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
  15 //class GlobalData;
  16 class GroupMap;
  17
  18 class AmovaCommand : public Command {
  19
  20 public:
  21         AmovaCommand(string);
  22         AmovaCommand();
  23         ~AmovaCommand();
  24         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  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
  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
  50