/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets whether or not to count stops in regions with ambiguous nucleotides that imply a stop OR an amino acid",
"[on; off]",
commandName,
"toggleCountEvenIfOthers")) {
countEvenIfOthers.toggleValue(parser.getFirstToken(arguments));
parametersChanged();
} else if (checker.compare(
this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
return matrixSourceTask;
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Hires the ExternalProcessRunner",
"[name of module]",
commandName,
"setExternalProcessRunner")) {
ExternalProcessRunner temp =
(ExternalProcessRunner)
replaceEmployee(
ExternalProcessRunner.class,
arguments,
"External Process Runner",
externalProcRunner);
if (temp != null) {
externalProcRunner = temp;
parametersChanged();
}
externalProcRunner.setProcessRequester(this);
return externalProcRunner;
} else return super.doCommand(commandName, arguments, checker);
}