New methods in treePanel

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index bb95476..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
@@ -221,10 +221,11 @@ public class Jalview2XML
                   tree.setThreshold(tp.treeCanvas.threshold);\r
 \r
                   tree.setFitToWindow(tp.fitToWindow.getState());\r
-                  tree.setFontName(tp.getFont().getName());\r
-                  tree.setFontSize(tp.getFont().getSize());\r
-                  tree.setFontStyle(tp.getFont().getStyle());\r
+                  tree.setFontName(tp.getTreeFont().getName());\r
+                  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
@@ -790,21 +791,18 @@ public class Jalview2XML
                     tp.fitToWindow_actionPerformed(null);\r
 \r
                     if(tree.getFontName()!=null)\r
-                      tp.setFont(new java.awt.Font(tree.getFontName(),\r
+                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
                                           tree.getFontStyle(),\r
                                           tree.getFontSize()));\r
                     else\r
-                      tp.setFont(new java.awt.Font(view.getFontName(),\r
+                      tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
                                             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.placeholdersMenu_actionPerformed(null);\r
-                    tp.bootstrapMenu.setState(tree.getShowBootstrap());\r
-                    tp.bootstrapMenu_actionPerformed(null);\r
-                    tp.distanceMenu.setState(tree.getShowDistances());\r
-                    tp.distanceMenu_actionPerformed(null);\r
                     tp.treeCanvas.threshold = tree.getThreshold();\r
 \r
                     if (tree.getCurrentTree())\r