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
  27         string getHelpString();
  28     string getOutputPattern(string);
  29     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"; }
  30         string getDescription()         { return "analysis of molecular variance"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         double runAMOVA(ofstream&, map<string, vector<int> >, double);
  37         double calcSSWithin(map<string, vector<int> >&);
  38         double calcSSTotal(map<string, vector<int> >&);
  39         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  40
  41         bool abort;
  42         vector<string> outputNames, Sets;
  43
  44         string outputDir, inputDir, designFileName, phylipFileName;
  45         GroupMap* designMap;
  46         vector< vector<double> > distanceMatrix;
  47         int iters;
  48         double experimentwiseAlpha;
  49 };
  50
  51 #endif
  52