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#ifndef RAREFACTSHAREDCOMMAND_H
#define RAREFACTSHAREDCOMMAND_H
/*
* rarefactsharedcommand.h
* Dotur
*
* Created by Sarah Westcott on 1/6/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "rarefact.h"
#include "display.h"
#include "validcalculator.h"
class RareFactSharedCommand : public Command {
public:
RareFactSharedCommand(string);
RareFactSharedCommand();
~RareFactSharedCommand() {}
vector<string> setParameters();
string getCommandName() { return "rarefaction.shared"; }
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.shared"; }
string getDescription() { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<SharedRAbundVector*> lookup;
int nIters, subsampleSize, iters;
string format;
float freq;
map<int, string> file2Group; //index in outputNames[i] -> group
bool abort, allLines, jumble, groupMode, subsample;
set<string> labels; //holds labels to be used
string label, calc, groups, outputDir, sharedfile, designfile;
vector<string> Estimators, Groups, outputNames, Sets;
int process(GroupMap&, string);
vector<string> createGroupFile(vector<string>&);
int subsampleLookup(vector<SharedRAbundVector*>&, string);
};
#endif
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