*/
public class ChimeraManager
{
- private static final boolean debug = true;
++ private static final boolean debug = false;
+
+ /*
+ * true: use REST API (recommended), false: use stdout/stdin (deprecated)
+ */
++ // TODO remove once definitely happy with using REST
+ private static final boolean USE_REST = true;
+
- // Port number for Chimera REST service
- private int restPort;
++ private int chimeraRestPort;
private Process chimera;
{
chimera = null;
currentModelsMap.clear();
- chimeraListenerThreads = null;
- if (!USE_REST)
++ if (USE_REST)
++ {
++ this.chimeraRestPort = 0;
++ }
++ else
+ {
+ chimeraListenerThread.requestStop();
+ chimeraListenerThread = null;
+ }
structureManager.clearOnChimeraExit();
}
// If no error, then Chimera was launched successfully
if (error.length() == 0)
{
- // Initialize the listener threads
- chimeraListenerThreads = new ListenerThreads(chimera,
- structureManager);
- chimeraListenerThreads.start();
+ if (USE_REST)
+ {
- this.restPort = getPortNumber();
++ this.chimeraRestPort = getPortNumber();
++ System.out.println("Chimera REST API on port " + chimeraRestPort);
+ }
+ else
+ {
+ // Initialize the listener threads
+ chimeraListenerThread = new ListenerThreads(chimera,
+ structureManager);
+ chimeraListenerThread.start();
+ }
// structureManager.initChimTable();
structureManager.setChimeraPathProperty(workingPath);
// TODO: [Optional] Check Chimera version and show a warning if below 1.8
}
/**
+ * Read and return the port number returned in the reply to --start RESTServer
+ */
+ private int getPortNumber()
+ {
+ int port = 0;
+ InputStream readChan = chimera.getInputStream();
+ BufferedReader lineReader = new BufferedReader(new InputStreamReader(
+ readChan));
+ String response = null;
+ try
+ {
+ // expect: REST server on host 127.0.0.1 port port_number
+ response = lineReader.readLine();
+ String [] tokens = response.split(" ");
+ if (tokens.length == 7 && "port".equals(tokens[5])) {
+ port = Integer.parseInt(tokens[6]);
- logger.info("Chimera REST service listening on port " + restPort);
++ logger.info("Chimera REST service listening on port "
++ + chimeraRestPort);
+ }
+ } catch (Exception e)
+ {
+ logger.error("Failed to get REST port number from " + response + ": "
+ + e.getMessage());
+ } finally
+ {
+ try
+ {
+ lineReader.close();
+ } catch (IOException e2)
+ {
+ }
+ }
+ return port;
+ }
+
+ /**
* Determine the color that Chimera is using for this model.
*
* @param model
} finally
{
busy = false;
+ if (debug)
+ {
+ System.out.println("Chimera command took "
+ + (System.currentTimeMillis() - startTime) + "ms: "
+ + command);
+ }
+
+ }
+ }
+
+ /**
+ * Sends the command to Chimera's REST API, and returns any response lines.
+ *
+ * @param command
+ * @return
+ */
+ protected List<String> sendRestCommand(String command)
+ {
+ // TODO start a separate thread to do this so we don't block?
- String restUrl = "http://127.0.0.1:" + this.restPort + "/run";
++ String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
+ List<NameValuePair> commands = new ArrayList<NameValuePair>(1);
+ commands.add(new BasicNameValuePair("command", command));
+
+ List<String> reply = new ArrayList<String>();
+ BufferedReader response = null;
+ try {
+ response = HttpClientUtils.doHttpUrlPost(restUrl,
+ commands);
+ String line = "";
+ while ((line = response.readLine()) != null) {
+ reply.add(line);
+ }
+ } catch (Exception e)
+ {
+ logger.error("REST call " + command + " failed: " + e.getMessage());
+ } finally
+ {
+ if (response != null)
+ {
+ try
+ {
+ response.close();
+ } catch (IOException e)
+ {
+ }
+ }
+ }
+ return reply;
+ }
+
+ /**
+ * Send a command to stdin of Chimera process, and optionally read any
+ * responses.
+ *
+ * @param command
+ * @param readReply
+ * @return
+ */
+ protected List<String> sendStdinCommand(String command, boolean readReply)
+ {
+ chimeraListenerThread.clearResponse(command);
+ String text = command.concat("\n");
+ try
+ {
+ // send the command
+ chimera.getOutputStream().write(text.getBytes());
+ chimera.getOutputStream().flush();
+ } catch (IOException e)
+ {
+ // logger.info("Unable to execute command: " + text);
+ // logger.info("Exiting...");
+ logger.warn("Unable to execute command: " + text);
+ logger.warn("Exiting...");
+ clearOnChimeraExit();
+ return null;
+ }
+ if (!readReply)
+ {
+ return null;
}
+ List<String> rsp = chimeraListenerThread.getResponse(command);
+ return rsp;
}
public StructureManager getStructureManager()
SequenceStructureBinding, StructureSelectionManagerProvider
{
++
++ private static final boolean debug = false;
++
private static final String PHOSPHORUS = "P";
private static final String ALPHACARBON = "CA";
}
if (selectioncom.length() > 0)
{
-- // TODO remove debug output
-- System.out.println("Select regions:\n" + selectioncom.toString());
-- System.out
-- .println("Superimpose command(s):\n" + command.toString());
++ if (debug)
++ {
++ System.out.println("Select regions:\n" + selectioncom.toString());
++ System.out.println("Superimpose command(s):\n"
++ + command.toString());
++ }
allComs.append("~display all; chain @CA|P; ribbon "
+ selectioncom.toString() + ";"+command.toString());
// selcom.append("; ribbons; ");
{
selectioncom.setLength(selectioncom.length() - 1);
}
-- System.out.println("Select regions:\n" + selectioncom.toString());
++ if (debug)
++ {
++ System.out.println("Select regions:\n" + selectioncom.toString());
++ }
allComs.append("; ~display all; chain @CA|P; ribbon "
+ selectioncom.toString() + "; focus");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
}
-- boolean debug = false;
--
private void log(String message)
{
System.err.println("## Chimera log: " + message);
git://source.jalview.org / jalview.git / commitdiff