import java.util.Map;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.pymol.PymolCommands;
private PymolManager pymolManager;
- private Thread pymolMonitor;
-
/*
* full paths to structure files opened in PyMOL
*/
public void closeViewer(boolean closePymol)
{
super.closeViewer(closePymol);
- if (closePymol)
- {
- pymolManager.exitPymol();
- }
pymolManager = null;
-
- if (pymolMonitor != null)
- {
- pymolMonitor.interrupt();
- }
}
public boolean launchPymol()
return true;
}
- boolean launched = pymolManager.launchPymol();
- if (launched)
+ Process pymol = pymolManager.launchPymol();
+ if (pymol != null)
{
// start listening for PyMOL selections - how??
+ startExternalViewerMonitor(pymol);
}
else
{
- System.err.println("Failed to launch PyMOL!");
+ Cache.log.error("Failed to launch PyMOL!");
}
- return launched;
+ return pymol != null;
}
public void openFile(PDBEntry pe)