private:
void printSharedData(vector<SharedRAbundVector*>, ofstream&);
- int createMisMatchFile(SharedListVector*, GroupMap*);
int readOrderFile();
bool isValidGroup(string, vector<string>);
int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
int createSharedFromListGroup(string);
int createSharedFromBiom(string);
string getTag(string&);
- vector<string> readRows(string, ifstream&, int&);
+ vector<string> readRows(string, int&);
int getDims(string, int&, int&);
- vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
+ vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
vector<string> Groups, outputNames, order;
set<string> labels;
- string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
+ string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile, countfile;
bool firsttime, pickedGroups, abort, allLines;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;