JAL-2023 fix for CDS shared dataset, robust load of split frame project

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 63e6787..56cf231 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -845,6 +845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * operation that affects the data in the current view (selection changed,
    * etc) to update the menus to reflect the new state.
    */
+  @Override
   public void setMenusForViewport()
   {
     setMenusFromViewport(viewport);
@@ -1401,6 +1402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.makeEPS(f);
   }
 
+  @Override
   public void createSVG(File f)
   {
     alignPanel.makeSVG(f);
@@ -1574,6 +1576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void addHistoryItem(CommandI command)
   {
     if (command.getSize() > 0)
@@ -3497,6 +3500,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param cs
    *          DOCUMENT ME!
    */
+  @Override
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
@@ -4752,8 +4756,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         try
         {
           // update our local dataset reference
-          Alignment ds = AlignFrame.this.getViewport().getAlignment()
-                  .getDataset();
+          AlignmentI alignment = AlignFrame.this.getViewport()
+                  .getAlignment();
+          Alignment ds = alignment.getDataset();
           Alignment prods = CrossRef
                   .findXrefSequences(sel, dna, source, ds);
           if (prods != null)
@@ -4806,7 +4811,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               if (dna)
               {
                 copyAlignment = AlignmentUtils.makeExonAlignment(
-                        sequenceSelection, cf);
+                        sequenceSelection, cf, alignment);
                 al.getCodonFrames().clear();
                 al.getCodonFrames().addAll(cf);
                 final StructureSelectionManager ssm = StructureSelectionManager
@@ -5755,6 +5760,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.firePropertyChange("alignment", null, al);
   }
 
+  @Override
   public void setShowSeqFeatures(boolean b)
   {
     showSeqFeatures.setSelected(b);