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//
// primerdesigncommand.h
// Mothur
//
// Created by Sarah Westcott on 1/18/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_primerdesigncommand_h
#define Mothur_primerdesigncommand_h
#include "command.hpp"
#include "listvector.hpp"
#include "inputdata.h"
#include "sequence.hpp"
#include "alignment.hpp"
#include "needlemanoverlap.hpp"
/**************************************************************************************************/
class PrimerDesignCommand : public Command {
public:
PrimerDesignCommand(string);
~PrimerDesignCommand(){}
vector<string> setParameters();
string getCommandName() { return "primer.design"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getOutputPattern(string);
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Primer.design"; }
string getDescription() { return "identify sequence fragments that are specific to particular OTUs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines, large;
int cutoff, pdiffs, length, processors, alignedLength;
string listfile, otulabel, namefile, countfile, fastafile, label;
double minTM, maxTM;
vector<string> outputNames;
char getBase(vector<unsigned int> counts, int size);
ListVector* getListVector();
set<string> getPrimer(Sequence);
int findMeltingPoint(string primer, double&, double&);
set<int> createProcesses(string, vector<double>&, vector<double>&, set<string>&, vector<Sequence>&, int, vector<string>&);
map<string, int> getSequenceBinAssignments(ListVector* list, map<string, int>& nameMap);
vector<Sequence> createProcessesConSeqs(map<string, int>&, map<string, int>&, vector<string>&);
int findIndex(string binLabel, vector<string> binLabels);
};
/**************************************************************************************************/
#endif
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