+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
package ext.edu.ucsf.rbvi.strucviz2.port;
import java.io.BufferedReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import ext.edu.ucsf.rbvi.strucviz2.*;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
/***************************************************
* 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);
- }
- }
- }
+public class ListenerThreads extends Thread
+{
+ private BufferedReader lineReader = null;
+
+ private Process chimera = null;
+
+ private Map<String, List<String>> replyLog = null;
+
+ private Logger logger;
+
+ private StructureManager structureManager = null;
+
+ private boolean stopMe = false;
+
+ /**
+ * Create a new listener thread to read the responses from Chimera
+ *
+ * @param chimera
+ * a handle to the Chimera Process
+ * @param structureManager
+ * a handle to the Chimera structure manager
+ */
+ public ListenerThreads(Process chimera, StructureManager structureManager)
+ {
+ this.chimera = chimera;
+ this.structureManager = structureManager;
+ replyLog = new HashMap<String, List<String>>();
+ // Get a line-oriented reader
+ InputStream 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 (!stopMe)
+ {
+ try
+ {
+ chimeraRead();
+ } catch (IOException e)
+ {
+ logger.warn("UCSF Chimera has exited: " + e.getMessage());
+ return;
+ } finally
+ {
+ if (lineReader != null)
+ {
+ try
+ {
+ lineReader.close();
+ } catch (IOException e)
+ {
+ }
+ }
+ }
+ }
+ }
+
+ public List<String> getResponse(String command)
+ {
+ List<String> reply;
+ // System.out.println("getResponse: "+command);
+ // TODO do we need a maximum wait time before aborting?
+ 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);
+ }
+ }
+ }
+
+ /**
+ * Set a flag that this thread should clean up and exit.
+ */
+ public void requestStop()
+ {
+ this.stopMe = true;
+ }
}
git://source.jalview.org / jalview.git / blobdiff