X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=f476d419dc11cb34f3b6a467c44ac3973e0d0e19;hb=f2d38aaebf121e49be29cb19ae01f1c6a36fe7e0;hp=fbe9ff8a59d60d9e7c34c4e7230da4a361b126e1;hpb=ffea8e06f34c1004671749a799722f64a83d8161;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index fbe9ff8..f476d41 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,15 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -34,7 +39,11 @@ import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -46,11 +55,12 @@ 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.List;
-import java.util.Vector;
 
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
@@ -121,6 +131,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   StructureSelectionManager ssm;
 
+  SearchResults lastSearchResults;
+
   /**
    * Creates a new SeqPanel object.
    * 
@@ -160,22 +172,29 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   int wrappedBlock = -1;
 
+  /**
+   * Returns the aligned sequence position (base 0) at the mouse position, or
+   * the closest visible one
+   * 
+   * @param evt
+   * @return
+   */
   int findRes(MouseEvent evt)
   {
     int res = 0;
     int x = evt.getX();
 
-    if (av.wrapAlignment)
+    if (av.getWrapAlignment())
     {
 
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = av.getCharHeight();
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += av.getCharHeight();
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
-              + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+              + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
       y -= hgap;
@@ -195,13 +214,18 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      if (x > seqCanvas.getWidth() + seqCanvas.getWidth())
+      if (x > seqCanvas.getX() + seqCanvas.getWidth())
       {
         // make sure we calculate relative to visible alignment, rather than
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
       res = (x / av.getCharWidth()) + av.getStartRes();
+      if (res > av.getEndRes())
+      {
+        // moused off right
+        res = av.getEndRes();
+      }
     }
 
     if (av.hasHiddenColumns())
@@ -218,16 +242,16 @@ public class SeqPanel extends JPanel implements MouseListener,
     int seq = 0;
     int y = evt.getY();
 
-    if (av.wrapAlignment)
+    if (av.getWrapAlignment())
     {
-      int hgap = av.charHeight;
-      if (av.scaleAboveWrapped)
+      int hgap = av.getCharHeight();
+      if (av.getScaleAboveWrapped())
       {
-        hgap += av.charHeight;
+        hgap += av.getCharHeight();
       }
 
-      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
-              + seqCanvas.getAnnotationHeight();
+      int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+              + hgap + seqCanvas.getAnnotationHeight();
 
       y -= hgap;
 
@@ -243,61 +267,33 @@ public class SeqPanel extends JPanel implements MouseListener,
     return seq;
   }
 
-  SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+  /**
+   * When all of a sequence of edits are complete, put the resulting edit list
+   * on the history stack (undo list), and reset flags for editing in progress.
+   */
+  void endEditing()
   {
-    Vector tmp = new Vector();
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (features != null)
+    try
     {
-      for (int i = 0; i < features.length; i++)
+      if (editCommand != null && editCommand.getSize() > 0)
       {
-        if (av.getFeaturesDisplayed() == null
-                || !av.getFeaturesDisplayed().containsKey(
-                        features[i].getType()))
-        {
-          continue;
-        }
-
-        if (features[i].featureGroup != null
-                && seqCanvas.fr.featureGroups != null
-                && seqCanvas.fr.featureGroups
-                        .containsKey(features[i].featureGroup)
-                && !((Boolean) seqCanvas.fr.featureGroups
-                        .get(features[i].featureGroup)).booleanValue())
-        {
-          continue;
-        }
-
-        if ((features[i].getBegin() <= res)
-                && (features[i].getEnd() >= res))
-        {
-          tmp.addElement(features[i]);
-        }
+        ap.alignFrame.addHistoryItem(editCommand);
+        av.firePropertyChange("alignment", null, av.getAlignment()
+                .getSequences());
       }
-    }
-
-    features = new SequenceFeature[tmp.size()];
-    tmp.copyInto(features);
-
-    return features;
-  }
-
-  void endEditing()
-  {
-    if (editCommand != null && editCommand.getSize() > 0)
+    } finally
     {
-      ap.alignFrame.addHistoryItem(editCommand);
-      av.firePropertyChange("alignment", null, av.getAlignment()
-              .getSequences());
+      /*
+       * Tidy up come what may...
+       */
+      startseq = -1;
+      lastres = -1;
+      editingSeqs = false;
+      groupEditing = false;
+      keyboardNo1 = null;
+      keyboardNo2 = null;
+      editCommand = null;
     }
-
-    startseq = -1;
-    lastres = -1;
-    editingSeqs = false;
-    groupEditing = false;
-    keyboardNo1 = null;
-    keyboardNo2 = null;
-    editCommand = null;
   }
 
