- if (option == JOptionPane.YES_OPTION)
- {
- // TODO : Fix multiple seq to one chain issue here.
- ap.getStructureSelectionManager().setMapping(seq, chains,
- alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
-
- // Now this ChimeraViewFrame is mapped to new sequences. We must add
- // them to the existing array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof ChimeraViewFrame)
- {
- final ChimeraViewFrame topView = ((ChimeraViewFrame) frame);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topView.jmb.pdbentry.length; pe++)
- {
- if (topView.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topView.jmb.addSequence(pe, seq);
- topView.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topView.useAlignmentPanelForColourbyseq(ap);
- topView.buildChimeraActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }