ReverseSeqsCommand::ReverseSeqsCommand(string option){
try {
- globaldata = GlobalData::getInstance();
abort = false;
//allow user to run help
string Array[] = {"fasta"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//check for required parameters
- fasta = validParameter->validFile(parameters, "fasta", true);
+ fasta = validParameter.validFile(parameters, "fasta", true);
if (fasta == "not open") { abort = true; }
- else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true; }
- else { globaldata->setFastaFile(fasta); globaldata->setFormat("fasta"); }
+ else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true; }
- delete validParameter;
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void ReverseSeqsCommand::help(){
try {
- cout << "The reverse.seqs command reads a fastafile and ...." << "\n";
- cout << "The reverse.seqs command parameter is fasta and it is required." << "\n";
- cout << "The reverse.seqs command should be in the following format: " << "\n";
- cout << "reverse.seqs(fasta=yourFastaFile) " << "\n";
+ mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+ mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+ mothurOut("The reverse.seqs command should be in the following format: \n");
+ mothurOut("reverse.seqs(fasta=yourFastaFile) \n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReverseSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//***************************************************************************************************************
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReverseSeqsCommand", "execute");
exit(1);
}
}