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#ifndef MERGEGROUPSCOMMAND_H
#define MERGEGROUPSCOMMAND_H
/*
* mergegroupscommand.h
* mothur
*
* Created by westcott on 1/24/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "designmap.h"
class MergeGroupsCommand : public Command {
#ifdef UNIT_TEST
friend class TestMergeGroupsCommand;
#endif
public:
MergeGroupsCommand(string);
~MergeGroupsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "merge.groups"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
string getDescription() { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
DesignMap* designMap;
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
string groups, label, inputDir, designfile, sharedfile, groupfile, countfile, method, fastafile;
vector<string> Groups, outputNames;
int process(SharedRAbundVectors*&, ofstream&, bool&);
int processSharedFile(DesignMap*&);
int processGroupFile(DesignMap*&);
int processCountFile(DesignMap*&);
int mergeAbund(vector<int>);
};
#endif
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