X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=056a602768b5debbb85d18bc5de50ad6c7af523e;hb=c643b4ce613987ceeea4e47cb570cc158b25a0cb;hp=a2c2bd9b8c87a5d7c2dcb7ee5c10dad9a3ca06b4;hpb=04d19d44b27b66c342e35b8933776b0ca7da9f35;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a2c2bd9..056a602 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -62,6 +62,7 @@ import java.awt.event.MouseWheelListener;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.ListIterator;
 
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
@@ -73,9 +74,9 @@ 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!! */
@@ -183,11 +184,12 @@ 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())
     {
 
@@ -202,7 +204,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       int y = evt.getY();
       y -= hgap;
-      x -= seqCanvas.LABEL_WEST;
+      x = Math.max(0, x - seqCanvas.LABEL_WEST);
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
@@ -211,10 +213,11 @@ 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 +227,7 @@ 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
@@ -260,15 +263,14 @@ 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 +287,8 @@ 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
     {
@@ -344,8 +346,7 @@ 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();
@@ -389,38 +390,11 @@ public class SeqPanel extends JPanel implements MouseListener,
     endEditing();
     if (av.getWrapAlignment())
     {
-      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
     }
     else
     {
-      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
-      {
-        ap.scrollUp(true);
-      }
-      while (seqCanvas.cursorY > av.getRanges().getEndSeq())
-      {
-        ap.scrollUp(false);
-      }
-      if (!av.getWrapAlignment())
-      {
-        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),
             seqCanvas.cursorX, seqCanvas.cursorY);
@@ -590,6 +564,7 @@ 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;
 
@@ -602,7 +577,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (!editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
+      doMouseReleasedDefineMode(evt, didDrag);
       return;
     }
 
@@ -642,7 +617,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < 0 || res < 0)
     {
@@ -696,17 +671,16 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     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);
+      // 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);
       if (ap.scrollToPosition(results, false))
       {
         seqCanvas.revalidate();
       }
+      ap.setToScrollComplementPanel(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
@@ -741,25 +715,28 @@ public class SeqPanel extends JPanel implements MouseListener,
       mouseDragged(evt);
     }
 
-    int res = findRes(evt);
+    final int column = findColumn(evt);
     int seq = findSeq(evt);
-    int pos;
-    if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+    if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
     {
       return;
     }
 
     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 +746,8 @@ 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"))
@@ -785,14 +763,20 @@ 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,
+              .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+      if (isGapped)
+      {
+        removeAdjacentFeatures(features, column + 1, sequence);
+      }
+      seqARep.appendFeatures(tooltipText, pos, features,
               this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
     if (tooltipText.length() == 6) // <html>
@@ -816,6 +800,35 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   }
 
+  /**
+   * Removes from the list of features any that start after, or end before, the
+   * given column position. This allows us to retain only those features
+   * adjacent to a gapped position that straddle the position. Contact features
+   * that 'straddle' the position are also removed, since they are not 'at' the
+   * position.
+   * 
+   * @param features
+   * @param column
+   *          alignment column (1..)
+   * @param sequence
+   */
+  protected void removeAdjacentFeatures(List<SequenceFeature> features,
+          final int column, SequenceI sequence)
+  {
+    // TODO should this be an AlignViewController method (and reused by applet)?
+    ListIterator<SequenceFeature> it = features.listIterator();
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (sf.isContactFeature()
+              || sequence.findIndex(sf.getBegin()) > column
+              || sequence.findIndex(sf.getEnd()) < column)
+      {
+        it.remove();
+      }
+    }
+  }
+
   private Point lastp = null;
 
   /*
@@ -832,8 +845,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     Point p = lastp;
     if (!event.isShiftDown() || p == null)
     {
-      p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
-              event.getX() + wdth, event.getY() - 20) : 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
@@ -859,17 +873,22 @@ 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
    *          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 seq)
   {
     StringBuilder text = new StringBuilder(32);
 
