/*.................................................................................................................*/
 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;
 }
Exemplo n.º 2
0
 /*.................................................................................................................*/
 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);
 }