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#ifndef SEQSUMMARYCOMMAND_H
#define SEQSUMMARYCOMMAND_H
/*
* seqcoordcommand.h
* Mothur
*
* Created by Pat Schloss on 5/30/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "command.hpp"
#include "sequence.hpp"
/**************************************************************************************************/
class SeqSummaryCommand : public Command {
public:
SeqSummaryCommand(string);
~SeqSummaryCommand(){}
vector<string> setParameters();
string getCommandName() { return "summary.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
string getDescription() { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string fastafile, namefile, countfile, summaryfile, contigsfile, alignfile;
int processors;
vector<string> outputNames;
};
#endif
/**************************************************************************************************/
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