ListVector* list;
InputData* input;
- string listfile, namefile, taxfile, label, outputDir;
+ string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
bool abort, allLines, probs;
int cutoff;
set<string> labels; //holds labels to be used
int readTaxonomyFile();
void removeConfidences(string&);
int process(ListVector*);
- string findConsensusTaxonomy(int, ListVector*, int&); // returns the name of the "representative" taxonomy of given bin
+ vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin
};