
+  }
 
   void numberPressed(char value)
   {
@@ -520,7 +536,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseReleased(MouseEvent evt)
   {
@@ -540,7 +556,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mousePressed(MouseEvent evt)
   {
@@ -598,13 +614,20 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (lastMessage == null || !lastMessage.equals(tmp))
     {
       // System.err.println("mouseOver Sequence: "+tmp);
-      ssm.mouseOverSequence(sequence, index, pos);
+      ssm.mouseOverSequence(sequence, index, pos, av);
     }
     lastMessage = tmp;
   }
 
   public void highlightSequence(SearchResults results)
   {
+    if (av.followHighlight)
+    {
+      if (ap.scrollToPosition(results, false))
+      {
+      seqCanvas.revalidate();
+      }
+    }
     seqCanvas.highlightSearchResults(results);
   }
 
@@ -618,7 +641,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseMoved(MouseEvent evt)
   {
@@ -679,42 +702,116 @@ public class SeqPanel extends JPanel implements MouseListener,
     // use aa to see if the mouse pointer is on a
     if (av.showSequenceFeatures)
     {
-      SequenceFeature[] features = findFeaturesAtRes(sequence
-              .getDatasetSequence(), sequence.findPosition(res));
+      int rpos;
+      SequenceFeature[] features = findFeaturesAtRes(
+              sequence.getDatasetSequence(),
+              rpos = sequence.findPosition(res));
+      appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
+              this.ap.seqPanel.seqCanvas.fr.minmax);
+    }
+    if (tooltipText.length() == 6) // <html></html>
+    {
+      setToolTipText(null);
+      lastTooltip = null;
+    }
+    else
+    {
+      tooltipText.append("</html>");
+      if (lastTooltip == null
+              || !lastTooltip.equals(tooltipText.toString()))
+      {
+        setToolTipText(tooltipText.toString());
+        lastTooltip = tooltipText.toString();
+      }
+
+    }
+
+  }
 
-      if (features != null)
+  private Point lastp = null;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+   */
+  public Point getToolTipLocation(MouseEvent event)
+  {
+    int x = event.getX(), w = getWidth();
+    int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
+    // close to edge
+    Point p = lastp;
+    if (!event.isShiftDown() || p == null)
+    {
+      p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
+              event.getX() + wdth, event.getY() - 20) : null;
+    }
+    /*
+     * TODO: try to modify position region is not obcured by tooltip
+     */
+    return lastp = p;
+  }
+
+  /**
+   * appends the features at rpos to the given stringbuffer ready for display in
+   * a tooltip
+   * 
+   * @param tooltipText2
+   * @param linkImageURL
+   * @param rpos
+   * @param features
+   *          TODO refactor to Jalview 'utilities' somehow.
+   */
+  public void appendFeatures(StringBuffer tooltipText2,
+          String linkImageURL, int rpos, SequenceFeature[] features)
+  {
+    appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
+  }
+
+  public void appendFeatures(StringBuffer tooltipText2, String string,
+          int rpos, SequenceFeature[] features, Hashtable minmax)
+  {
+    String tmpString;
+    if (features != null)
+    {
+      for (int i = 0; i < features.length; i++)
       {
-        for (int i = 0; i < features.length; i++)
+        if (features[i].getType().equals("disulfide bond"))
         {
-          if (features[i].getType().equals("disulfide bond"))
+          if (features[i].getBegin() == rpos
+                  || features[i].getEnd() == rpos)
           {
-            if (features[i].getBegin() == sequence.findPosition(res)
-                    || features[i].getEnd() == sequence.findPosition(res))
+            if (tooltipText2.length() > 6)
             {
-              if (tooltipText.length() > 6)
-              {
-                tooltipText.append("<br>");
-              }
-              tooltipText.append("disulfide bond " + features[i].getBegin()
-                      + ":" + features[i].getEnd());
-              if (features[i].links != null)
-              {
-                tooltipText.append(" <img src=\"" + linkImageURL + "\">");
-              }
+              tooltipText2.append("<br>");
+            }
+            tooltipText2.append("disulfide bond " + features[i].getBegin()
+                    + ":" + features[i].getEnd());
+            if (features[i].links != null)
+            {
+              tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
             }
           }
-          else
+        }
+        else
+        {
+          if (tooltipText2.length() > 6)
           {
-            if (tooltipText.length() > 6)
+            tooltipText2.append("<br>");
+          }
+          // TODO: remove this hack to display link only features
+          boolean linkOnly = features[i].getValue("linkonly") != null;
+          if (!linkOnly)
+          {
+            tooltipText2.append(features[i].getType() + " ");
+            if (rpos != 0)
             {
-              tooltipText.append("<br>");
+              // we are marking a positional feature
+              tooltipText2.append(features[i].begin);
             }
-
-            tooltipText.append(features[i].getType() + " "
-                    + features[i].begin);
             if (features[i].begin != features[i].end)
             {
-              tooltipText.append(" " + features[i].end);
+              tooltipText2.append(" " + features[i].end);
             }
 
