X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=9ab6419f7884999750c0e069b90c7df4a4cc17fd;hb=1e5d09b1f43f8a86a4906cd1a410bee9ff07294f;hp=d2d55f8c7c182a05893ded920e784ff11ee0aca4;hpb=5ad6d650b6726eb880d8342d19711e626f6ae2f0;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d2d55f8..9ab6419 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -156,7 +156,7 @@ public class Jalview2XML
         AlignViewport av = af.viewport;
 
         JalviewModel object = new JalviewModel();
-        object.setVamsasModel(new VamsasModel());
+        object.setVamsasModel(new jalview.binding.VamsasModel());
 
         object.setCreationDate(new java.util.Date(timeStamp));
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
@@ -225,6 +225,7 @@ public class Jalview2XML
                   tree.setFontSize(tp.getTreeFont().getSize());
                   tree.setFontStyle(tp.getTreeFont().getStyle());
                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
                   tree.setShowDistances(tp.distanceMenu.getState());
 
@@ -798,13 +799,10 @@ public class Jalview2XML
                                             view.getFontStyle(),
                                             tree.getFontSize()));
 
+                    tp.showPlaceholders(tree.getMarkUnlinked());
+                    tp.showBootstrap(tree.getShowBootstrap());
+                    tp.showDistances(tree.getShowDistances());
 
-                    tp.placeholdersMenu.setState(tree.getMarkUnlinked());
-                    tp.treeCanvas.setMarkPlaceholders(tree.getMarkUnlinked());
-                    tp.bootstrapMenu.setState(tree.getShowBootstrap());
-                    tp.treeCanvas.setShowBootstrap(tree.getShowBootstrap());
-                    tp.distanceMenu.setState(tree.getShowDistances());
-                    tp.treeCanvas.setShowDistances(tree.getShowDistances());
                     tp.treeCanvas.threshold = tree.getThreshold();
 
                     if (tree.getCurrentTree())