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#ifndef CLUSTERSPLITCOMMAND_H
#define CLUSTERSPLITCOMMAND_H
/*
* clustersplitcommand.h
* Mothur
*
* Created by westcott on 5/19/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
#include "sparsedistancematrix.h"
#include "readcluster.h"
#include "splitmatrix.h"
#include "readphylip.h"
#include "readcolumn.h"
#include "readmatrix.hpp"
#include "inputdata.h"
#include "clustercommand.h"
#include "clusterclassic.h"
#include "vsearchfileparser.h"
#include "opticluster.h"
#include "calculator.h"
class ClusterSplitCommand : public Command {
public:
ClusterSplitCommand(string);
~ClusterSplitCommand() = default;
vector<string> setParameters();
string getCommandName() { return "cluster.split"; }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getOutputPattern(string);
string getCommonQuestions();
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/Cluster.split"; }
string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
string file, method, fileroot, tag, namefile, countfile, distfile, format, timing, taxFile, fastafile, inputDir, vsearchLocation, metricName, initialize, type;
double cutoff, splitcutoff, stableMetric;
int precision, length, processors, taxLevelCutoff, maxIters, numSingletons;
bool abort, classic, runCluster, deleteFiles, isList, cutoffNotSet, makeDist, runsensSpec, showabund;
void printData(ListVector*);
vector<string> createProcesses(vector< map<string, string> >, set<string>&);
int mergeLists(vector<string>, map<double, int>, ListVector*);
map<double, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
int createMergedDistanceFile(vector< map<string, string> >);
string readFile(vector< map<string, string> >&);
string printFile(string, vector< map<string, string> >&);
int getLabels(string, set<string>& listLabels);
int runSensSpec();
};
#endif
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