X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolManager.java;h=05d5bcc0befbf51376b9d509fdaf74a350068811;hb=d654b1f014790b7ae25e6eec631847170a930987;hp=6a014a56c8464a4083a0168d31e083e8dc2c25de;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git
diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 6a014a5..05d5bcc 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.pymol;
import java.io.BufferedReader;
@@ -14,6 +34,7 @@ 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;
@@ -59,14 +80,13 @@ public class PymolManager
protected static List getPymolPaths(String os)
{
List pathList = new ArrayList<>();
-
- String userPath = Cache
- .getDefault(Preferences.PYMOL_PATH, null);
+
+ String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
if (userPath != null)
{
pathList.add(userPath);
}
-
+
/*
* add default installation paths
*/
@@ -140,7 +160,7 @@ public class PymolManager
int rc = conn.getResponseCode();
if (rc != HttpURLConnection.HTTP_OK)
{
- Cache.error(
+ Console.error(
String.format("Error status from %s: %d", rpcUrl, rc));
return result;
}
@@ -158,7 +178,7 @@ public class PymolManager
} catch (SocketException e)
{
// thrown when 'quit' command is sent to PyMol
- Cache.warn(String.format("Request to %s returned %s", rpcUrl,
+ Console.warn(String.format("Request to %s returned %s", rpcUrl,
e.toString()));
} catch (Exception e)
{
@@ -169,12 +189,12 @@ public class PymolManager
{
out.close();
}
- if (Cache.isTraceEnabled())
+ if (Console.isTraceEnabled())
{
- Cache.trace("Sent: " + command.toString());
+ Console.trace("Sent: " + command.toString());
if (result != null)
{
- Cache.trace("Received: " + result);
+ Console.trace("Received: " + result);
}
}
}
@@ -251,12 +271,12 @@ public class PymolManager
this.pymolXmlRpcPort = getPortNumber();
if (pymolXmlRpcPort > 0)
{
- Cache.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.error(error);
+ Console.error(error);
pymolProcess.destroy();
pymolProcess = null;
}
@@ -300,7 +320,7 @@ public class PymolManager
}
} catch (Exception e)
{
- Cache.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());
@@ -315,10 +335,10 @@ public class PymolManager
}
if (port == 0)
{
- Cache.error("Failed to start PyMOL with XMLRPC, response was: "
+ Console.error("Failed to start PyMOL with XMLRPC, response was: "
+ responses);
}
- Cache.error("PyMOL started with XMLRPC on port " + port);
+ Console.info("PyMOL started with XMLRPC on port " + port);
return port;
}