             if (features[i].getDescription() != null
@@ -722,17 +819,20 @@ public class SeqPanel extends JPanel implements MouseListener,
                             .getType()))
             {
               tmpString = features[i].getDescription();
-              int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+              String tmp2up=tmpString.toUpperCase();
+              int startTag = tmp2up.indexOf("<HTML>");
               if (startTag > -1)
               {
                 tmpString = tmpString.substring(startTag + 6);
+                tmp2up = tmp2up.substring(startTag+6);
               }
-              int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+              int endTag = tmp2up.indexOf("</BODY>");
               if (endTag > -1)
               {
                 tmpString = tmpString.substring(0, endTag);
+                tmp2up = tmp2up.substring(0, endTag);
               }
-              endTag = tmpString.toUpperCase().indexOf("</HTML>");
+              endTag = tmp2up.indexOf("</HTML>");
               if (endTag > -1)
               {
                 tmpString = tmpString.substring(0, endTag);
@@ -740,7 +840,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
               if (startTag > -1)
               {
-                tooltipText.append("; " + tmpString);
+                tooltipText2.append("; " + tmpString);
               }
               else
               {
@@ -752,50 +852,44 @@ public class SeqPanel extends JPanel implements MouseListener,
                   tmpString = tmpString.replaceAll("<", "&lt;");
                   tmpString = tmpString.replaceAll(">", "&gt;");
 
-                  tooltipText.append("; ");
-                  tooltipText.append(tmpString);
+                  tooltipText2.append("; ");
+                  tooltipText2.append(tmpString);
 
                 }
                 else
                 {
-                  tooltipText.append("; " + tmpString);
+                  tooltipText2.append("; " + tmpString);
                 }
               }
             }
+            // check score should be shown
+            if (features[i].getScore() != Float.NaN)
+            {
+              float[][] rng = (minmax == null) ? null : ((float[][]) minmax
+                      .get(features[i].getType()));
+              if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
+              {
+                tooltipText2.append(" Score=" + features[i].getScore());
+              }
+            }
             if (features[i].getValue("status") != null)
             {
               String status = features[i].getValue("status").toString();
               if (status.length() > 0)
               {
-                tooltipText.append("; (" + features[i].getValue("status")
+                tooltipText2.append("; (" + features[i].getValue("status")
                         + ")");
               }
             }
-
-            if (features[i].links != null)
-            {
-              tooltipText.append(" <img src=\"" + linkImageURL + "\">");
-            }
-
           }
+          if (features[i].links != null)
+          {
+            tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+          }
+
         }
       }
     }
-
-    if (tooltipText.length() == 6) // <html></html>
-    {
-      setToolTipText(null);
-    }
-    else
-    {
-      tooltipText.append("</html>");
-      if (lastTooltip == null
-              || !lastTooltip.equals(tooltipText.toString()))
-        setToolTipText(tooltipText.toString());
-
-      lastTooltip = tooltipText.toString();
-    }
-
   }
 
