protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem();
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
* @param links
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
- Vector groupLinks)
+ public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links,
+ final Vector groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
colours.add(userDefinedColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
+ colours.add(purinePyrimidineColour);
+ //colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
}
}
else
- {
- structureMenu.remove(viewStructureMenu);
+ {
+ if(ap.av.alignment.isNucleotide()==false){
+ structureMenu.remove(viewStructureMenu);
+ }
// structureMenu.remove(colStructureMenu);
}
+
+ 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);
+ }
menuItem = new JMenuItem("Hide Sequences");
menuItem.addActionListener(new java.awt.event.ActionListener()
{
clustalColour.setSelected(true);
}
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)
+ {
+ purinePyrimidineColour.setSelected(true);
+ }
+ /* else if (sg.cs instanceof CovariationColourScheme)
+ {
+ covariationColour.setSelected(true);
+ }*/
else
{
noColourmenuItem.setSelected(true);
final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
final JMenuItem gpdbview;
structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures."));
+ gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
gpdbview.addActionListener(new ActionListener()
{
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(purinePyrimidineColour);
+ //colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
BLOSUM62Colour_actionPerformed();
}
});
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+ /*
+ covariationColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ covariationColour_actionPerformed();
+ }
+ });*/
+
conservationMenuItem.setText("Conservation");
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
getGroup().cs = new NucleotideColourScheme();
refresh();
}
-
+
+ protected void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+ /*
+ protected void covariationColour_actionPerformed()
+ {
+ getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
+ refresh();
+ }
+*/
/**
* DOCUMENT ME!
*