REmove commented out lines

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ee038fc..bdd255c 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -684,6 +684,7 @@ public class Jalview2XML
     }\r
     else\r
     {\r
+      af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
       af.viewport.setShowAnnotation(view.getShowAnnotation());\r
       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
     }\r
@@ -737,28 +738,6 @@ public class Jalview2XML
 \r
     //LOAD TREES\r
     ///////////////////////////////////////\r
- /*   JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
-for(int t=0; t<frames.length; t++)\r
-{\r
-  if (frames[t] instanceof TreePanel)\r
-  {\r
-    TreePanel tp = (TreePanel) frames[t];\r
-    if(tp.treeCanvas.av.alignment==jal)\r
-    {\r
-      Tree tree = new Tree();\r
-      tree.setTitle(tp.getTitle());\r
-      tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));\r
-      tree.setNewick(tp.getTree().toString());\r
-      tree.setThreshold(tp.treeCanvas.threshold);\r
-\r
-      tree.setHeight(tp.getHeight());\r
-      tree.setWidth(tp.getWidth());\r
-      tree.setXpos(tp.getX());\r
-      tree.setYpos(tp.getY());\r
-\r
-      jms.addTree(tree);\r
-    }\r
-*/\r
     if (jms.getTreeCount() > 0)\r
     {\r
       try\r