New methods in treePanel

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