   void setCursorRow()
@@ -381,7 +377,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     endEditing();
-    if (av.wrapAlignment)
+    if (av.getWrapAlignment())
     {
       ap.scrollToWrappedVisible(seqCanvas.cursorX);
     }
@@ -395,7 +391,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         ap.scrollUp(false);
       }
-      if (!av.wrapAlignment)
+      if (!av.getWrapAlignment())
       {
         while (seqCanvas.cursorX < av.getColumnSelection()
                 .adjustForHiddenColumns(av.startRes))
@@ -515,6 +511,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   void insertNucAtCursor(boolean group, String nuc)
   {
+    // TODO not called - delete?
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX;
@@ -605,7 +602,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     lastMousePress = evt.getPoint();
 
-    if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+    if (SwingUtilities.isMiddleMouseButton(evt))
     {
       mouseWheelPressed = true;
       return;
@@ -663,20 +660,46 @@ public class SeqPanel extends JPanel implements MouseListener,
     lastMessage = tmp;
   }
 
+  /**
+   * Highlight the mapped region described by the search results object (unless
+   * unchanged). This supports highlight of protein while mousing over linked
+   * cDNA and vice versa. The status bar is also updated to show the location of
+   * the start of the highlighted region.
+   */
   @Override
   public void highlightSequence(SearchResults results)
   {
-    if (av.followHighlight)
+    if (results == null || results.equals(lastSearchResults))
     {
+      return;
+    }
+    lastSearchResults = results;
+
+    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))
       {
         seqCanvas.revalidate();
       }
     }
+    setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
   }
 
   @Override
+  public VamsasSource getVamsasSource()
+  {
+    return this.ap == null ? null : this.ap.av;
+  }
+
+  @Override
   public void updateColours(SequenceI seq, int index)
   {
     System.out.println("update the seqPanel colours");
@@ -744,14 +767,14 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       int rpos;
-      SequenceFeature[] features = findFeaturesAtRes(
-              sequence.getDatasetSequence(),
-              rpos = sequence.findPosition(res));
+      List<SequenceFeature> features = ap.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      rpos = sequence.findPosition(res));
       seqARep.appendFeatures(tooltipText, rpos, features,
-              this.ap.getSeqPanel().seqCanvas.fr.minmax);
+              this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
     }
     if (tooltipText.length() == 6) // <html></html>
     {
@@ -781,6 +804,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    * 
    * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
    */
+  @Override
   public Point getToolTipLocation(MouseEvent event)
   {
     int x = event.getX(), w = getWidth();
@@ -801,6 +825,20 @@ public class SeqPanel extends JPanel implements MouseListener,
   String lastTooltip;
 
   /**
+   * 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
+   */
+  private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
+
+  /**
+   * set if av.getSelectionGroup() refers to a group that is defined on the
+   * alignment view, rather than a transient selection
+   */
+  private boolean editingDefinedGroup = false;  // TODO: refactor to avcontroller or viewModel
+
+  /**
    * Set status message in alignment panel
    * 
    * @param sequence
@@ -813,42 +851,86 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   int setStatusMessage(SequenceI sequence, int res, int seq)
   {
-    int pos = -1;
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
-            + sequence.getName());
+    StringBuilder text = new StringBuilder(32);
 
-    Object obj = null;
+    /*
+     * Sequence number (if known), and sequence name.
+     */
+    String seqno = seq == -1 ? "" : " " + (seq + 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())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
-              + "");
-      if (obj != null)
+      residue = ResidueProperties.nucleotideName.get(displayChar);
+      if (residue != null)
       {
-        text.append(" Nucleotide: ");
+        text.append(" Nucleotide: ").append(residue);
       }
     }
     else
     {
-      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-      if (obj != null)
+      residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+              .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
+              .get(displayChar));
+      if (residue != null)
       {
-        text.append("  Residue: ");
+        text.append(" Residue: ").append(residue);
       }
     }
 
