X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=6fbed49e014db3e2f6e52d614d9c0618e11890e3;hb=b4d2b6a2ed131265ed599db27de9b82aaf010400;hp=f1e4d135d3cc7b4eadb222e51c25f28b80e695cc;hpb=1c595b732e537e1b9ba60dec40f8e34f93d4cb74;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index f1e4d13..6fbed49 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,7 @@ import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -59,7 +60,9 @@ 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 java.util.ListIterator;
 
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
@@ -181,11 +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())
     {
 
@@ -200,7 +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)
@@ -209,10 +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
+              + Math.min(cwidth - 1, startOffset + x / av.getCharWidth());
     }
     else
     {
@@ -222,7 +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
@@ -232,7 +237,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(res);
     }
 
     return res;
@@ -338,20 +344,23 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
+
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
     if (av.hasHiddenColumns()
-            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ && !hidden.isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+      while (!hidden.isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+              || !hidden.isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -387,32 +396,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
-      {
-        av.getRanges().scrollUp(true);
-      }
-      while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq())
-      {
-        av.getRanges().scrollUp(false);
-      }
-
-      while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(av.getRanges().getStartRes()))
-      {
-        if (!av.getRanges().scrollRight(false))
-        {
-          break;
-        }
-      }
-      while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(av.getRanges().getEndRes()))
-      {
-        if (!av.getRanges().scrollRight(true))
-        {
-          break;
-        }
-      }
-
+      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
@@ -582,6 +566,7 @@ 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;
 
@@ -594,7 +579,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (!editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
+      doMouseReleasedDefineMode(evt, didDrag);
       return;
     }
 
@@ -634,7 +619,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < 0 || res < 0)
     {
@@ -692,12 +677,12 @@ public class SeqPanel extends JPanel implements MouseListener,
       // 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.setDontScrollComplement(true);
+      ap.setToScrollComplementPanel(false);
       if (ap.scrollToPosition(results, false))
       {
         seqCanvas.revalidate();
       }
-      ap.setDontScrollComplement(false);
+      ap.setToScrollComplementPanel(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
@@ -732,25 +717,28 @@ 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>
@@ -760,7 +748,8 @@ 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"))
@@ -776,14 +765,20 @@ 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>
@@ -807,6 +802,35 @@ 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;
 
   /*
@@ -850,17 +874,22 @@ 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);
 
@@ -872,36 +901,34 @@ 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;
   }
 
@@ -942,30 +969,36 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
+   * {@inheritDoc}
    */
   @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (mouseWheelPressed)
     {
+      boolean inSplitFrame = ap.av.getCodingComplement() != null;
+      boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
+
       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()))
       {
+        /*
+         * on drag up or down, decrement or increment font size
+         */
         int fontSize = av.font.getSize();
+        boolean fontChanged = false;
 
         if (evt.getY() < lastMousePress.getY())
         {
+          fontChanged = true;
           fontSize--;
         }
         else if (evt.getY() > lastMousePress.getY())
         {
+          fontChanged = true;
           fontSize++;
         }
 
@@ -974,24 +1007,56 @@ public class SeqPanel extends JPanel implements MouseListener,
           fontSize = 1;
         }
 
-        av.setFont(
-                new Font(av.font.getName(), av.font.getStyle(), fontSize),
-                true);
-        av.setCharWidth(oldWidth);
-        ap.fontChanged();
+        if (fontChanged)
+        {
+          Font newFont = new Font(av.font.getName(), av.font.getStyle(),
+                  fontSize);
+          av.setFont(newFont, true);
+          av.setCharWidth(oldWidth);
+          ap.fontChanged();
+          if (copyChanges)
+          {
+            ap.av.getCodingComplement().setFont(newFont, true);
+            SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+                    .getSplitViewContainer();
+            splitFrame.adjustLayout();
+            splitFrame.repaint();
+          }
+        }
       }
       else
       {
+        /*
+         * on drag left or right, decrement or increment character width
+         */
+        int newWidth = 0;
         if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
         {
-          av.setCharWidth(av.getCharWidth() - 1);
+          newWidth = av.getCharWidth() - 1;
+          av.setCharWidth(newWidth);
         }
         else if (evt.getX() > lastMousePress.getX())
         {
-          av.setCharWidth(av.getCharWidth() + 1);
+          newWidth = av.getCharWidth() + 1;
+          av.setCharWidth(newWidth);
+        }
+        if (newWidth > 0)
+        {
+          ap.paintAlignment(false);
+          if (copyChanges)
+          {
+            /*
+             * need to ensure newWidth is set on cdna, regardless of which
+             * panel the mouse drag happened in; protein will compute its 
+             * character width as 1:1 or 3:1
+             */
+            av.getCodingComplement().setCharWidth(newWidth);
+            SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+                    .getSplitViewContainer();
+            splitFrame.adjustLayout();
+            splitFrame.repaint();
+          }
         }
-
-        ap.paintAlignment(false);
       }
 
