X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=2c40e1ce271b60cf181da4b11446da1764b7a4ab;hb=b28bddf12e2791a019fba9c233d46407deb65976;hp=a76c7e0fe69e2f6be247a716b6c40e26dec2ed1c;hpb=81316c6cc11e29c893d55e87ebd16d9ecd09c1f3;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index a76c7e0..2c40e1c 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -27,15 +27,9 @@ import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
  */
 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)
-   */
-  private static final boolean USE_REST = true;
-
-  // Port number for Chimera REST service
-  private int restPort;
+  private int chimeraRestPort;
 
   private Process chimera;
 
@@ -224,10 +218,14 @@ public class ChimeraManager
                     modelNumbers[0], modelNumbers[1]);
             currentModelsMap.put(modelNumber, newModel);
             models.add(newModel);
+
+            //
             // patch for Jalview - set model name in Chimera
+            //
             sendChimeraCommand("setattr M name " + modelName + " #"
                     + modelNumbers[0], false);
             // end patch for Jalview
+
             modelNumbers = null;
           }
         }
@@ -370,11 +368,7 @@ public class ChimeraManager
   {
     chimera = null;
     currentModelsMap.clear();
-    if (!USE_REST)
-    {
-      chimeraListenerThread.requestStop();
-      chimeraListenerThread = null;
-    }
+      this.chimeraRestPort = 0;
     structureManager.clearOnChimeraExit();
   }
 
@@ -545,13 +539,11 @@ public class ChimeraManager
         List<String> args = new ArrayList<String>();
         args.add(chimeraPath);
         args.add("--start");
-        args.add(USE_REST ? "RESTServer" : "ReadStdin");
+        args.add("RESTServer");
         ProcessBuilder pb = new ProcessBuilder(args);
         chimera = pb.start();
         error = "";
         workingPath = chimeraPath;
-        logger.info("Starting " + chimeraPath + " with "
-                + (USE_REST ? "REST API" : "stdin/stdout"));
         break;
       } catch (Exception e)
       {
@@ -562,17 +554,9 @@ public class ChimeraManager
     // If no error, then Chimera was launched successfully
     if (error.length() == 0)
     {
-      if (USE_REST)
-      {
-        this.restPort = getPortNumber();
-      }
-      else
-      {
-        // Initialize the listener threads
-        chimeraListenerThread = new ListenerThreads(chimera,
-                structureManager);
-        chimeraListenerThread.start();
-      }
+      this.chimeraRestPort = getPortNumber();
+      System.out.println("Chimera REST API started on port "
+              + chimeraRestPort);
       // structureManager.initChimTable();
       structureManager.setChimeraPathProperty(workingPath);
       // TODO: [Optional] Check Chimera version and show a warning if below 1.8
@@ -603,7 +587,8 @@ public class ChimeraManager
       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)
     {
@@ -760,22 +745,17 @@ public class ChimeraManager
       } catch (InterruptedException q)
       {
       }
-      ;
     }
     busy = true;
     long startTime = System.currentTimeMillis();
     try
     {
-      if (USE_REST)
-      {
-        return sendRestCommand(command);
-      }
-      else
-      {
-        return sendStdinCommand(command, reply);
-      }
+      return sendRestCommand(command);
     } finally
     {
+      /*
+       * Make sure busy flag is reset come what may!
+       */
       busy = false;
       if (debug)
       {
@@ -796,7 +776,7 @@ public class ChimeraManager
   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));