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#ifndef AMOVACOMMAND_H
#define AMOVACOMMAND_H
/*
* amovacommand.h
* mothur
*
* Created by westcott on 2/7/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
class GroupMap;
class AmovaCommand : public Command {
public:
AmovaCommand(string);
AmovaCommand();
~AmovaCommand() {}
vector<string> setParameters();
string getCommandName() { return "amova"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
string getDescription() { return "analysis of molecular variance"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
double runAMOVA(ofstream&, map<string, vector<int> >, double);
double calcSSWithin(map<string, vector<int> >&);
double calcSSTotal(map<string, vector<int> >&);
map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
bool abort;
vector<string> outputNames, Sets;
string outputDir, inputDir, designFileName, phylipFileName;
GroupMap* designMap;
vector< vector<double> > distanceMatrix;
int iters;
double experimentwiseAlpha;
};
#endif
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