X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolManager.java;h=1acce5e3ae789f863672604e2a54d419a1c86a70;hp=26c780d5bde3bf7dcc920e879d65d154180fe659;hb=483ecb5e4541537778844529cc93204f9124b68d;hpb=2fb924ec0d110eb3ca6c3fb06efa27acd34b2750

diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 26c780d..1acce5e 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 <http://www.gnu.org/licenses/>.
+ * 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<String> getPymolPaths(String os)
   {
     List<String> 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
      */
@@ -81,6 +101,18 @@ public class PymolManager
     else if (os.startsWith("Windows"))
     {
       // todo Windows installation path(s)
+    	for (String root : new String[]
+      {
+        String.format("%s\\AppData\\Local", System.getProperty("user.home")),
+    		"\\Program Files", "C:\\Program Files", "\\Program Files (x86)",
+    		"C:\\Program Files (x86)" })
+    	{
+    	  for (String binary : new String [] {"PyMOLWinWithConsole.bat", "PyMOLWin.exe"})
+    	  {
+          pathList.add(String.format("%s\\Schrodinger\\PyMOL2\\%s", root, binary));
+    	  }
+    	}
+
     }
     else if (os.startsWith("Mac"))
     {
@@ -140,7 +172,7 @@ 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 +190,7 @@ 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 +201,14 @@ public class PymolManager
       {
         out.close();
       }
+      if (Console.isTraceEnabled())
+      {
+        Console.trace("Sent: " + command.toString());
+        if (result != null)
+        {
+          Console.trace("Received: " + result);
+        }
+      }
     }
     return result;
   }
@@ -243,12 +283,12 @@ 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 +332,7 @@ 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 +347,10 @@ 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.info("PyMOL started with XMLRPC on port " + port);
     return port;
   }