//**********************************************************************************************************************
-SystemCommand::SystemCommand(string option){
+SystemCommand::SystemCommand(string option) {
try {
abort = false;
if(option == "help") { help(); abort = true; }
else {
- //valid paramters for this command
- string Array[] = {"command"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+ else {
+ //check for outputdir and inputdir parameters
+ int commaPos = option.find_first_of(',');
+
+ //if there is a comma then grab string up to that pos
+ if (commaPos != option.npos) {
+ option = option.substr(0, commaPos);
+ }
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ command = option;
}
-
- //check for required parameters
- command = validParameter.validFile(parameters, "command", false);
- if (command == "not found") { mothurOut("command is a required parameter."); mothurOutEndLine(); abort = true; }
}
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "SystemCommand");
+ m->errorOut(e, "SystemCommand", "SystemCommand");
exit(1);
}
}
void SystemCommand::help(){
try {
- mothurOut("The system command allows you to execute a system command from within mothur.\n");
- mothurOut("The system command parameter is command and it is required.\n");
- mothurOut("The system command should be in the following format: system(command=yourCommand).\n");
- mothurOut("Example system(command=clear).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. command), '=' and parameters (i.e.yourCommand).\n\n");
+ m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
+ m->mothurOut("The system has no parameters.\n");
+ m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
+ m->mothurOut("Example system(clear).\n");
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "help");
+ m->errorOut(e, "SystemCommand", "help");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "execute");
+ m->errorOut(e, "SystemCommand", "execute");
exit(1);
}
}