class MatrixOutputCommand : public Command {
public:
- MatrixOutputCommand(string);
+ MatrixOutputCommand(string);
+ MatrixOutputCommand();
~MatrixOutputCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
void printSims(ostream&);
- void process(vector<SharedRAbundVector*>);
+ int process(vector<SharedRAbundVector*>);
GlobalData* globaldata;
ReadOTUFile* read;
InputData* input;
ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
- string exportFileName;
+ string exportFileName, output;
int numGroups;
ofstream out;
bool abort, allLines;
set<string> labels; //holds labels to be used
string outputFile, calc, groups, label, outputDir;
- vector<string> Estimators, Groups; //holds estimators to be used
+ vector<string> Estimators, Groups, outputNames; //holds estimators to be used
+ map<string, vector<string> > outputTypes;
};