X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fpymol%2FPymolManager.java;h=358e360c66d4e1e8f93e14166a77c9180c75dc67;hb=14e1f9dbb9c7a4535734fd3be7ddeee2a5ae72dc;hp=e3b913b608ae6750483fb6103fb8cef99101ff5f;hpb=aa643d0f2f5f506df2771e216af1618549d32050;p=jalview.git
diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index e3b913b..358e360 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;
@@ -14,8 +34,8 @@ 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;
public class PymolManager
@@ -59,14 +79,13 @@ 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
*/
@@ -80,7 +99,23 @@ 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")), // default user path
+ "\\ProgramData", "C:\\ProgramData", // this is the default install
+ // path "for everyone"
+ System.getProperty("user.home"), "\\Program Files",
+ "C:\\Program Files", "\\Program Files (x86)",
+ "C:\\Program Files (x86)" })
+ {
+ for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
+ {
+ for (String binary : new String[] { "PyMOLWinWithConsole.bat" })
+ {
+ pathList.add(String.format("%s\\%s\\%s", root, path, binary));
+ }
+ }
+ }
}
else if (os.startsWith("Mac"))
{
@@ -108,17 +143,6 @@ public class PymolManager
return launched;
}
- public void exitPymol()
- {
- if (isPymolLaunched() && pymolProcess != null)
- {
- sendCommand(new StructureCommand("quit"), false);
- }
- pymolProcess = null;
- // currentModelsMap.clear();
- this.pymolXmlRpcPort = 0;
- }
-
/**
* Sends the command to Pymol; if requested, tries to get and return any
* replies, else returns null
@@ -151,7 +175,7 @@ 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;
}
@@ -169,7 +193,7 @@ 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)
{
@@ -180,6 +204,14 @@ public class PymolManager
{
out.close();
}
+ if (Console.isTraceEnabled())
+ {
+ Console.trace("Sent: " + command.toString());
+ if (result != null)
+ {
+ Console.trace("Received: " + result);
+ }
+ }
}
return result;
}
@@ -211,13 +243,13 @@ public class PymolManager
return sb.toString();
}
- public boolean launchPymol()
+ public Process launchPymol()
{
// todo pull up much of this
// Do nothing if already launched
if (isPymolLaunched())
{
- return true;
+ return pymolProcess;
}
String error = "Error message: ";
@@ -244,20 +276,28 @@ public class PymolManager
break;
} catch (Exception e)
{
- // pPymol could not be started using this path
+ // Pymol could not be started using this path
error += e.getMessage();
}
}
- if (error.length() == 0)
+
+ if (pymolProcess != null)
{
this.pymolXmlRpcPort = getPortNumber();
- System.out.println(
- "PyMOL XMLRPC started on port " + pymolXmlRpcPort);
- return (pymolXmlRpcPort > 0);
+ if (pymolXmlRpcPort > 0)
+ {
+ Console.info("PyMOL XMLRPC started on port " + pymolXmlRpcPort);
+ }
+ else
+ {
+ error += "Failed to read PyMOL XMLRPC port number";
+ Console.error(error);
+ pymolProcess.destroy();
+ pymolProcess = null;
+ }
}
- // logger.warn(error);
- return false;
+ return pymolProcess;
}
private int getPortNumber()
@@ -295,9 +335,8 @@ public class PymolManager
}
} catch (Exception e)
{
- System.err.println(
- "Failed to get REST port number from " + responses + ": "
- + e.getMessage());
+ Console.error("Failed to get REST port number from " + responses
+ + ": " + e.getMessage());
// logger.error("Failed to get REST port number from " + responses + ": "
// + e.getMessage());
} finally
@@ -311,10 +350,10 @@ public class PymolManager
}
if (port == 0)
{
- System.err.println("Failed to start PyMOL with XMLRPC, response was: "
+ Console.error("Failed to start PyMOL with XMLRPC, response was: "
+ responses);
}
- System.err.println("PyMOL started with XMLRPC on port " + port);
+ Console.info("PyMOL started with XMLRPC on port " + port);
return port;
}