   String lastTooltip;
@@ -804,11 +898,11 @@ public class SeqPanel extends JPanel implements MouseListener,
    * Set status message in alignment panel
    * 
    * @param sequence
-   *                aligned sequence object
+   *          aligned sequence object
    * @param res
-   *                alignment column
+   *          alignment column
    * @param seq
-   *                index of sequence in alignment
+   *          index of sequence in alignment
    * @return position of res in sequence
    */
   int setStatusMessage(SequenceI sequence, int res, int seq)
@@ -852,7 +946,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseDragged(MouseEvent evt)
   {
@@ -862,8 +956,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       // Which is bigger, left-right or up-down?
       if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
-              .getX()
-              - lastMousePress.getX()))
+              .getX() - lastMousePress.getX()))
       {
         int fontSize = av.font.getSize();
 
@@ -881,9 +974,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           fontSize = 1;
         }
 
-        av
-                .setFont(new Font(av.font.getName(), av.font.getStyle(),
-                        fontSize));
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
         av.charWidth = oldWidth;
         ap.fontChanged();
       }
@@ -930,11 +1021,11 @@ public class SeqPanel extends JPanel implements MouseListener,
     if ((res < av.getAlignment().getWidth()) && (res < lastres))
     {
       // dragLeft, delete gap
-      editSequence(false, res);
+      editSequence(false, false,res);
     }
     else
     {
-      editSequence(true, res);
+      editSequence(true, false,res);
     }
 
     mouseDragging = true;
@@ -944,7 +1035,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
-  synchronized void editSequence(boolean insertGap, int startres)
+  //TODO: Make it more clever than many booleans
+  synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
   {
     int fixedLeft = -1;
     int fixedRight = -1;
@@ -1229,10 +1321,11 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
           { seq }, lastres, startres - lastres, av.alignment, true);
-        }
+         }
       }
       else
       {
+    	if(!editSeq){
         // dragging to the left
         if (fixedColumns && fixedRight != -1)
         {
@@ -1266,6 +1359,21 @@ public class SeqPanel extends JPanel implements MouseListener,
             { seq }, startres, max, av.alignment, true);
           }
         }
+    	}else{//insertGap==false AND editSeq==TRUE;
+    		if (fixedColumns && fixedRight != -1)
+            {
+              for (int j = lastres; j < startres; j++)
+              {
+                insertChar(j, new SequenceI[]
+                { seq }, fixedRight);
+              }
+              }
+            else
+            {
+              editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+              { seq }, lastres, startres - lastres, av.alignment, true);
+             }
+    	}
       }
     }
 
@@ -1320,7 +1428,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseEntered(MouseEvent e)
   {
@@ -1340,7 +1448,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void mouseExited(MouseEvent e)
   {
@@ -1357,24 +1465,26 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   public void mouseClicked(MouseEvent evt)
   {
+    SequenceGroup sg = null;
     SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
     if (evt.getClickCount() > 1)
     {
-      if (av.getSelectionGroup().getSize() == 1
-              && av.getSelectionGroup().getEndRes()
-                      - av.getSelectionGroup().getStartRes() < 2)
+      sg = av.getSelectionGroup();
+      if (sg != null && sg.getSize() == 1
+              && sg.getEndRes() - sg.getStartRes() < 2)
       {
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(sequence
-              .getDatasetSequence(), sequence.findPosition(findRes(evt)));
+      SequenceFeature[] features = findFeaturesAtRes(
+              sequence.getDatasetSequence(),
+              sequence.findPosition(findRes(evt)));
 
