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#ifndef CLASSIFYOTUSCOMMAND_H
#define CLASSIFYOTUSCOMMAND_H
/*
* classifyotucommand.h
* Mothur
*
* Created by westcott on 6/1/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
#include "counttable.h"
class ClassifyOtuCommand : public Command {
public:
ClassifyOtuCommand(string);
~ClassifyOtuCommand() = default;
vector<string> setParameters();
string getCommandName() { return "classify.otu"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
string getDescription() { return "find the concensus taxonomy for each OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
GroupMap* groupMap;
CountTable* ct;
ListVector* list;
InputData* input;
string listfile, namefile, taxfile, label, groupfile, basis, countfile, output;
bool abort, allLines, probs, persample, relabund;
int cutoff, threshold, printlevel;
set<string> labels; //holds labels to be used
vector<string> outputNames, groups;
map<string, string> nameMap;
map<string, string> taxMap;
int process(ListVector*);
int processTaxMap();
vector<string> findConsensusTaxonomy(vector<string>, int&, string&, string); // returns the name of the "representative" taxonomy of given bin
};
#endif
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