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The command-line interface is still limited to the essential.
For now, the program processes only one argument. This should be the
name of a file that contains a genetic network definition (that should
otherwise be typed in the Editor window). If there are no errors, this
class will send the result of the simulation (all componentamounts for all
requested timepoints) to an outputfile (named: inputfile's name + "_out"
+ inputfile's extension), just like the Graphical Interface's menu-item
"Export states to textfile" would do.If
there are errors in the network definition, the error is printed
to the outputfile. The error message will always start with the text
"Error", so an automated processor of the result file can check for this
text.
If there are other errors that are not caused by the network
definition's contents (like I/O-errors), then the program does not write
these to the outputfile, but prints an error message to the commandline
instead, and exits with errorcode1.
This is how you simulate a file's definition text via the command-line:
java
-jar simplex.jar networkDef.txt
Note that "java -jar simplex.jar" is just the
basic clause to tell the Java Runtime Environment that it should run the
compressed file "simplex.jar". Everything that follows this clause is
passed to SIM-plex as arguments. Here, "networkDef.txt" is the
one and only argument.
If you don't give any arguments, SIM-plex
will start up normally and show its graphical interface. At command-line
this is done like this:
java
-jar simplex.jar
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