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