From 434c0972af516df9b66fed52acb86fe08de0c3b3 Mon Sep 17 00:00:00 2001
From: janengelhardt <engelhardt87@googlemail.com>
Date: Mon, 18 Jul 2011 02:54:33 +0200
Subject: [PATCH] JAL-842: some bugfixes;

Change-Id: Ia349eeb750da7b51673a76be805737e4356524e7
---
 src/jalview/gui/AppVarna.java        |    3 ++-
 src/jalview/gui/AppVarnaBinding.java |   12 +-----------
 2 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index bc83400..81ea76c 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -106,9 +106,10 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
 	  StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
 	  StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
 	  for(int i=0;i<rnaTrim.getSeq().length();i++){
+		  //TODO: Jalview utility for gap detection java.utils.isGap()
+		  //TODO: Switch to jalview rna datamodel
 		  if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
 			  if(!rnaTrim.findPair(i).isEmpty()){
-				  System.out.println(rnaTrim.findPair(i));
 				  int m=rnaTrim.findPair(i).get(1);
 				  int l=rnaTrim.findPair(i).get(0);
 				  
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 493e4a7..c235fc1 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -261,17 +261,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 			public void actionPerformed(ActionEvent e) {
 				FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 				sel.rna.setSequence("A");
-				/*try {
-				RNA nRNA = new RNA(generateDefaultName());
-				nRNA.setRNA(_seq.getText(), _str.getText());
-				nRNA.drawRNARadiate(vp.getConfig());
-				_rnaList.add(new VARNAConfig(),nRNA,true);
-				} catch (ExceptionUnmatchedClosingParentheses e1) {
-					JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
-				} catch (ExceptionFileFormatOrSyntax e1) {
-					JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
-				}*/
-			}
+				}
 		});
 		
 		//_seqPanel.setLayout(new BorderLayout());
-- 
1.7.10.2