//**********************************************************************************************************************
vector<string> ClusterDoturCommand::getValidParameters(){
try {
- string AlignArray[] = {"phylip","cutoff","precision","method","outputdir","inputdir"};
+ string AlignArray[] = {"phylip","name","hard","cutoff","precision","method","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
return myArray;
}
else {
//valid paramters for this command
- string Array[] = {"phylip","cutoff","precision","method","outputdir","inputdir"};
+ string Array[] = {"phylip","name","cutoff","hard","precision","method","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
oldRAbund = *rabund;
oldList = *list;
- double saveCutoff = cutoff;
+ //double saveCutoff = cutoff;
int estart = time(NULL);
- while (cluster->getSmallDist() < cutoff && cluster->getNSeqs() > 0){
-
+ 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; }
cluster->update(cutoff);
delete cluster; delete nameMap; delete list; delete rabund;
- if (saveCutoff != cutoff) {
- if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
- else { saveCutoff = m->roundDist(saveCutoff, precision); }
- m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
- }
+ //if (saveCutoff != cutoff) {
+ // if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
+ // else { saveCutoff = m->roundDist(saveCutoff, precision); }
+ // m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
+ //}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();