       if (features != null && features.length > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(), features[0]
-                .getEnd());
+        highlight.addResult(sequence, features[0].getBegin(),
+                features[0].getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
       if (features != null && features.length > 0)
@@ -1398,13 +1508,14 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       ap.scrollUp(true);
     }
+    // TODO Update tooltip for new position.
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void doMousePressedDefineMode(MouseEvent evt)
   {
@@ -1477,8 +1588,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence
-              .getDatasetSequence(), sequence.findPosition(res));
+      SequenceFeature[] allFeatures = findFeaturesAtRes(
+              sequence.getDatasetSequence(), sequence.findPosition(res));
       Vector links = new Vector();
       for (int i = 0; i < allFeatures.length; i++)
       {
@@ -1514,6 +1625,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
+
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1548,7 +1660,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
@@ -1557,48 +1669,42 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
+    stretchGroup.recalcConservation(); // always do this - annotation has own
+                                       // state
     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();
+        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+                stretchGroup.getSequences(av.hiddenRepSequences),
+                stretchGroup.getWidth());
       }
 
       if (stretchGroup.cs.conservationApplied())
       {
-        SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
-                .getName());
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                stretchGroup.getName());
       }
       else
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
-                .getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                stretchGroup.getName());
       }
-      PaintRefresher.Refresh(this, av.getSequenceSetId());
-      ap.paintAlignment(true);
     }
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    ap.paintAlignment(true);
 
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
-
+    av.sendSelection();
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
@@ -1791,4 +1897,99 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
   }
+
+  /**
+   * modify current selection according to a received message.
+   */
+  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+          SelectionSource source)
+  {
+    // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+    // handles selection messages...
+    // TODO: extend config options to allow user to control if selections may be
+    // shared between viewports.
+    if (av == source
+            || !av.followSelection
+            || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+            || (source instanceof AlignViewport && ((AlignViewport) source)
+                    .getSequenceSetId().equals(av.getSequenceSetId())))
+    {
+      return;
+    }
+    // do we want to thread this ? (contention with seqsel and colsel locks, I
+    // suspect)
+    // rules are: colsel is copied if there is a real intersection between
+    // sequence selection
+    boolean repaint = false, copycolsel = true;
+    // if (!av.isSelectionGroupChanged(false))
+    {
+      SequenceGroup sgroup = null;
+      if (seqsel != null && seqsel.getSize()>0)
+      {
+        if (av.alignment == null)
+        {
+          jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+                  + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+                  + " 's alignment is NULL! returning immediatly.");
+          return;
+        }
+        sgroup = seqsel.intersect(av.alignment,
+                (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+        if ((sgroup == null || sgroup.getSize() == 0)
+                || (colsel == null || colsel.size() == 0))
+        {
+          // don't copy columns if the region didn't intersect.
+          copycolsel = false;
+        }
+      }
+      if (sgroup != null && sgroup.getSize() > 0)
+      {
+        av.setSelectionGroup(sgroup);
+      }
+      else
+      {
+        av.setSelectionGroup(null);
+      }
+      av.isSelectionGroupChanged(true);
+      repaint = true;
+    }
+    if (copycolsel)
+    {
+      // the current selection is unset or from a previous message
+      // so import the new colsel.
+      if (colsel == null || colsel.size() == 0)
+      {
+        if (av.colSel != null)
+        {
+          av.colSel.clear();
+          repaint=true;
+        }
+      }
+      else
+      {
+        // TODO: shift colSel according to the intersecting sequences
+        if (av.colSel == null)
+        {
+          av.colSel = new ColumnSelection(colsel);
+        }
+        else
+        {
+          av.colSel.setElementsFrom(colsel);
+        }
+      }
+      av.isColSelChanged(true);
+      repaint = true;
+    }
+    if (copycolsel && av.hasHiddenColumns
+            && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+    {
+      System.err.println("Bad things");
+    }
+    if (repaint)
+    {
+      // probably finessing with multiple redraws here
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
+      // ap.paintAlignment(false);
+    }
+  }
 }