From fccecccb08422b8bd8c9d541632edd9dbee2641f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Jun 2005 14:59:27 +0000
Subject: [PATCH] REmove commented out lines

---
 src/jalview/gui/Jalview2XML.java |   23 +----------------------
 1 file changed, 1 insertion(+), 22 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ee038fc..bdd255c 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -684,6 +684,7 @@ public class Jalview2XML
     }
     else
     {
+      af.annotationPanelMenuItem.setState(view.getShowAnnotation());
       af.viewport.setShowAnnotation(view.getShowAnnotation());
       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
     }
@@ -737,28 +738,6 @@ public class Jalview2XML
 
     //LOAD TREES
     ///////////////////////////////////////
- /*   JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-for(int t=0; t<frames.length; t++)
-{
-  if (frames[t] instanceof TreePanel)
-  {
-    TreePanel tp = (TreePanel) frames[t];
-    if(tp.treeCanvas.av.alignment==jal)
-    {
-      Tree tree = new Tree();
-      tree.setTitle(tp.getTitle());
-      tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
-      tree.setNewick(tp.getTree().toString());
-      tree.setThreshold(tp.treeCanvas.threshold);
-
-      tree.setHeight(tp.getHeight());
-      tree.setWidth(tp.getWidth());
-      tree.setXpos(tp.getX());
-      tree.setYpos(tp.getY());
-
-      jms.addTree(tree);
-    }
-*/
     if (jms.getTreeCount() > 0)
     {
       try
-- 
1.7.10.2