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#ifndef COuNTSEQSCOMMAND_H
#define COuNTSEQSCOMMAND_H
/*
* countseqscommand.h
* Mothur
*
* Created by westcott on 6/1/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "groupmap.h"
class CountSeqsCommand : public Command {
public:
CountSeqsCommand(string);
~CountSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "count.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
string getDescription() { return "makes a count file from a names or shared file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string namefile, groupfile, groups, sharedfile, countfile;
bool abort, allLines, compress;
vector<string> Groups, outputNames;
set<string> labels;
unsigned long long process(string);
map<int, string> processNameFile(string);
map<int, string> getGroupNames(string, set<string>&);
unsigned long long processShared(vector<SharedRAbundVector*>& lookup, map<string, string> variables, vector<string>);
};
#endif
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