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#ifndef BINSEQCOMMAND_H
#define BINSEQCOMMAND_H
/*
* binsequencecommand.h
* Mothur
*
* Created by Sarah Westcott on 4/3/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
#include "fastamap.h"
#include "groupmap.h"
#include "counttable.h"
#include "getseqscommand.h"
class BinSeqCommand : public Command {
public:
BinSeqCommand(string);
~BinSeqCommand();
vector<string> setParameters();
string getCommandName() { return "bin.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
string getDescription() { return "maps sequences to otus"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
CountTable ct;
bool abort, allLines;
set<string> labels; //holds labels to be used
string filename, fastafile, listfile, countfile, label;
vector<string> outputNames;
int process(ListVector*, FastaMap&);
};
#endif
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