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#ifndef OTUASSOCIATIONCOMMAND_H
#define OTUASSOCIATIONCOMMAND_H
/*
* otuassociationcommand.h
* Mothur
*
* Created by westcott on 1/19/12.
* Copyright 2012 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
class OTUAssociationCommand : public Command {
public:
OTUAssociationCommand(string);
~OTUAssociationCommand(){}
vector<string> setParameters();
string getCommandName() { return "otu.association"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
string getDescription() { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, method;
bool abort, pickedGroups, allLines;
double cutoff;
set<string> labels;
vector< vector< double> > metadata;
vector<string> outputNames, Groups, metadataLabels;
void processShared();
void process(SharedRAbundVectors*&);
void processRelabund();
void process(SharedRAbundFloatVectors*&);
void readMetadata();
};
#endif
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