-    if (obj != null)
+    int pos = -1;
+    if (residue != null)
     {
       pos = sequence.findPosition(res);
-      if (obj != "")
-      {
-        text.append(obj + " (" + pos + ")");
-      }
+      text.append(" (").append(Integer.toString(pos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
     return pos;
   }
 
   /**
+   * Set the status bar message to highlight the first matched position in
+   * search results.
+   * 
+   * @param results
+   */
+  private void setStatusMessage(SearchResults results)
+  {
+    AlignmentI al = this.av.getAlignment();
+    int sequenceIndex = al.findIndex(results);
+    if (sequenceIndex == -1)
+    {
+      return;
+    }
+    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    for (Match m : results.getResults())
+    {
+      SequenceI seq = m.getSequence();
+      if (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
+
+      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);
+        return;
+      }
+    }
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @param evt
@@ -859,7 +941,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     if (mouseWheelPressed)
     {
-      int oldWidth = av.charWidth;
+      int oldWidth = av.getCharWidth();
 
       // Which is bigger, left-right or up-down?
       if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
@@ -881,26 +963,28 @@ public class SeqPanel extends JPanel implements MouseListener,
           fontSize = 1;
         }
 
-        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
-        av.charWidth = oldWidth;
+        av.setFont(
+                new Font(av.font.getName(), av.font.getStyle(), fontSize),
+                true);
+        av.setCharWidth(oldWidth);
         ap.fontChanged();
       }
       else
       {
-        if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+        if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
         {
-          av.charWidth--;
+          av.setCharWidth(av.getCharWidth() - 1);
         }
         else if (evt.getX() > lastMousePress.getX())
         {
-          av.charWidth++;
+          av.setCharWidth(av.getCharWidth() + 1);
         }
 
         ap.paintAlignment(false);
       }
 
       FontMetrics fm = getFontMetrics(av.getFont());
-      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+      av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
 
       lastMousePress = evt.getPoint();
 
@@ -963,13 +1047,14 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    StringBuffer message = new StringBuffer();
+    StringBuilder message = new StringBuilder(64);
     if (groupEditing)
     {
       message.append("Edit group:");
       if (editCommand == null)
       {
-        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
+        editCommand = new EditCommand(
+                MessageManager.getString("action.edit_group"));
       }
     }
     else
@@ -982,7 +1067,8 @@ 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 }));
       }
     }
 
@@ -1103,8 +1189,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(groupSeqs[g]
-                      .getCharAt(fixedRight - j)))
+              if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -1166,7 +1251,7 @@ public class SeqPanel extends JPanel implements MouseListener,
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+            if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1188,8 +1273,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
-                  startres, startres - lastres, av.getAlignment(), true);
+          appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
+                  - lastres);
         }
       }
       else
@@ -1204,8 +1289,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
-                  startres, lastres - startres, av.getAlignment(), true);
+          appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
+                  - startres);
         }
 
       }
@@ -1220,14 +1305,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           for (int j = lastres; j < startres; j++)
           {
-            insertChar(j, new SequenceI[]
-            { seq }, fixedRight);
+            insertChar(j, new SequenceI[] { seq }, fixedRight);
           }
         }
         else
         {
-          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres, av.getAlignment(), true);
+          appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+                  startres - lastres);
         }
       }
       else
@@ -1239,13 +1323,12 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = lastres; j > startres; j--)
             {
-              if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+              if (!Comparison.isGap(seq.getCharAt(startres)))
               {
                 endEditing();
                 break;
               }
-              deleteChar(startres, new SequenceI[]
-              { seq }, fixedRight);
+              deleteChar(startres, new SequenceI[] { seq }, fixedRight);
             }
           }
           else
@@ -1254,7 +1337,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             int max = 0;
             for (int m = startres; m < lastres; m++)
             {
-              if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+              if (!Comparison.isGap(seq.getCharAt(m)))
               {
                 break;
               }
@@ -1263,9 +1346,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (max > 0)
             {
-              editCommand.appendEdit(Action.DELETE_GAP,
-                      new SequenceI[]
-                      { seq }, startres, max, av.getAlignment(), true);
+              appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+                      startres, max);
             }
           }
         }
@@ -1275,14 +1357,13 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = lastres; j < startres; j++)
             {
-              insertChar(j, new SequenceI[]
-              { seq }, fixedRight);
+              insertChar(j, new SequenceI[] { seq }, fixedRight);
             }
           }
           else
           {
-            editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
-            { seq }, lastres, startres - lastres, av.getAlignment(), true);
+            appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+                    startres - lastres);
           }
         }
       }
@@ -1302,7 +1383,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
-        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
         {
           // Theres a space, so break and insert the gap
           break;
@@ -1317,22 +1398,36 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
-            av.getAlignment(), true);
+    appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
+
+    appendEdit(Action.INSERT_GAP, seq, j, 1);
+
+  }
+
+  /**
+   * Helper method to add and perform one edit action.
+   * 
+   * @param action
+   * @param seq
+   * @param pos
+   * @param count
+   */
+  protected void appendEdit(Action action, SequenceI[] seq, int pos,
+          int count)
+  {
 
