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#ifndef SUMMARYCOMMAND_H
#define SUMMARYCOMMAND_H
/*
* summarycommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "sabundvector.hpp"
#include "inputdata.h"
#include "calculator.h"
#include "validcalculator.h"
class SummaryCommand : public Command {
public:
SummaryCommand(string);
~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:
vector<Calculator*> sumCalculators;
int abund, size, iters, subsampleSize, alpha;
bool abort, allLines, groupMode, subsample, withReplacement;
set<string> labels; //holds labels to be used
string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
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&);
void fillEstimators();
};
#endif
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