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#ifndef CLUSTERDOTURCOMMAND_H
#define CLUSTERDOTURCOMMAND_H
/*
* clusterdoturcommand.h
* Mothur
*
* Created by westcott on 10/27/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "nameassignment.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
class ClusterDoturCommand : public Command {
public:
ClusterDoturCommand(string);
~ClusterDoturCommand(){}
vector<string> setParameters();
string getCommandName() { return "cluster.classic"; }
string getCommandCategory() { return "Clustering"; }
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.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
string getDescription() { return "cluster your sequences into OTUs using DOTUR’s method"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, sim;
string method, fileroot, tag, phylipfile, namefile, countfile;
double cutoff;
int precision, length;
ofstream sabundFile, rabundFile, listFile;
NameAssignment* nameMap;
ListVector* list;
RAbundVector* rabund;
RAbundVector oldRAbund;
ListVector oldList;
void printData(string label, map<string, int>&, bool&);
vector<string> outputNames;
};
#endif
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