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[mothur.git] / homovacommand.h

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+#ifndef HOMOVACOMMAND_H
+#define HOMOVACOMMAND_H
+
+/*
+ *  homovacommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/8/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+//class GlobalData;
+class GroupMap;
+
+class HomovaCommand : public Command {
+       
+public:
+       HomovaCommand(string);
+       HomovaCommand();
+       ~HomovaCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "homova";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
+       string getDescription()         { return "homova"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       double runHOMOVA(ofstream& , map<string, vector<int> >, double);
+       double calcSigleSSWithin(vector<int>);
+       double calcBValue(map<string, vector<int> >, vector<double>&);
+       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