-    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
-            av.getAlignment(), true);
+    final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+            av.getAlignment().getGapCharacter());
 
+    editCommand.appendEdit(edit, av.getAlignment(), true, null);
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
-            av.getAlignment(), true);
+    appendEdit(Action.DELETE_GAP, seq, j, 1);
 
-    editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
-            av.getAlignment(), true);
+    appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
   }
 
   /**
@@ -1390,21 +1485,23 @@ public class SeqPanel extends JPanel implements MouseListener,
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(
-              sequence.getDatasetSequence(),
-              sequence.findPosition(findRes(evt)));
+      List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      sequence.findPosition(findRes(evt)));
 
-      if (features != null && features.length > 0)
+      if (features != null && features.size() > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(),
-                features[0].getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(), features
+                .get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
-      if (features != null && features.length > 0)
+      if (features != null && features.size() > 0)
       {
-        seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
-        { sequence }, features, false, ap);
+        seqCanvas.getFeatureRenderer().amendFeatures(
+                new SequenceI[] { sequence },
+                features.toArray(new SequenceFeature[features.size()]),
+                false, ap);
 
         seqCanvas.highlightSearchResults(null);
       }
@@ -1455,7 +1552,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     startWrapBlock = wrappedBlock;
 
-    if (av.wrapAlignment && seq > av.getAlignment().getHeight())
+    if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("label.cannot_edit_annotations_in_wrapped_view"),
@@ -1486,10 +1583,12 @@ public class SeqPanel extends JPanel implements MouseListener,
               && (res < stretchGroup.getEndRes()))
       {
         av.setSelectionGroup(stretchGroup);
+        editingDefinedGroup = true;
       }
       else
       {
         stretchGroup = null;
+        editingDefinedGroup = false;
       }
     }
     else if (!stretchGroup.getSequences(null).contains(sequence)
@@ -1508,6 +1607,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                   && (allGroups[i].getEndRes() >= res))
           {
             stretchGroup = allGroups[i];
+            editingDefinedGroup = true;
             break;
           }
         }
@@ -1517,23 +1617,24 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     }
 
-    if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+    if (evt.isPopupTrigger())
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(
-              sequence.getDatasetSequence(), sequence.findPosition(res));
-      Vector links = new Vector();
-      for (int i = 0; i < allFeatures.length; i++)
+      List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+              .findFeaturesAtRes(sequence.getDatasetSequence(),
+                      sequence.findPosition(res));
+      List<String> links = new ArrayList<String>();
+      for (SequenceFeature sf : allFeatures)
       {
-        if (allFeatures[i].links != null)
+        if (sf.links != null)
         {
-          for (int j = 0; j < allFeatures[i].links.size(); j++)
+          for (String link : sf.links)
           {
-            links.addElement(allFeatures[i].links.elementAt(j));
+            links.add(link);
           }
         }
       }
 
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+      PopupMenu pop = new PopupMenu(ap, null, links);
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
@@ -1556,7 +1657,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       sg.setEndRes(res);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
-
+      editingDefinedGroup = false;
       stretchGroup = sg;
 
       if (av.getConservationSelected())
@@ -1599,9 +1700,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       return;
     }
-
-    stretchGroup.recalcConservation(); // always do this - annotation has own
-                                       // state
+    // always do this - annotation has own state
+    // but defer colourscheme update until hidden sequences are passed in
+    boolean vischange = stretchGroup.recalcConservation(true);
+    needOverviewUpdate |= vischange && editingDefinedGroup;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1619,8 +1721,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());
-    ap.paintAlignment(true);
-
+    ap.paintAlignment(needOverviewUpdate);
+    needOverviewUpdate =false;
+    editingDefinedGroup = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1674,6 +1777,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
     else if (changeStartRes)
@@ -1681,6 +1785,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
 