       FontMetrics fm = getFontMetrics(av.getFont());
@@ -1008,7 +1073,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (res < 0)
     {
@@ -1141,8 +1206,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.hasHiddenColumns())
     {
       fixedColumns = true;
-      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+      int y1 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryLeft(startres);
+      int y2 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryRight(startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1217,8 +1284,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns() && startres < av
-                    .getColumnSelection().getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns() && startres < av.getAlignment()
+                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1482,6 +1549,11 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
+  /**
+   * Handler for double-click on a position with one or more sequence features.
+   * Opens the Amend Features dialog to allow feature details to be amended, or
+   * the feature deleted.
+   */
   @Override
   public void mouseClicked(MouseEvent evt)
   {
@@ -1496,24 +1568,38 @@ 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 != null && features.size() > 0)
+      if (!features.isEmpty())
       {
+        /*
+         * 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());
         seqCanvas.highlightSearchResults(highlight);
-      }
-      if (features != null && features.size() > 0)
-      {
-        seqCanvas.getFeatureRenderer().amendFeatures(
-                new SequenceI[] { sequence },
-                features.toArray(new SequenceFeature[features.size()]),
-                false, ap);
 
+        /*
+         * open the Amend Features dialog; clear highlighting afterwards,
+         * whether changes were made or not
+         */
+        List<SequenceI> seqs = Collections.singletonList(sequence);
+        seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+                ap);
         seqCanvas.highlightSearchResults(null);
       }
     }
@@ -1557,7 +1643,7 @@ 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;
@@ -1616,7 +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;
@@ -1668,17 +1754,17 @@ public class SeqPanel extends JPanel implements MouseListener,
    * 
    * @param evt
    * @param res
-   * @param sequence
+   * @param sequences
    */
   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)
@@ -1695,12 +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)
     {
@@ -1709,7 +1798,8 @@ 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,
@@ -1743,7 +1833,7 @@ 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)
@@ -1946,7 +2036,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
     // handles selection messages...
@@ -1954,7 +2044,20 @@ public class SeqPanel extends JPanel implements MouseListener,
     // shared between viewports.
     boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
             .getSequenceSetId().equals(av.getSequenceSetId())));
-    if (iSentTheSelection || !av.followSelection)
+
+    if (iSentTheSelection)
+    {
+      // respond to our own event by updating dependent dialogs
+      if (ap.getCalculationDialog() != null)
+      {
+        ap.getCalculationDialog().validateCalcTypes();
+      }
+
+      return;
+    }
+
+    // process further ?
+    if (!av.followSelection)
     {
       return;
     }
@@ -1971,7 +2074,7 @@ public class SeqPanel extends JPanel implements MouseListener,
      * Check for selection in a view of which this one is a dna/protein
      * complement.
      */
-    if (selectionFromTranslation(seqsel, colsel, source))
+    if (selectionFromTranslation(seqsel, colsel, hidden, source))
     {
       return;
     }
@@ -2034,7 +2137,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       av.isColSelChanged(true);
@@ -2043,8 +2147,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getColumnSelection()
-                    .getHiddenColumns() == null))
+            && (av.getAlignment().getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }
@@ -2054,6 +2157,13 @@ public class SeqPanel extends JPanel implements MouseListener,
       PaintRefresher.Refresh(this, av.getSequenceSetId());
       // ap.paintAlignment(false);
     }
+
+    // lastly, update dependent dialogs
+    if (ap.getCalculationDialog() != null)
+    {
+      ap.getCalculationDialog().validateCalcTypes();
+    }
+
   }
 
   /**
@@ -2066,7 +2176,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -2089,9 +2200,19 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * Map column selection
      */
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
-            av);
+    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+    // av);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
+    av.getAlignment().setHiddenColumns(hs);
+
+    // lastly, update any dependent dialogs
+    if (ap.getCalculationDialog() != null)
+    {
+      ap.getCalculationDialog().validateCalcTypes();
+    }
 
     PaintRefresher.Refresh(this, av.getSequenceSetId());