homovacommand.h

   1 #ifndef HOMOVACOMMAND_H
   2 #define HOMOVACOMMAND_H
   3
   4 /*
   5  *  homovacommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 2/8/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 //class GlobalData;
  17 class GroupMap;
  18
  19 class HomovaCommand : public Command {
  20
  21 public:
  22         HomovaCommand(string);
  23         HomovaCommand();
  24         ~HomovaCommand(){}
  25
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "homova";                                      }
  28         string getCommandCategory()             { return "Hypothesis Testing";          }
  29
  30         string getHelpString();
  31     string getOutputPattern(string);
  32         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"; }
  33         string getDescription()         { return "homova"; }
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         double runHOMOVA(ofstream& , map<string, vector<int> >, double);
  40         double calcSigleSSWithin(vector<int>);
  41         double calcBValue(map<string, vector<int> >, vector<double>&);
  42         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  43
  44         bool abort;
  45         vector<string> outputNames, Sets;
  46
  47         string outputDir, inputDir, designFileName, phylipFileName;
  48         GroupMap* designMap;
  49         vector< vector<double> > distanceMatrix;
  50         int iters;
  51         double experimentwiseAlpha;
  52 };
  53
  54 #endif