anosimcommand.h

   1 #ifndef ANOSIMCOMMAND_H
   2 #define ANOSIMCOMMAND_H
   3
   4 /*
   5  *  anosimcommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 2/14/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "command.hpp"
  15
  16 class GroupMap;
  17
  18 class AnosimCommand : public Command {
  19
  20 public:
  21         AnosimCommand(string);
  22         AnosimCommand();
  23         ~AnosimCommand();
  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         bool abort;
  33         GroupMap* designMap;
  34         map<string, vector<string> > outputTypes;
  35         string outputDir, inputDir, designFileName, phylipFileName;
  36
  37         vector<vector<double> > convertToRanks(vector<vector<double> >);
  38         double calcR(vector<vector<double> >, map<string, vector<int> >);
  39         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  40         double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
  41
  42         vector< vector<double> > distanceMatrix;
  43         vector<string> outputNames;
  44         int iters;
  45         double experimentwiseAlpha;
  46         vector< vector<string> > namesOfGroupCombos;
  47
  48
  49 };
  50
  51 #endif
  52
  53
  54