vector<string> setParameters();
string getCommandName() { return "make.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
vector<string> setParameters();
string getCommandName() { return "make.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
string getDescription() { return "make a shared file from a list and group file"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
string getDescription() { return "make a shared file from a list and group file"; }
int readOrderFile();
bool isValidGroup(string, vector<string>);
int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
int readOrderFile();
bool isValidGroup(string, vector<string>);
int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
- vector<SharedRAbundVector*> readData(string, string, ifstream&, vector<string>&, int);
+ vector<SharedRAbundVector*> readData(string, string, string, vector<string>&, int);
- 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;
bool firsttime, pickedGroups, abort, allLines;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;