//check for required parameters
inFastaName = validParameter.validFile(parameters, "fasta", true);
if (inFastaName == "not open") { abort = true; }
- else if (inFastaName == "not found") { inFastaName = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true; }
+ else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true; }
oldNameMapFName = validParameter.validFile(parameters, "name", true);
if (oldNameMapFName == "not open") { abort = true; }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
exit(1);
}
}
void DeconvoluteCommand::help(){
try {
- cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
- cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n";
- cout << "If the sequence is unique the second column will just contain its name. " << "\n";
- cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
- cout << "The unique.seqs command should be in the following format: " << "\n";
- cout << "unique.seqs(fasta=yourFastaFile) " << "\n";
+ mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+ mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
+ mothurOut("If the sequence is unique the second column will just contain its name. \n");
+ mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+ mothurOut("The unique.seqs command should be in the following format: \n");
+ mothurOut("unique.seqs(fasta=yourFastaFile) \n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "DeconvoluteCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/**************************************************************************************/
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "DeconvoluteCommand", "execute");
exit(1);
}
}