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#ifndef SETCURRENTCOMMAND_H
#define SETCURRENTCOMMAND_H
/*
* setcurrentcommand.h
* Mothur
*
* Created by westcott on 3/16/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
class SetCurrentCommand : public Command {
public:
SetCurrentCommand(string);
~SetCurrentCommand() = default;
vector<string> setParameters();
string getCommandName() { return "set.current"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
string getDescription() { return "set current files for mothur"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
bool abort;
string clearTypes;
vector<string> types;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summaryfile, currentFile, samplefile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, filefile, constaxonomyfile, contigsreportfile, clrfile;
int readCurrentFiles();
};
#endif
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