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#ifndef GETSHAREDOTUCOMMAND_H
#define GETSHAREDOTUCOMMAND_H
/*
* getsharedotucommand.h
* Mothur
*
* Created by westcott on 9/22/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "listvector.hpp"
#include "sequence.hpp"
#include "groupmap.h"
#include "counttable.h"
#include "inputdata.h"
//**********************************************************************************************************************
class GetSharedOTUCommand : public Command {
public:
GetSharedOTUCommand(string);
~GetSharedOTUCommand() = default;
vector<string> setParameters();
string getCommandName() { return "get.sharedseqs"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getRequiredCommand() { return "none"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
ListVector* list;
GroupMap* groupMap;
CountTable* ct;
set<string> labels;
string fastafile, label, groups, listfile, groupfile, sharedfile, output, userGroups, format, countfile;
bool abort, allLines, unique;
vector<string> Groups;
map<string, string> groupFinder;
map<string, string>::iterator it;
vector<Sequence> seqs;
vector<string> outputNames;
int process(ListVector*);
int process(SharedRAbundVectors*&);
int runShared();
};
//**********************************************************************************************************************
#endif
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