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#ifndef GETGROUPSCOMMAND_H
#define GETGROUPSCOMMAND_H
/*
* getgroupscommand.h
* Mothur
*
* Created by westcott on 11/10/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "groupmap.h"
class GetGroupsCommand : public Command {
#ifdef UNIT_TEST
friend class TestGetGroupsCommand;
#endif
public:
GetGroupsCommand(string);
~GetGroupsCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.groups"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
string getDescription() { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
unordered_set<string> names;
map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
//then the other files need to change the unique name in their file to match.
//only add the names that need to be changed to keep the map search quick
string sets, accnosfile, countfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, groups, sharedfile, phylipfile, columnfile, flowfile;
bool abort;
vector<string> outputNames, Groups, Sets;
GroupMap* groupMap;
void readFasta();
void readFlow();
void readName();
void readGroup();
void readList();
void readTax();
void fillNames();
void readShared();
void readDesign();
void readPhylip();
void readColumn();
void fillGroupsFromDesign();
};
#endif
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