#include "sharedrabundvector.h"
#include "inputdata.h"
#include "calculator.h"
-#include "readotu.h"
#include "validcalculator.h"
-class GlobalData;
-
class SummarySharedCommand : public Command {
public:
SummarySharedCommand(string);
- ~SummarySharedCommand();
- int execute();
- void help();
+ SummarySharedCommand();
+ ~SummarySharedCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "summary.shared"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
+ string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
struct linePair {
int end;
};
vector<linePair> lines;
- GlobalData* globaldata;
- ReadOTUFile* read;
vector<Calculator*> sumCalculators;
InputData* input;
- ValidCalculators* validCalculator;
bool abort, allLines, mult, all, createPhylip;
set<string> labels; //holds labels to be used
- string label, calc, groups;
+ string label, calc, groups, sharedfile;
vector<string> Estimators, Groups, outputNames;
vector<SharedRAbundVector*> lookup;
string format, outputDir;