@@ -1714,6 +1819,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
+        needOverviewUpdate |= editingDefinedGroup;
       }
       else
       {
@@ -1723,6 +1829,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
         stretchGroup.addSequence(nextSeq, false);
+        needOverviewUpdate |= editingDefinedGroup;
       }
     }
 
@@ -1838,57 +1945,72 @@ 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.
-    if (av == source
-            || !av.followSelection
-            || (av.isSelectionGroupChanged(false) || av
-                    .isColSelChanged(false))
-            || (source instanceof AlignViewport && ((AlignViewport) source)
-                    .getSequenceSetId().equals(av.getSequenceSetId())))
+    boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
+            .getSequenceSetId().equals(av.getSequenceSetId())));
+    if (iSentTheSelection || !av.followSelection)
     {
       return;
     }
+
+    /*
+     * Ignore the selection if there is one of our own pending.
+     */
+    if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+    {
+      return;
+    }
+
+    /*
+     * Check for selection in a view of which this one is a dna/protein
+     * complement.
+     */
+    if (selectionFromTranslation(seqsel, colsel, source))
+    {
+      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))
+    /*
+     * only copy colsel if there is a real intersection between
+     * sequence selection and this panel's alignment
+     */
+    boolean repaint = false;
+    boolean copycolsel = false;
+
+    SequenceGroup sgroup = null;
+    if (seqsel != null && seqsel.getSize() > 0)
     {
-      SequenceGroup sgroup = null;
-      if (seqsel != null && seqsel.getSize() > 0)
+      if (av.getAlignment() == null)
       {
-        if (av.getAlignment() == 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.getAlignment(),
-                (av.hasHiddenRows()) ? av.getHiddenRepSequences() : 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);
+        Cache.log.warn("alignviewport av SeqSetId="
+                + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+                + " 's alignment is NULL! returning immediately.");
+        return;
       }
-      else
+      sgroup = seqsel.intersect(av.getAlignment(),
+              (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+      if ((sgroup != null && sgroup.getSize() > 0))
       {
-        av.setSelectionGroup(null);
+        copycolsel = true;
       }
-      av.isSelectionGroupChanged(true);
-      repaint = true;
     }
+    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 (colsel == null || colsel.isEmpty())
       {
         if (av.getColumnSelection() != null)
         {
@@ -1911,6 +2033,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       av.isColSelChanged(true);
       repaint = true;
     }
+
     if (copycolsel
             && av.hasHiddenColumns()
             && (av.getColumnSelection() == null || av.getColumnSelection()
@@ -1918,11 +2041,53 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       System.err.println("Bad things");
     }
-    if (repaint)
+    if (repaint) // always true!
     {
       // probably finessing with multiple redraws here
       PaintRefresher.Refresh(this, av.getSequenceSetId());
       // ap.paintAlignment(false);
     }
   }
+
+  /**
+   * If this panel is a cdna/protein translation view of the selection source,
+   * tries to map the source selection to a local one, and returns true. Else
+   * returns false.
+   * 
+   * @param seqsel
+   * @param colsel
+   * @param source
+   */
+  protected boolean selectionFromTranslation(SequenceGroup seqsel,
+          ColumnSelection colsel, SelectionSource source)
+  {
+    if (!(source instanceof AlignViewportI))
+    {
+      return false;
+    }
+    final AlignViewportI sourceAv = (AlignViewportI) source;
+    if (sourceAv.getCodingComplement() != av
+            && av.getCodingComplement() != sourceAv)
+    {
+      return false;
+    }
+
+    /*
+     * Map sequence selection
+     */
+    SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+    av.setSelectionGroup(sg);
+    av.isSelectionGroupChanged(true);
+
+    /*
+     * Map column selection
+     */
+    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+            av);
+    av.setColumnSelection(cs);
+
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+    return true;
+  }
 }