X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fpicking%2FPickEndPoint.java;h=b5b0a9a78629031dc365999a3ef545af09b21bef;hb=f5306591821b5f6d4e381ff30b647bd149d51f43;hp=ac45278e011fdb945dd39a476463573e8aa7fb91;hpb=7f5605c5ced2a123e747cb2fdfc3fafbe72dee9f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/picking/PickEndPoint.java b/src/uk/ac/vamsas/client/picking/PickEndPoint.java
index ac45278..b5b0a9a 100644
--- a/src/uk/ac/vamsas/client/picking/PickEndPoint.java
+++ b/src/uk/ac/vamsas/client/picking/PickEndPoint.java
@@ -4,15 +4,19 @@ import java.io.*;
 import java.net.*;
 import java.util.logging.*;
 
+import org.apache.commons.logging.Log;
+
 class PickEndPoint extends Thread
 {
-	private Logger logger = Logger.getLogger("uk.ac.vamsas.client.picking");
+	private Log logger = org.apache.commons.logging.LogFactory.getLog(uk.ac.vamsas.client.picking.PickEndPoint.class);
 	
 	private Socket socket;
 	private int rPort;
 	private BufferedWriter os;
 	private BufferedReader in;
-
+	/**
+   * reference to server or null if no comms session active
+   */
 	private SocketManager manager;	
 	
 	PickEndPoint(SocketManager manager, Socket s)
@@ -37,15 +41,15 @@ class PickEndPoint extends Thread
 			in = new BufferedReader(new InputStreamReader(socket.getInputStream()));
 		
 			// Start the thread to listen for incoming messages
-//			logger.info("CLIENT: connection successful to port "
-//				+ socket.getPort() + " via port " + socket.getLocalPort());
+			logger.debug("CLIENT: connection successful to port "
+				+ socket.getPort() + " via port " + socket.getLocalPort());
 			start();
 			
 			return true;
 		}
 		catch (Exception e)
 		{
-			//logger.info("CLIENT: connection failed: " + e);
+			logger.info("CLIENT: connection failed: " + e);
 			return false;
 		}
 	}
@@ -67,7 +71,7 @@ class PickEndPoint extends Thread
 		{
 			//logger.info("CLIENT: failed to send");
 			
-			// TODO: terminate the connection on a failed send or retry?
+			// TODO: terminate the connection on a failed send or retry? (Has this been done? JBP)
 			terminate();
 		}
 	}
@@ -77,7 +81,7 @@ class PickEndPoint extends Thread
 	{
 		try
 		{
-			while (true)
+			while (manager!=null)
 			{
 				String str = in.readLine();				
 				//logger.info("CLIENT: recv " + str + " from " + rPort);
@@ -98,27 +102,38 @@ class PickEndPoint extends Thread
 			// terminate this endpoint (if this is server side)
 			//logger.info("CLIENT: read failed: " + e);
 						
-			terminate();
+			terminate(); // this may not be necessary - probably caused infinite loop on terminate() without null checks
 		}
 	}
 	
-	private void terminate()
+	void terminate()
 	{
-		try { socket.close(); }
-		catch (IOException e) {}
-		
-		//logger.info("CLIENT: closing connection to port " + socket.getPort());
-		manager.removeEndPoint(this);
+    SocketManager mgr=manager;
+    manager=null; // stops receive thread
+		if (socket!=null) {
+      try { socket.close(); }
+      catch (IOException e) {}
+      socket=null;
+    }
+    //logger.info("CLIENT: closing connection to port " + socket.getPort());
+		// terminate() can be called by the socket manager to shutdown the connection,
+    // or the receive thread after an exception has been received
+    // (which includes the above case when the socket is closed.
+    //  so we only want to removeEndPoint once - for the initial call to terminate()
+    if (mgr!=null)
+      mgr.removeEndPoint(this);
 	}
 	
 	private Message strToMessage(String str)
 	{
 		try
 		{
-			if (str.startsWith("CUSTOM_"))
-				return new CustomMessage(str.substring(7));
+      if (str==null || str.length()==1)
+        return null;
+			if (str.startsWith("CUSTOM"))
+				return new CustomMessage(str.substring(6));
 		
-			if (str.startsWith("MOUSEOVER_"))
+			if (str.startsWith("MOUSEOVER"))
 				return new MouseOverMessage(str);
 		}
 		catch (Exception e)