}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
+ String alreadyMapped = jmb.ssm.alreadyMappedToFile(
pdbentry.getId());
if (alreadyMapped != null)
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
+ jmb.ssm.setMapping(seq, chains, alreadyMapped,
AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
}
// /////////////////////////////////
- jmb = new AppJmolBinding(this, new PDBEntry[]
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq }, null, null);
addAlignmentPanel(ap);
{
for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
{
- cap.appendText(StructureSelectionManager
- .getStructureSelectionManager().printMapping(
+ cap.appendText(jmb.printMapping(
jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}