--- /dev/null
+package ext.edu.ucsf.rbvi.strucviz2.port;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import ext.edu.ucsf.rbvi.strucviz2.*;
+
+/***************************************************
+ * Thread Classes *
+ **************************************************/
+
+/**
+ * Reply listener thread
+ */
+public class ListenerThreads extends Thread {
+ private InputStream readChan = null;
+ private BufferedReader lineReader = null;
+ private Process chimera = null;
+ private Map<String, List<String>> replyLog = null;
+ private Logger logger;
+ private StructureManager structureManager = null;
+
+ /**
+ * Create a new listener thread to read the responses from Chimera
+ *
+ * @param chimera
+ * a handle to the Chimera Process
+ * @param log
+ * a handle to a List to post the responses to
+ * @param chimeraObject
+ * a handle to the Chimera Object
+ */
+ public ListenerThreads(Process chimera, StructureManager structureManager) {
+ this.chimera = chimera;
+ this.structureManager = structureManager;
+ replyLog = new HashMap<String, List<String>>();
+ // Get a line-oriented reader
+ readChan = chimera.getInputStream();
+ lineReader = new BufferedReader(new InputStreamReader(readChan));
+ logger = LoggerFactory.getLogger(ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads.class);
+ }
+
+ /**
+ * Start the thread running
+ */
+ public void run() {
+ // System.out.println("ReplyLogListener running");
+ while (true) {
+ try {
+ chimeraRead();
+ } catch (IOException e) {
+ logger.warn("UCSF Chimera has exited: " + e.getMessage());
+ return;
+ }
+ }
+ }
+
+ public List<String> getResponse(String command) {
+ List<String> reply;
+ // System.out.println("getResponse: "+command);
+ while (!replyLog.containsKey(command)) {
+ try {
+ Thread.currentThread().sleep(100);
+ } catch (InterruptedException e) {
+ }
+ }
+
+ synchronized (replyLog) {
+ reply = replyLog.get(command);
+ // System.out.println("getResponse ("+command+") = "+reply);
+ replyLog.remove(command);
+ }
+ return reply;
+ }
+
+ public void clearResponse(String command) {
+ try {
+ Thread.currentThread().sleep(100);
+ } catch (InterruptedException e) {
+ }
+ if (replyLog.containsKey(command))
+ replyLog.remove(command);
+ return;
+ }
+
+ /**
+ * Read input from Chimera
+ *
+ * @return a List containing the replies from Chimera
+ */
+ private void chimeraRead() throws IOException {
+ if (chimera == null)
+ return;
+
+ String line = null;
+ while ((line = lineReader.readLine()) != null) {
+ // System.out.println("From Chimera-->" + line);
+ if (line.startsWith("CMD")) {
+ chimeraCommandRead(line.substring(4));
+ } else if (line.startsWith("ModelChanged: ")) {
+ (new ModelUpdater()).start();
+ } else if (line.startsWith("SelectionChanged: ")) {
+ (new SelectionUpdater()).start();
+ } else if (line.startsWith("Trajectory residue network info:")) {
+ (new NetworkUpdater(line)).start();
+ }
+ }
+ return;
+ }
+
+ private void chimeraCommandRead(String command) throws IOException {
+ // Generally -- looking for:
+ // CMD command
+ // ........
+ // END
+ // We return the text in between
+ List<String> reply = new ArrayList<String>();
+ boolean updateModels = false;
+ boolean updateSelection = false;
+ boolean importNetwork = false;
+ String line = null;
+
+ synchronized (replyLog) {
+ while ((line = lineReader.readLine()) != null) {
+ // System.out.println("From Chimera (" + command + ") -->" + line);
+ if (line.startsWith("CMD")) {
+ logger.warn("Got unexpected command from Chimera: " + line);
+
+ } else if (line.startsWith("END")) {
+ break;
+ }
+ if (line.startsWith("ModelChanged: ")) {
+ updateModels = true;
+ } else if (line.startsWith("SelectionChanged: ")) {
+ updateSelection = true;
+ } else if (line.length() == 0) {
+ continue;
+ } else if (!line.startsWith("CMD")) {
+ reply.add(line);
+ } else if (line.startsWith("Trajectory residue network info:")) {
+ importNetwork = true;
+ }
+ }
+ replyLog.put(command, reply);
+ }
+ if (updateModels)
+ (new ModelUpdater()).start();
+ if (updateSelection)
+ (new SelectionUpdater()).start();
+ if (importNetwork) {
+ (new NetworkUpdater(line)).start();
+ }
+ return;
+ }
+
+ /**
+ * Model updater thread
+ */
+ class ModelUpdater extends Thread {
+
+ public ModelUpdater() {
+ }
+
+ public void run() {
+ structureManager.updateModels();
+ structureManager.modelChanged();
+ }
+ }
+
+ /**
+ * Selection updater thread
+ */
+ class SelectionUpdater extends Thread {
+
+ public SelectionUpdater() {
+ }
+
+ public void run() {
+ try {
+ logger.info("Responding to chimera selection");
+ structureManager.chimeraSelectionChanged();
+ } catch (Exception e) {
+ logger.warn("Could not update selection", e);
+ }
+ }
+ }
+
+ /**
+ * Selection updater thread
+ */
+ class NetworkUpdater extends Thread {
+
+ private String line;
+
+ public NetworkUpdater(String line) {
+ this.line = line;
+ }
+
+ public void run() {
+ try {
+// ((TaskManager<?, ?>) structureManager.getService(TaskManager.class))
+// .execute(new ImportTrajectoryRINTaskFactory(structureManager, line)
+// .createTaskIterator());
+ } catch (Exception e) {
+ logger.warn("Could not import trajectory network", e);
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff