X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=3f64ff1129e3a111267b6dde9b42a812abb15469;hb=dc24bc768061f6e08be77d7e18709da98c6f9428;hp=7b8ade66b621da54b43a9ba2756f47ebd214b59d;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 7b8ade6..3f64ff1 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -135,6 +135,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
+
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
@@ -272,11 +274,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
        */
       if (viewport != null && viewport.getAlignment() != null)
       {
-        if (proxyColourScheme != null)
-        {
-          viewport.applyFeaturesStyle(proxyColourScheme);
-        }
         ((AlignViewport) viewport).addAlignment(al, title);
+        viewport.applyFeaturesStyle(proxyColourScheme);
       }
       else
       {
@@ -298,8 +297,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
-          ColourSchemeI cs = ColourSchemeMapper
-                  .getJalviewColourScheme(colourSchemeName, al);
+          af.setMenusForViewport();
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
           if (cs != null)
           {
             af.changeColour(cs);
@@ -321,7 +321,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         af.currentFileFormat = format;
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText(MessageManager
+        af.setStatus(MessageManager
                 .getString("label.successfully_pasted_alignment_file"));
 
         try