amovacommand.h

   1 #ifndef AMOVACOMMAND_H
   2 #define AMOVACOMMAND_H
   3
   4 /*
   5  *  amovacommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 2/7/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 class GroupMap;
  15
  16 class AmovaCommand : public Command {
  17
  18 public:
  19         AmovaCommand(string);
  20         AmovaCommand();
  21         ~AmovaCommand() {}
  22
  23         vector<string> setParameters();
  24         string getCommandName()                 { return "amova";                                       }
  25         string getCommandCategory()             { return "Hypothesis Testing";          }
  26         string getHelpString();
  27
  28         int execute();
  29         void help() { m->mothurOut(getHelpString()); }
  30
  31 private:
  32         double runAMOVA(ofstream&, map<string, vector<int> >, double);
  33         double calcSSWithin(map<string, vector<int> >&);
  34         double calcSSTotal(map<string, vector<int> >&);
  35         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  36
  37         bool abort;
  38         vector<string> outputNames;
  39
  40         string outputDir, inputDir, designFileName, phylipFileName;
  41         GroupMap* designMap;
  42         vector< vector<double> > distanceMatrix;
  43         int iters;
  44         double experimentwiseAlpha;
  45 };
  46
  47 #endif
  48