From 9de5a036e2a12a895cece39abda685841b219ad3 Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Mon, 25 Jul 2011 14:46:35 +0200
Subject: [PATCH] some print statements to test things

Change-Id: I0730499d395e8f84b9cfd9ec2aaaa7283fc4b1fa
---
 src/jalview/gui/PopupMenu.java          |    9 +++++----
 src/jalview/io/AppletFormatAdapter.java |    2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 82ce835..9de51ea 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -264,14 +264,14 @@ public class PopupMenu extends JPopupMenu
     	  AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
     	  String rnastruc=new String();
     	  for(int i=0; i<aa.length;i++){
-    		  if(aa[i]._rnasecstr != null){
+    		  if(aa[i].getRNAStruc() != null){
     			  rnastruc=aa[i].getRNAStruc();
     			  break;
     		  }
     	  }
-    	  
-    	  SequenceGroup a = aa[0].groupRef;
 
+    	  AlignmentAnnotation a[] = seq.getAnnotation();
+    	  
     	  //TODO: make rnastrucF a bit more nice
     	  final String rnastrucF=rnastruc;
     	  menuItem = new JMenuItem();
@@ -280,8 +280,9 @@ public class PopupMenu extends JPopupMenu
     	  {
     		  public void actionPerformed(ActionEvent e)
     		  {
-    			  System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
+    			  //System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
     			  //TODO: VARNA does'nt print gaps in the sequence
+    			  
     			  new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName(),ap);
     		  }
 		  	});	  
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index e9574fc..fc1d870 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -67,7 +67,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "stk" }; // ,
+      "sto,stk" }; // ,
 
   // ".blast"
   // };
-- 
1.7.10.2