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#ifndef CORRAXESCOMMAND_H
#define CORRAXESCOMMAND_H
/*
* corraxescommand.h
* Mothur
*
* Created by westcott on 12/22/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sharedrabundvectors.hpp"
#include "sharedrabundfloatvectors.hpp"
#include "inputdata.h"
class CorrAxesCommand : public Command {
public:
CorrAxesCommand(string);
~CorrAxesCommand(){}
vector<string> setParameters();
string getCommandName() { return "corr.axes"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "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/Corr.axes"; }
string getDescription() { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, method;
bool abort, pickedGroups;
int numaxes;
set<string> names;
vector<string> outputNames, Groups;
SharedRAbundFloatVectors* lookupFloat;
vector<string> metadataLabels;
int getSharedFloat(InputData*);
int getMetadata();
map<string, vector<float> > readAxes();
int calcPearson(map<string, vector<float> >&, ofstream&);
int calcSpearman(map<string, vector<float> >&, ofstream&);
int calcKendall(map<string, vector<float> >&, ofstream&);
};
#endif
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