private:
bool abort;
- string listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
+ string sharedfile, listfile, groupfile, repfastafile, repnamesfile, contaxonomyfile, label, outputDir;
vector<string> outputNames;
vector<int> readFasta(vector<Sequence>&);
- vector<int> readTax(vector<string>&);
+ vector<int> readTax(vector<string>&, vector<string>&);
ListVector* getList();
+ vector<SharedRAbundVector*> getShared();
+ int findIndex(vector<string>&, string);
};