m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+ }
+
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
}
return 0;
bool wroteSomething = false;
bool taxonsHasConfidence = false;
- vector< map<string, int> > searchTaxons;
+ vector< map<string, float> > searchTaxons;
string noConfidenceTaxons = taxons;
int hasConPos = taxons.find_first_of('(');
if (hasConPos != string::npos) {
if (pos != string::npos) { //if yes, then are the confidences okay
bool remove = false;
- vector< map<string, int> > usersTaxon = getTaxons(newtax);
+ vector< map<string, float> > usersTaxon = getTaxons(newtax);
//the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
//we want to "line them up", so we will find the the index where the searchstring starts
}
}
/**************************************************************************************************/
-vector< map<string, int> > RemoveLineageCommand::getTaxons(string tax) {
+vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
try {
- vector< map<string, int> > t;
+ vector< map<string, float> > t;
string taxon = "";
int taxLength = tax.length();
for(int i=0;i<taxLength;i++){
newtaxon = taxon;
confidence = "0";
}
- int con = 0;
+ float con = 0;
convert(confidence, con);
- map<string, int> temp;
+ map<string, float> temp;
temp[newtaxon] = con;
t.push_back(temp);