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#ifndef INDICATORCOMMAND_H
#define INDICATORCOMMAND_H
/*
* indicatorcommand.h
* Mothur
*
* Created by westcott on 11/12/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "readtree.h"
#include "counttable.h"
#include "inputdata.h"
#include "designmap.h"
//**********************************************************************************************************************
struct sharedIndexes {
int treatmentIndex;
int sampleIndex;
sharedIndexes() : treatmentIndex(0), sampleIndex(0) {}
sharedIndexes(int g, int o) : treatmentIndex(g), sampleIndex(o) {}
bool operator<(const sharedIndexes& rhs) const {
return rhs.treatmentIndex < this->treatmentIndex || (rhs.treatmentIndex == this->treatmentIndex && rhs.sampleIndex < this->sampleIndex);
}
bool operator>(const sharedIndexes& rhs) const {
return rhs.treatmentIndex > this->treatmentIndex || (rhs.treatmentIndex == this->treatmentIndex && rhs.sampleIndex > this->sampleIndex);
}
bool operator=(const sharedIndexes& rhs) const {
return ((rhs.treatmentIndex == this->treatmentIndex) && (rhs.sampleIndex == this->sampleIndex));
}
};
//**********************************************************************************************************************
class IndicatorCommand : public Command {
public:
IndicatorCommand(string);
~IndicatorCommand(){}
vector<string> setParameters();
string getCommandName() { return "indicator"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
string getDescription() { return "calculate the indicator value for each OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
DesignMap* designMap;
string treefile, sharedfile, relabundfile, groups, label, inputFileName, designfile;
bool abort;
int iters, processors;
vector<string> outputNames, Groups, namesSeqs;
set<string> getDescendantList(Tree*&, int, map<int, set<string> >, map<int, set<int> >&);
map<int, float> getDistToRoot(Tree*&);
vector< map<sharedIndexes, vector<int> > > randomizeGroupings(vector<int>, int);
SharedRAbundVectors* getShared();
SharedRAbundFloatVectors* getSharedFloat();
int GetIndicatorSpecies(Tree*&);
int GetIndicatorSpecies();
vector<float> getPValues(vector< vector<SharedRAbundFloatVector*> >&, vector< vector<string> >&, int, vector<float>);
vector<float> getPValues(vector< vector<SharedRAbundVector*> >&, vector< vector<string> >&, int, vector<float>);
};
/**************************************************************************************************/
#endif
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