- void printSharedData();
- GlobalData* globaldata;
- ReadOTUFile* read;
- SharedListVector* SharedList;
- InputData* input;
- Shared* shared;
- map<string, SharedRAbundVector*>::iterator it;
- ofstream out;
- string filename;
+ void printSharedData(vector<SharedRAbundVector*>, ofstream&);
+ int createMisMatchFile(SharedListVector*, GroupMap*);
+ int readOrderFile();
+ bool isValidGroup(string, vector<string>);
+ int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+ int ListGroupSameSeqs(vector<string>&, SharedListVector*);
+ int createSharedFromListGroup(string);
+ int createSharedFromBiom(string);
+ string getTag(string&);
+ vector<string> readRows(string, ifstream&, int&);
+ int getDims(string, int&, int&);
+ vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
+
+ vector<string> Groups, outputNames, order;
+ set<string> labels;
+ string fileroot, outputDir, listfile, groupfile, biomfile, ordergroupfile;
+ bool firsttime, pickedGroups, abort, allLines;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;