string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "0.05"; }
- convert(temp, threshold);
+ m->mothurConvert(temp, threshold);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
}
}
//get set names
string setA = namesOfGroupCombos[c][0];
string setB = namesOfGroupCombos[c][1];
- cout << setA << '\t' << setB << endl;
+ //cout << setA << '\t' << setB << endl;
//get filename
string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
}
}
- for (int i = 0; i < subset.size(); i++) { cout << designMap->getGroup(subset[i]->getGroup()) << endl; }
- cout << setACount << endl;
+ //for (int i = 0; i < subset.size(); i++) { cout << designMap->getGroup(subset[i]->getGroup()) << endl; }
+ //cout << setACount << endl;
if ((setACount == 0) || (setBCount == 0)) {
m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();