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#ifndef LISTSEQSCOMMAND_H
#define LISTSEQSCOMMAND_H
/*
* listseqscommand.h
* Mothur
*
* Created by Sarah Westcott on 7/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
class ListSeqsCommand : public Command {
public:
ListSeqsCommand(string);
~ListSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "list.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
string getDescription() { return "lists sequences from a list, fasta, name, group, count, fastq, taxonomy, alignreport or contigsreport file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
vector<string> fastafiles, namefiles, groupfiles, countfiles, alignfiles, listfiles, taxfiles, fastqfiles, contigsreportfiles, qualityfiles;
string format, inputFileName;
bool abort;
void process(vector<string> files, unordered_set<string>&);
void process(vector<string> files, unordered_set<string>&, void f(unordered_set<string>&, ifstream&, MothurOut*&));
};
#endif
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