#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();
- ~SummaryCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~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;
int abund, size;
bool abort, allLines, groupMode;
set<string> labels; //holds labels to be used
- string label, calc, outputDir;
+ string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
vector<string> inputFileNames, outputNames;
- map<string, vector<string> > outputTypes;
vector<string> groups;
vector<string> parseSharedFile(string);