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#ifndef CLUSTERCOMMAND_H
#define CLUSTERCOMMAND_H
/*
* clustercommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
#include "sparsedistancematrix.h"
#include "counttable.h"
/* The cluster() command:
The cluster command outputs a .list , .rabund and .sabund files.
The cluster command parameter options are method, cuttoff and precision. No parameters are required.
The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).
The acceptable methods are furthest, nearest and average. If you do not provide a method the default algorithm is furthest neighbor.
The cluster() command outputs three files *.list, *.rabund, and *.sabund. */
class ClusterCommand : public Command {
public:
ClusterCommand(string);
ClusterCommand();
~ClusterCommand();
vector<string> setParameters();
string getCommandName() { return "cluster"; }
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"; }
string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
Cluster* cluster;
SparseDistanceMatrix* matrix;
ListVector* list;
RAbundVector* rabund;
RAbundVector oldRAbund;
ListVector oldList;
bool abort, hard, sim;
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
double cutoff;
float adjust;
string showabund, timing;
int precision, length;
ofstream sabundFile, rabundFile, listFile;
bool print_start;
time_t start;
unsigned long loops;
void printData(string label);
vector<string> outputNames;
int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};
#endif
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