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#ifndef Mothur_sortseqscommand_h
#define Mothur_sortseqscommand_h
//
// sortseqscommand.h
// Mothur
//
// Created by Sarah Westcott on 2/3/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "counttable.h"
class SortSeqsCommand : public Command {
public:
SortSeqsCommand(string);
~SortSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "sort.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
string getDescription() { return "puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
map<string, int> names;
string accnosfile, fastafile, namefile, taxfile, qualfile, flowfile;
bool abort, large;
vector<string> outputNames;
int readFasta();
int readFlow();
int readName();
int readTax();
int readQual();
};
#endif
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