});
viewMenu.add(seqColourBy);
viewMenu.add(fitToWindow);
- viewMenu.add(highlightSelection);
final ItemListener handler;
JMenu alpanels = new ViewSelectionMenu(
SequenceI[][] seqs)
{
createProgressBar();
+ // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
.getAllPDBEntries();
if (pdbrefs != null && pdbrefs.size() > 0)
{
+ // FIXME: SequenceI.PDBEntry[0] chain mapping used for
+ // ChimeraViewFrame. Is this even used ???
+
chain = pdbrefs.get(0).getChainCode();
}
}
*/
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
+ // FIXME: this is duplicated code with Jmol frame ?
String filePath = null;
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
}
@Override
- protected void highlightSelection_actionPerformed()
- {
- jmb.highlightSelection(getAlignmentPanel());
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.CHIMERA;