#include "sabundvector.hpp"
#include "inputdata.h"
#include "calculator.h"
-#include "readotu.h"
#include "validcalculator.h"
-class GlobalData;
-
class SummaryCommand : public Command {
public:
SummaryCommand(string);
- ~SummaryCommand();
- int execute();
- void help();
+ SummaryCommand();
+ ~SummaryCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "summary.single"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
vector<Calculator*> sumCalculators;
InputData* input;
- ValidCalculators* validCalculator;
SAbundVector* sabund;
- string outputFileName;
- ofstream outputFileHandle;
int abund, size;
- bool abort, allLines;
+ bool abort, allLines, groupMode;
set<string> labels; //holds labels to be used
- string label, calc;
+ string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
+ vector<string> inputFileNames, outputNames;
+ vector<string> groups;
+
+ vector<string> parseSharedFile(string);
+ string createGroupSummaryFile(int, int, vector<string>&);
+
};
#endif