Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[jalview.git] / src / jalview / ext / pymol / PymolManager.java

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 26c780d..db71269 100644 (file)
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -14,6 +14,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.gui.Preferences;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
@@ -140,7 +141,7 @@ public class PymolManager
       int rc = conn.getResponseCode();
       if (rc != HttpURLConnection.HTTP_OK)
       {
-        Cache.log.error(
+        Console.error(
                 String.format("Error status from %s: %d", rpcUrl, rc));
         return result;
       }
@@ -158,7 +159,7 @@ public class PymolManager
     } catch (SocketException e)
     {
       // thrown when 'quit' command is sent to PyMol
-      Cache.log.warn(String.format("Request to %s returned %s", rpcUrl,
+      Console.warn(String.format("Request to %s returned %s", rpcUrl,
               e.toString()));
     } catch (Exception e)
     {
@@ -169,6 +170,14 @@ public class PymolManager
       {
         out.close();
       }
+      if (Console.isTraceEnabled())
+      {
+        Console.trace("Sent: " + command.toString());
+        if (result != null)
+        {
+          Console.trace("Received: " + result);
+        }
+      }
     }
     return result;
   }
@@ -243,12 +252,12 @@ public class PymolManager
       this.pymolXmlRpcPort = getPortNumber();
       if (pymolXmlRpcPort > 0)
       {
-        Cache.log.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+        Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
       }
       else
       {
         error += "Failed to read PyMOL XMLRPC port number";
-        Cache.log.error(error);
+        Console.error(error);
         pymolProcess.destroy();
         pymolProcess = null;
       }
@@ -292,7 +301,7 @@ public class PymolManager
       }
     } catch (Exception e)
     {
-      Cache.log.error("Failed to get REST port number from " + responses
+      Console.error("Failed to get REST port number from " + responses
               + ": " + e.getMessage());
       // logger.error("Failed to get REST port number from " + responses + ": "
       // + e.getMessage());
@@ -307,10 +316,10 @@ public class PymolManager
     }
     if (port == 0)
     {
-      Cache.log.error("Failed to start PyMOL with XMLRPC, response was: "
+      Console.error("Failed to start PyMOL with XMLRPC, response was: "
               + responses);
     }
-    Cache.log.error("PyMOL started with XMLRPC on port " + port);
+    Console.error("PyMOL started with XMLRPC on port " + port);
     return port;
   }