*
*/
-#include <iostream>
-#include <fstream>
-#include <vector>
+
#include "command.hpp"
#include "sharedrabundvector.h"
#include "inputdata.h"
#include "calculator.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "sharedlistvector.h"
+#include "validcalculator.h"
+#include "sharedutilities.h"
/*The summary.shared() command
The summary.shared command can only be executed after a successful read.shared command.
int execute();
private:
- void getGroupComb();
- void getSharedVectors();
-
GlobalData* globaldata;
- ReadMatrix* read;
+ ReadOTUFile* read;
+ SharedUtil* util;
vector<Calculator*> sumCalculators;
InputData* input;
+ ValidCalculators* validCalculator;
SharedListVector* SharedList;
SharedOrderVector* order;
vector<SharedRAbundVector*> lookup;
- SharedRAbundVector* shared1, shared2;
- string outputFileName;
- ofstream outputFileHandle;
- vector<string> groupComb;
+ string outputFileName, format, outAllFileName;
+ ofstream outputFileHandle, outAll;
+ bool mult;
};