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#ifndef NORMALIZESHAREDCOMMAND_H
#define NORMALIZESHAREDCOMMAND_H
/*
* normalizesharedcommand.h
* Mothur
*
* Created by westcott on 9/15/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "sharedrabundvector.h"
class NormalizeSharedCommand : public Command {
public:
NormalizeSharedCommand(string);
NormalizeSharedCommand();
~NormalizeSharedCommand() {}
vector<string> setParameters();
string getCommandName() { return "normalize.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
string getDescription() { return "normalize samples in a shared or relabund file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
InputData* input;
vector<SharedRAbundVector*> lookup;
vector<SharedRAbundFloatVector*> lookupFloat;
bool abort, allLines, pickedGroups, makeRelabund;
set<string> labels; //holds labels to be used
string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
int norm;
vector<string> Groups, outputNames;
int normalize(vector<SharedRAbundVector*>&);
int normalize(vector<SharedRAbundFloatVector*>&);
int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
};
#endif
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