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         struct linePair {
  36                 int start;
  37                 int num;
  38                 linePair(int i, int j) : start(i), num(j) {}
  39         };
  40         vector<linePair> lines;
  41
  42         GlobalData* globaldata;
  43         GroupMap* designMap;
  44         map<string, vector<string> > outputTypes;
  45
  46         vector< vector<double> > matrix;
  47         bool abort, allLines, pickedGroups;
  48         set<string> labels; //holds labels to be used
  49         string format, groups, label, outputDir, inputDir, designfile, sets, phylipfile, calc, sharedfile;
  50         vector<string> Groups, outputNames, Sets;
  51         vector< vector<string> > namesOfGroupCombos;
  52         int iters, processors;
  53         vector<Calculator*> calculators;
  54
  55         int driver(int, int, vector<SharedRAbundVector*>, string);
  56         int driver(int, int, vector<string>, string, vector< vector<double> >&);
  57         int process(vector<SharedRAbundVector*>);
  58         int calcAmova(ofstream&, int, vector<string>);
  59         double calcWithin(vector< vector<double> >&, int, vector<string>);
  60         double calcTotal(int);
  61 };
  62
  63 #endif
  64