Merge branch 'Release_2_8_3_Branch' of https://source.jalview.org/git/jalview into...

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8beb26f..8e77111 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1133,7 +1133,7 @@ public class Jalview2XML
       view.setShowGroupConservation(av.isShowGroupConservation());
       view.setShowNPfeatureTooltip(av.isShowNPFeats());
       view.setShowDbRefTooltip(av.isShowDBRefs());
-      view.setFollowHighlight(av.followHighlight);
+      view.setFollowHighlight(av.isFollowHighlight());
       view.setFollowSelection(av.followSelection);
       view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
       if (av.getFeaturesDisplayed() != null)
@@ -2263,6 +2263,13 @@ public class Jalview2XML
     int height = (int) (dnaFrame.getBounds().getHeight()
             + proteinFrame.getBounds().getHeight() + 50);
     Desktop.addInternalFrame(splitFrame, title, width, height);
+
+    /*
+     * And compute cDNA consensus (couldn't do earlier with consensus as
+     * mappings were not yet present)
+     */
+    proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+
     return splitFrame;
   }
 
@@ -3452,7 +3459,7 @@ public class Jalview2XML
                       (OutOfMemoryError) ex.getCause());
               if (sview != null && sview.isVisible())
               {
-                sview.closeViewer();
+                sview.closeViewer(false);
                 sview.setVisible(false);
                 sview.dispose();
               }
@@ -3837,7 +3844,7 @@ public class Jalview2XML
     }
     if (view.hasFollowHighlight())
     {
-      af.viewport.followHighlight = view.getFollowHighlight();
+      af.viewport.setFollowHighlight(view.getFollowHighlight());
     }
     if (view.hasFollowSelection())
     {