//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine();
abort = true;
}
- }
+ }else { m->setPhylipFile(phylipfile); }
//check for optional parameter and set defaults
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
string temp;
temp = validParameter.validFile(parameters, "precision", false);
if (temp == "not found") { temp = "100"; }
//saves precision legnth for formatting below
length = temp.length();
- convert(temp, precision);
+ m->mothurConvert(temp, precision);
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
int estart = time(NULL);
while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
- if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
cluster->update(cutoff);