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#ifndef PRECLUSTERCOMMAND_H
#define PRECLUSTERCOMMAND_H
/*
* preclustercommand.h
* Mothur
*
* Created by westcott on 12/21/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sequence.hpp"
#include "sequenceparser.h"
#include "sequencecountparser.h"
#include "alignment.hpp"
#include "gotohoverlap.hpp"
#include "needlemanoverlap.hpp"
#include "noalign.hpp"
#include "filters.h"
#include "getseqscommand.h"
//************************************************************/
class PreClusterCommand : public Command {
public:
PreClusterCommand(string);
~PreClusterCommand(){}
vector<string> setParameters();
string getCommandName() { return "pre.cluster"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nhttp://www.mothur.org/wiki/Pre.cluster"; }
string getDescription() { return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
int diffs, length, processors;
float match, misMatch, gapOpen, gapExtend, alpha, delta, error_rate, indel_prob, max_indels;
vector<float> error_dist;
bool abort, bygroup;
string fastafile, namefile, groupfile, countfile, pc_method, align_method, align, clump;
vector<string> outputNames;
void createProcessesGroups(map<string, vector<string> >&, vector<string>, string, string);
unordered_set<string> mergeGroupCounts(string, string);
void printFasta(string newFastaFileName, unordered_set<string> accnosFile);
};
/**************************************************************************************************/
#endif
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