//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
}
}
}
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
- convert(temp, window);
+ m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; }
- convert(temp, increment);
+ m->mothurConvert(temp, increment);
}
}
catch(exception& e) {
chimera->getChimeras();
- if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
#ifdef USE_MPI
MPI_File outMPI;
#endif
- if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); delete chimera; return 0; }
+ if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(outputFileName); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete chimera; return 0; }
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();