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#ifndef RAREFACTCOMMAND_H
#define RAREFACTCOMMAND_H
/*
* rarefactcommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "ordervector.hpp"
#include "inputdata.h"
#include "rarefact.h"
#include "display.h"
#include "validcalculator.h"
class RareFactCommand : public Command {
public:
RareFactCommand(string);
~RareFactCommand(){}
vector<string> setParameters();
string getCommandName() { return "rarefaction.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
string getDescription() { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<Display*> rDisplays;
int nIters, abund, processors, alpha;
float freq;
bool abort, allLines, groupMode;
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, map<string, set<int> >&);
vector<string> createGroupFile(vector<string>&, map<int, string>);
void fillRDisplays(map<string, string>, map<int, string>&, int);
};
#endif
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