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[mothur.git] / anosimcommand.h

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+#ifndef ANOSIMCOMMAND_H
+#define ANOSIMCOMMAND_H
+
+/*
+ *  anosimcommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/14/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+class GroupMap;
+
+class AnosimCommand : public Command {
+       
+public:
+       AnosimCommand(string);
+       AnosimCommand();
+       ~AnosimCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "anosim";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+       string getDescription()         { return "analysis of similarity"; }
+       
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
+       
+private:
+       bool abort;
+       GroupMap* designMap;
+       string outputDir, inputDir, designFileName, phylipFileName;
+       
+       vector<vector<double> > convertToRanks(vector<vector<double> >);
+       double calcR(vector<vector<double> >, map<string, vector<int> >);
+       map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+       double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
+       
+       vector< vector<double> > distanceMatrix;
+       vector<string> outputNames;
+       int iters;
+       double experimentwiseAlpha;
+       vector< vector<string> > namesOfGroupCombos;
+       
+       
+};
+
+#endif
+
+
+