import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
-import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.httpserver.AbstractRequestHandler;
import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
+import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureSelectionManager;
public static final String CHIMERA_FEATURE_GROUP = "Chimera";
- // Chimera clause to exclude alternate locations in atom selection
- private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
-
- private static final boolean debug = false;
-
- private static final String PHOSPHORUS = "P";
-
- private static final String ALPHACARBON = "CA";
-
/*
* Object through which we talk to Chimera
*/
String lastHighlightCommand;
- private Thread chimeraMonitor;
-
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
}
/**
- * 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 = chimeraManager.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();
- }
-
- /**
* Start a dedicated HttpServer to listen for Chimera notifications, and tell it
* to start listening
*/
* Close down the Jalview viewer and listener, and (optionally) the associated
* Chimera window.
*/
+ @Override
public void closeViewer(boolean closeChimera)
{
- getSsm().removeStructureViewerListener(this, this.getStructureFiles());
- if (closeChimera)
- {
- chimeraManager.exitChimera();
- }
+ super.closeViewer(closeChimera);
if (this.chimeraListener != null)
{
chimeraListener.shutdown();
chimeraListener = null;
}
+ chimeraManager.clearOnChimeraExit();
chimeraManager = null;
-
- if (chimeraMonitor != null)
- {
- chimeraMonitor.interrupt();
- }
- releaseUIResources();
}
/**
boolean launched = chimeraManager.launchChimera(getChimeraPaths());
if (launched)
{
- startChimeraProcessMonitor();
+ startExternalViewerMonitor(chimeraManager.getChimeraProcess());
}
else
{
*
* @return
*/
- public boolean isChimeraRunning()
+ @Override
+ public boolean isViewerRunning()
{
return chimeraManager.isChimeraLaunched();
}
if (getResponse)
{
reply = lastReply;
- if (debug)
- {
- log("Response from command ('" + cmd + "') was:\n" + lastReply);
- }
+ Cache.log.debug(
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
}
return reply;
atomSpecs.add(spec);
} catch (IllegalArgumentException e)
{
- System.err.println("Failed to parse atomspec: " + atomSpec);
+ Cache.log.error("Failed to parse atomspec: " + atomSpec);
}
}
return atomSpecs;
}
/**
- * Ask Chimera to save its session to the given file. Returns true if
- * successful, else false.
- *
- * @param filepath
- * @return
- */
- public boolean saveSession(String filepath)
- {
- if (isChimeraRunning())
- {
- /*
- * Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
- * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
- */
- String command = getCommandGenerator().saveSession(filepath)
- .getCommand();
- List<String> reply = chimeraManager.sendChimeraCommand(command, true);
- if (reply.contains("Session written"))
- {
- return true;
- }
- else
- {
- Cache.log
- .error("Error saving Chimera session: " + reply.toString());
- }
- }
- return false;
- }
-
- /**
- * Ask Chimera to open a session file. Returns true if successful, else false.
- * The filename must have a .py (Chimera) or .cxs (ChimeraX) extension for
- * this command to work.
- *
- * @param filepath
- * @return
- */
- public boolean openSession(String filepath)
- {
- /*
- * Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html
- * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
- */
- executeCommand(getCommandGenerator().loadFile(filepath), true);
- // todo: test for failure - how?
- return true;
- }
-
- /**
* Send a 'show' command for all atoms in the currently selected columns
*
* TODO: pull up to abstract structure viewer interface
/**
* Constructs and send commands to Chimera to set attributes on residues for
- * features visible in Jalview
+ * features visible in Jalview.
+ * <p>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * <p>
+ * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
*
* @param avp
* @return
public int sendFeaturesToViewer(AlignmentViewPanel avp)
{
// TODO refactor as required to pull up to an interface
- String[] files = getStructureFiles();
- if (files == null)
- {
- return 0;
- }
+ Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
+ avp);
List<StructureCommandI> commands = getCommandGenerator()
- .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
+ .setAttributes(featureValues);
if (commands.size() > 10)
{
sendCommandsByFile(commands);
return CHIMERA_SESSION_EXTENSION;
}
+ @Override
public String getHelpURL()
{
return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
git://source.jalview.org / jalview.git / blobdiff