}
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
- convert(itersString, iters);
+ m->mothurConvert(itersString, iters);
string temp = validParameter.validFile(parameters, "distance", false);
if (temp == "not found") { phylip = false; outputForm = ""; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
if (!random) { iters = 0; } //turn off random calcs
}
util = new SharedUtil();
string s; //to make work with setgroups
- vector<string> Groups = m->getGroups();
+ Groups = m->getGroups();
vector<string> nameGroups = tmap->getNamesOfGroups();
util->setGroups(Groups, nameGroups, s, numGroups, "weighted"); //sets the groups the user wants to analyze
util->getCombos(groupComb, Groups, numComp);
+ m->setGroups(Groups);
delete util;
weighted = new Weighted(tmap, includeRoot);