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[mothur.git] / amovacommand.h

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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 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;
+
+       string outputDir, inputDir, designFileName, phylipFileName;
+       GroupMap* designMap;
+       vector< vector<double> > distanceMatrix;
+       int iters;
+       double experimentwiseAlpha;
+};
+
+#endif
+