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 #include "inputdata.h"
  15 #include "sharedrabundvector.h"
  16 #include "validcalculator.h"
  17 #include "readphylipvector.h"
  18
  19 class GlobalData;
  20
  21 class AmovaCommand : public Command {
  22
  23 public:
  24         AmovaCommand(string);
  25         AmovaCommand();
  26         ~AmovaCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35         double runAMOVA(ofstream&, map<string, vector<int> >, double);
  36         double calcSSWithin(map<string, vector<int> >&);
  37         double calcSSTotal(map<string, vector<int> >&);
  38         map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
  39
  40
  41         bool abort;
  42         GlobalData* globaldata;
  43         map<string, vector<string> > outputTypes;
  44         vector<string> outputNames;
  45
  46         string outputDir, inputDir, designFileName, phylipFileName;
  47         GroupMap* designMap;
  48         vector< vector<double> > distanceMatrix;
  49         int iters;
  50         double experimentwiseAlpha;
  51
  52 //      struct linePair {
  53 //              int start;
  54 //              int num;
  55 //              linePair(int i, int j) : start(i), num(j) {}
  56 //      };
  57 //      vector<linePair> lines;
  58 //
  59 //      vector< vector<string> > namesOfGroupCombos;
  60 //      vector<string> Groups, outputNames, Sets;
  61 //      int processors;
  62 //      string groups, sets, calc, sharedfile, label, allLines, pickedGroups;
  63 //      vector<Calculator*> calculators;
  64 //      set<string> labels; //holds labels to be used
  65 //      int driver(int, int, vector<SharedRAbundVector*>, string);
  66 //      int driver(int, int, vector<string>, string, vector< vector<double> >&);
  67 //      int process(vector<SharedRAbundVector*>);
  68 };
  69
  70 #endif
  71