X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=ef01a5092e88f99125d1306bdb5b841e31b3d05a;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=c83f1aa184dbafc924b695471f9fc64ca97aca97;hpb=10e637daad8983c41db8679baabea5563d7371f4;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index c83f1aa..ef01a50 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -371,15 +371,14 @@ public class Jalview2XML_V1
     af.viewport.setColourText(view.getShowColourText());
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.setFont(new java.awt.Font(view.getFontName(), view
-            .getFontStyle(), view.getFontSize()));
-    af.alignPanel.fontChanged();
+    af.viewport.setFont(
+            new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+                    .getFontSize()), true);
 
     af.viewport.setRenderGaps(view.getRenderGaps());
     af.viewport.setWrapAlignment(view.getWrapAlignment());
-    af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-    af.viewport.setShowAnnotation(view.getShowAnnotation());
-    af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+    af.viewport.setShowAnnotation(view.isShowAnnotation());
     af.viewport.setShowBoxes(view.getShowBoxes());
     af.viewport.setShowText(view.getShowText());
 
@@ -405,6 +404,7 @@ public class Jalview2XML_V1
 
     af.viewport.setGlobalColourScheme(cs);
     af.viewport.setColourAppliesToAllGroups(false);
+    af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {