- string treefile, taxonomyfile, groupfile, namefile, outputDir;
+ string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);