X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2Fport%2FListenerThreads.java;h=2b2ce48d742b94140227a65775a78174b303aa05;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=883d53645a73e894d6de97eb5721f017e74b5359;hpb=d3a2fdc864b586b5c604335dd715ec215b679197;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java b/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java
index 883d536..2b2ce48 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/port/ListenerThreads.java
@@ -21,207 +21,282 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 /**
  * 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);
+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))
+    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;
-	}
+    return reply;
+  }
 
-	/**
-	 * Read input from Chimera
-	 * 
-	 * @return a List containing the replies from Chimera
-	 */
-	private void chimeraRead() throws IOException {
-		if (chimera == null)
+  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)
+    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)
+    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);
-			}
-		}
-	}
+    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;
+  }
 }