//This Function parses through the command line and pulls out the command then sends the options to the parseGlobalData
CommandOptionParser::CommandOptionParser(string input){
try {
+ m = MothurOut::getInstance();
+
int openParen = input.find_first_of('(');
int closeParen = input.find_last_of(')');
optionString = "";
commandString = input.substr(0, openParen); //commandString contains everything before "("
optionString = input.substr((openParen+1), (closeParen-openParen-1)); //optionString contains everything between "(" and ")".
}
- else if (openParen == -1) { cout << "You are missing (" << endl; }
- else if (closeParen == -1) { cout << "You are missing )" << endl; }
+ else if (openParen == -1) { m->mothurOut("You are missing ("); m->mothurOutEndLine(); }
+ else if (closeParen == -1) { m->mothurOut("You are missing )"); m->mothurOutEndLine(); }
//GlobalData* globaldata = GlobalData::getInstance();
//globaldata->parseGlobalData(commandString, optionString); //parser to separate and check options
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CommandOptionParser class Function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "CommandOptionParser", "CommandOptionParser");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CommandOptionParser class function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************