import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
*/
private long loadNotifiesHandled = 0;
+ private Thread chimeraMonitor;
+
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
- viewer = new ChimeraManager(
- new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ viewer = new ChimeraManager(new StructureManager(true));
+ }
+
+ /**
+ * Starts a thread that waits for the Chimera process to finish, so that we
+ * can then close the associated resources. This avoids leaving orphaned
+ * Chimera viewer panels in Jalview if the user closes Chimera.
+ */
+ protected void startChimeraProcessMonitor()
+ {
+ final Process p = viewer.getChimeraProcess();
+ chimeraMonitor = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ p.waitFor();
+ JalviewStructureDisplayI display = getViewer();
+ if (display != null)
+ {
+ display.closeViewer(false);
+ }
+ } catch (InterruptedException e)
+ {
+ // exit thread if Chimera Viewer is closed in Jalview
+ }
+ }
+ });
+ chimeraMonitor.start();
}
/**
}
viewer = null;
+ if (chimeraMonitor != null)
+ {
+ chimeraMonitor.interrupt();
+ }
releaseUIResources();
}
/**
* Launch Chimera, unless an instance linked to this object is already
- * running. Returns true if chimera is successfully launched, or already
+ * running. Returns true if Chimera is successfully launched, or already
* running, else false.
*
* @return
*/
public boolean launchChimera()
{
- if (!viewer.isChimeraLaunched())
- {
- return viewer.launchChimera(StructureManager.getChimeraPaths());
- }
if (viewer.isChimeraLaunched())
{
return true;
}
- log("Failed to launch Chimera!");
- return false;
+
+ boolean launched = viewer.launchChimera(StructureManager
+ .getChimeraPaths());
+ if (launched)
+ {
+ startChimeraProcessMonitor();
+ }
+ else
+ {
+ log("Failed to launch Chimera!");
+ }
+ return launched;
}
/**
}
return -1;
}
+
+ /**
+ * Queries Chimera for its list of residue attributes and returns their names
+ *
+ * @return
+ */
+ public List<String> getResidueAttributes()
+ {
+ List<String> result = new ArrayList<String>();
+ List<String> atts = sendChimeraCommand("list resattr", true);
+ for (String att : atts)
+ {
+ /*
+ * expect lines like "resattr chi1" - we just one the second bit
+ */
+ String[] tokens = att.split(" ");
+ result.add(tokens[tokens.length - 1]);
+ }
+ return result;
+ }
}