-
- if(ap.av.alignment.isNucleotide()==true){
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- String rnastruc=new String();
- for(int i=0; i<aa.length;i++){
- if(aa[i]._rnasecstr != null){
- rnastruc=aa[i].getRNAStruc();
- break;
- }
- }
-
- //TODO: make rnastrucF a bit more nice
- final String rnastrucF=rnastruc;
- menuItem = new JMenuItem();
- menuItem.setText("RNA structure");
- menuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- 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());
- }
- });
- viewStructureMenu.add(menuItem);
- }