From f2469e3ede414575d5e8cd510ed5c916095b55bf Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Thu, 30 Jun 2011 16:54:40 +0200
Subject: [PATCH] Varna external frame bug solved

Change-Id: Ie60149059d664fb63d6bd99d748c1f34c1b01703
---
 src/jalview/gui/AppVarna.java  |   24 ++++++------------------
 src/jalview/gui/PopupMenu.java |    1 +
 2 files changed, 7 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 524ac82..7a1e206 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -49,14 +49,6 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
   VARNAPanel varnaPanel;
   
   String name;
-
-  //JSplitPane splitPane;
-
-  //RenderPanel renderPanel;
-
-  //AlignmentPanel ap;
-
-  //Vector atomsPicked = new Vector();
   
   /*public AppVarna(){
 	  vab = new AppVarnaBinding(); 
@@ -75,8 +67,8 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 	  }
 	  rnaList.add(rna1);
 	  
-	  //vab = new AppVarnaBinding(rnaList);
-	  vab = new AppVarnaBinding(seq,struc);
+	  vab = new AppVarnaBinding(rnaList);
+	  //vab = new AppVarnaBinding(seq,struc);
 	  name=this.name;
 	  initVarna();	  
   }
@@ -86,21 +78,17 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 	  //vab.setFinishedInit(false);
 	  varnaPanel=vab.get_varnaPanel();
 	  setBackground(Color.white);
-	  System.out.println("vp: "+vab.get_varnaPanel().getName());
-	  //varnaPanel.setVisible(true);
 	  getContentPane().setLayout(new BorderLayout());
 	  getContentPane().add(varnaPanel, BorderLayout.CENTER);
-	  setVisible(true);
+	  
 	  varnaPanel.addVARNAListener(this);
-	  jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);  
+	  jalview.gui.Desktop.addInternalFrame(this,name,getBounds().width, getBounds().height);
+	  this.pack();
+	  this.setVisible(true);
 	  //showPanel(true);
   }
   
   public void showPanel(boolean show){
-	  //vab.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-	  //vab.pack();
-	  //vab.setVisible(show);
-	    
 	  varnaPanel.setVisible(show);
   }
   
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 948f684..2ac304b 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -269,6 +269,7 @@ public class PopupMenu extends JPopupMenu
     			  break;
     		  }
     	  }
+
     	  //TODO: make rnastrucF a bit more nice
     	  final String rnastrucF=rnastruc;
     	  menuItem = new JMenuItem();
-- 
1.7.10.2