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JAL-4281 reinstate access to legacy id width calculation so we can import old files...
[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
e10fc9d
..
ddc8d84
100644
(file)
--- a/
src/jalview/ext/pymol/PymolManager.java
+++ b/
src/jalview/ext/pymol/PymolManager.java
@@
-112,7
+112,8
@@
public class PymolManager
{
for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
{
{
for (String path : new String[] { "Schrodinger\\PyMOL2", "PyMOL" })
{
- for (String binary : new String [] {"PyMOLWinWithConsole.bat", "Scripts\\pymol.exe", "PyMOLWin.exe"})
+ for (String binary : new String[] { "PyMOLWinWithConsole.bat",
+ "Scripts\\pymol.exe", "PyMOLWin.exe" })
{
pathList.add(String.format("%s\\%s\\%s", root, path, binary));
}
{
pathList.add(String.format("%s\\%s\\%s", root, path, binary));
}
@@
-157,7
+158,7
@@
public class PymolManager
boolean getReply)
{
String postBody = getPostRequest(command);
boolean getReply)
{
String postBody = getPostRequest(command);
- // System.out.println(postBody);// debug
+ // jalview.bin.Console.outPrintln(postBody);// debug
String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
PrintWriter out = null;
BufferedReader in = null;
String rpcUrl = "http://127.0.0.1:" + this.pymolXmlRpcPort;
PrintWriter out = null;
BufferedReader in = null;
@@
-271,15
+272,16
@@
public class PymolManager
}
List<String> args = new ArrayList<>();
args.add(pymolPath);
}
List<String> args = new ArrayList<>();
args.add(pymolPath);
-
+
// Windows PyMOLWin.exe needs an extra argument
// Windows PyMOLWin.exe needs an extra argument
- if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT).endsWith("\\pymolwin.exe"))
+ if (Platform.isWin() && pymolPath.toLowerCase(Locale.ROOT)
+ .endsWith("\\pymolwin.exe"))
{
args.add("+2");
}
args.add("-R"); // https://pymolwiki.org/index.php/RPC
ProcessBuilder pb = new ProcessBuilder(args);
{
args.add("+2");
}
args.add("-R"); // https://pymolwiki.org/index.php/RPC
ProcessBuilder pb = new ProcessBuilder(args);
- Console.debug("Running PyMOL as "+String.join(" ", pb.command()));
+ Console.debug("Running PyMOL as " + String.join(" ", pb.command()));
pymolProcess = pb.start();
error = "";
break;
pymolProcess = pb.start();
error = "";
break;