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         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         double runHOMOVA(ofstream& , map<string, vector<int> >, double);
  34         double calcSigleSSWithin(vector<int>);
  35         double calcBValue(map<string, vector<int> >, vector<double>&);
  36         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  37
  38         bool abort;
  39         map<string, vector<string> > outputTypes;
  40         vector<string> outputNames;
  41
  42         string outputDir, inputDir, designFileName, phylipFileName;
  43         GroupMap* designMap;
  44         vector< vector<double> > distanceMatrix;
  45         int iters;
  46         double experimentwiseAlpha;
  47 };
  48
  49 #endif