cyclient.command.quit
cyclient.command.quit(self,verbose=False)
This command causes Cytoscape to exit. It is typically used at the end of a script file.
verbose
print more
cyclient.command.pause
cyclient.command.pause(self, message=None, verbose=False)
The pause command displays a dialog with the text provided in the message argument and waits for the user to click OK
message
a message to display. default=Noneverbose
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cyclient.command.run
cyclient.command.run(self,script_file,args=None,verbose=False)
The run command will execute a command script from the file pointed to by the file argument, which should contain Cytoscape commands, one per line. Arguments to the script are provided by the args argument.
script_file
file to runargs: enter the script arguments as key
value pairs separated by commas. eg. "arg1:value1,arg2:value2"verbose
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cyclient.command.echo
cyclient.command.echo(self, variableName, verbose=False)
The echo command will display the value of the variable specified by the variableName argument, or all variables if variableName is not provided.
variableName
The name of the variable or '*' to display the value of all variables.verbose
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cyclient.command.sleep
cyclient.command.sleep(self,duration,verbose=False)
The sleep command will pause processing for a period of time as specified by duration seconds. It is typically used as part of a command script.
duration
enter the time in seconds to sleepverbose
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cyclient.command.open_dialog
cyclient.command.open_dialog(self, verbose=False)
The command line dialog provides a field to enter commands and view results. It also provides the help command to display namespaces, commands, and arguments.
verbose
print more
cyclient.session.createSessionFile
cyclient.session.createSessionFile(file, verbose=None)
Saves the current session to a file. If successful, the session file location will be returned.
file
Session file location as an absolute path-
verbose
print more -
returns
200: successful operation
cyclient.session.deleteSession
cyclient.session.deleteSession(verbose=None)
This deletes the current session and initializes a new one. A message is returned to indicate the success of the deletion.
-
verbose
print more -
returns
200: successful operation
cyclient.session.getSessionFromFile
cyclient.session.getSessionFromFile(file, verbose=None)
Loads a session from a local file and returns the session file name
file
Session file location as an absolute path-
verbose
print more -
returns
200: successful operation
cyclient.session.getSessionName
cyclient.session.getSessionName(verbose=None)
Returns the file name for the current Cytoscape session.
-
verbose
print more -
returns
200: successful operation
cyclient.session.runGarbageCollection
cyclient.session.runGarbageCollection(verbose=None)
Manually call Java's System.gc() to free up unused memory. This process happens automatically, but may be useful to call explicitly for testing or evaluation purposes.
-
verbose
print more -
returns
204: Successful Garbage Collection