if (aa[i].getRNAStruc() != null)
{
final String rnastruc = aa[i].getRNAStruc();
-
+ final String structureLine=aa[i].label;
menuItem = new JMenuItem();
- menuItem.setText("RNA structure - consensus");
+ menuItem.setText("2D RNA "+structureLine);
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
.getName(), ap);
}
});
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText("RNA structure - "+seq.getName());
+ menuItem.setText("2D RNA - "+seq.getName());
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
- new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+ new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
.getName(), ap);
}
});
{
SequenceGroup sg = getGroup();
sg.cs = new ClustalxColourScheme(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- ap.av.getAlignment().getWidth());
+ sg,ap.av.getHiddenRepSequences());
refresh();
}
public void discoverPDB_actionPerformed()
{
- // TODO: test: verify PDB sequence discovery behaves correctly for group selections
final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
{ sequence }