_alignwith = new Vector<AlignmentPanel>();
}
+ // save As not yet implemented
+ savemenu.setVisible(false);
+
ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
// TODO : Fix multiple seq to one chain issue here.
ap.getStructureSelectionManager().setMapping(seq, chains,
alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
+ if (ap.getSeqPanel().seqCanvas.fr != null)
{
- ap.seqPanel.seqCanvas.fr.featuresAdded();
+ ap.getSeqPanel().seqCanvas.fr.featuresAdded();
ap.paintAlignment(true);
}
jmb.setFinishedInit(false);
// TODO: consider waiting until the structure/view is fully loaded before
// displaying
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(true),
getBounds().width, getBounds().height);
if (command == null)
{
jmb.centerViewer(toshow);
}
+ /**
+ * Close down this instance of Jalview's Chimera viewer, giving the user the
+ * option to close the associated Chimera window (process). They may wish to
+ * keep it open until they have had an opportunity to save any work.
+ */
public void closeViewer()
{
- jmb.closeViewer();
+ if (jmb.isChimeraRunning())
+ {
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_chimera", new Object[]
+ { jmb.getViewerTitle(false) });
+ prompt = JvSwingUtils.wrapTooltip(true, prompt);
+ int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ MessageManager.getString("label.close_viewer"),
+ JOptionPane.YES_NO_OPTION);
+ jmb.closeViewer(confirm == JOptionPane.YES_OPTION);
+ }
ap = null;
_aps.clear();
_alignwith.clear();
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '"
+ errormsgs.append("When retrieving pdbfiles for '"
+ thePdbEntry.getId() + "'");
}
if (errormsgs.length() > 0)
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- }
- if (progressBar != null)
+ } finally
{
- progressBar.setProgressBar(
- MessageManager.getString("label.state_completed"), hdl);
+ if (progressBar != null)
+ {
+ progressBar
+ .setProgressBar(
+ pdbid
+ + " "
+ + MessageManager
+ .getString("label.state_completed"),
+ hdl);
+ }
}
/*
* If PDB data were saved and are not invalid (empty alignment), return the
}
setChainMenuItems(jmb.chainNames);
- this.setTitle(jmb.getViewerTitle());
+ this.setTitle(jmb.getViewerTitle(true));
if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
viewerActionMenu.setVisible(true);