JAL-842: some bugfixes;

Change-Id: Ia349eeb750da7b51673a76be805737e4356524e7

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index bc83400..81ea76c 100644 (file)
--- 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 (file)
--- 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());