#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();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
+ string getDescription() { return "generate summary file that has the calculator value for each line in the OTU data"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
- GlobalData* globaldata;
- ReadOTUFile* read;
vector<Calculator*> sumCalculators;
InputData* input;
- ValidCalculators* validCalculator;
SAbundVector* sabund;
- int abund, size;
+ int abund, size, iters, subsampleSize;
- bool abort, allLines;
+ bool abort, allLines, groupMode, subsample;
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;
+ vector<string> inputFileNames, outputNames;
vector<string> groups;
vector<string> parseSharedFile(string);
+ vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
+ int process(SAbundVector*&, ofstream&, ofstream&);
};