public:
MetaStatsCommand(string);
+ MetaStatsCommand();
~MetaStatsCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair> lines;
+
GlobalData* globaldata;
GroupMap* designMap;
ReadOTUFile* read;
InputData* input;
vector<SharedRAbundVector*> lookup;
+ map<string, vector<string> > outputTypes;
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
- string groups, label, outputDir, inputDir, designfile;
- vector<string> Groups, outputNames;
- int iters, g;
+ string groups, label, outputDir, inputDir, designfile, sets;
+ vector<string> Groups, outputNames, Sets;
+ vector< vector<string> > namesOfGroupCombos;
+ int iters, processors;
float threshold;
int process(vector<SharedRAbundVector*>&);
- int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+ int driver(int, int, vector<SharedRAbundVector*>&);
};
#endif