JSAPResult workaround for using command line arguments as a alternative to parameter files

Currently I need 2 checks for pulling parameter values either from the command line or from a parameter file. Can we simplify that somehow?

Example:

if (args.userSpecified(AStalavistaSettings.GEN_DIR.getName())||
args.userSpecified(AStalavistaSettings.GEN_DIR.getLongOption()))

{ // acceptableIntrons= true; if (args.userSpecified(AStalavistaSettings.GEN_DIR.getName())) Graph.overrideSequenceDirPath= args.getFile(AStalavistaSettings.GEN_DIR.getName()).getAbsolutePath(); else Graph.overrideSequenceDirPath= args.getFile(AStalavistaSettings.GEN_DIR.getLongOption()).getAbsolutePath(); }