@@ -881,36 +900,34 @@ public class SeqPanel extends JPanel implements MouseListener,
             .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())
+    final String displayChar = String.valueOf(sequence.getCharAt(column));
+    boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+    int pos = sequence.findPosition(column);
+
+    if (!isGapped)
     {
-      residue = ResidueProperties.nucleotideName.get(displayChar);
-      if (residue != null)
+      boolean nucleotide = av.getAlignment().isNucleotide();
+      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(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
+
     return pos;
   }
 
@@ -964,8 +981,8 @@ 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
@@ -1055,7 +1072,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (res < 0)
     {
@@ -1125,8 +1142,9 @@ 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 +1161,8 @@ 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;
 
@@ -1333,8 +1350,8 @@ 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 +1366,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
-                  - startres);
+          appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+                  lastres - startres);
         }
 
       }
@@ -1550,9 +1567,20 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
+      int column = findColumn(evt);
+      boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+
+      /*
+       * 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)));
+                      sequence.findPosition(column));
+      if (isGapped)
+      {
+        removeAdjacentFeatures(features, column, sequence);
+      }
 
       if (!features.isEmpty())
       {
@@ -1560,8 +1588,8 @@ public class SeqPanel extends JPanel implements MouseListener,
          * highlight the first feature at the position on the alignment
          */
         SearchResultsI highlight = new SearchResults();
-        highlight.addResult(sequence, features.get(0).getBegin(), features
-                .get(0).getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(),
+                features.get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
 
         /*
@@ -1570,7 +1598,7 @@ public class SeqPanel extends JPanel implements MouseListener,
          */
         List<SequenceI> seqs = Collections.singletonList(sequence);
         seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
-                ap, null);
+                ap);
         seqCanvas.highlightSearchResults(null);
       }
     }
@@ -1584,23 +1612,23 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (e.isShiftDown())
       {
-        ap.scrollRight(true);
+        av.getRanges().scrollRight(true);
 
       }
-      else
+      else if (!av.getWrapAlignment())
       {
-        ap.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
     else
     {
       if (e.isShiftDown())
       {
-        ap.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
-      else
+      else if (!av.getWrapAlignment())
       {
-        ap.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
     // TODO Update tooltip for new position.
@@ -1614,7 +1642,7 @@ 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;
@@ -1623,8 +1651,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     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 +1702,7 @@ 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;
@@ -1729,13 +1758,13 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   void showPopupMenu(MouseEvent evt)
   {
-    final int res = findRes(evt);
+    final int res = 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>();
+    List<String> links = new ArrayList<>();
     for (SequenceFeature sf : allFeatures)
     {
       if (sf.links != null)
@@ -1752,12 +1781,15 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * 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)
     {
@@ -1766,13 +1798,15 @@ public class SeqPanel extends JPanel implements MouseListener,
     // 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();
+    needOverviewUpdate |= 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())
       {
@@ -1800,7 +1834,7 @@ 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)
@@ -1968,23 +2002,22 @@ public class SeqPanel extends JPanel implements MouseListener,
           if (mouseDragging && (evt.getY() < 0)
                   && (av.getRanges().getStartSeq() > 0))
           {
-            running = ap.scrollUp(true);
+            running = av.getRanges().scrollUp(true);
           }
 
-          if (mouseDragging && (evt.getY() >= getHeight())
-                  && (av.getAlignment().getHeight() > av.getRanges()
-                          .getEndSeq()))
+          if (mouseDragging && (evt.getY() >= getHeight()) && (av
+                  .getAlignment().getHeight() > av.getRanges().getEndSeq()))
           {
-            running = ap.scrollUp(false);
+            running = av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && (evt.getX() < 0))
           {
-            running = ap.scrollRight(false);
+            running = av.getRanges().scrollRight(false);
           }
           else if (mouseDragging && (evt.getX() >= getWidth()))
           {
-            running = ap.scrollRight(true);
+            running = av.getRanges().scrollRight(true);
           }
         }
 
@@ -2009,8 +2042,10 @@ 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 +2055,13 @@ 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 +2147,8 @@ 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");
     }