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
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "anosim";                                      }
  27         string getCommandCategory()             { return "Hypothesis Testing";          }
  28
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
  32         string getDescription()         { return "analysis of similarity"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37 private:
  38         bool abort;
  39         GroupMap* designMap;
  40         string outputDir, inputDir, designFileName, phylipFileName;
  41
  42         vector<vector<double> > convertToRanks(vector<vector<double> >);
  43         double calcR(vector<vector<double> >, map<string, vector<int> >);
  44         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  45         double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
  46
  47         vector< vector<double> > distanceMatrix;
  48         vector<string> outputNames;
  49         int iters;
  50         double experimentwiseAlpha;
  51         vector< vector<string> > namesOfGroupCombos;
  52
  53
  54 };
  55
  56 #endif
  57
  58
  59