bayesian.h

   1 #ifndef BAYESIAN_H
   2 #define BAYESIAN_H
   3
   4 /*
   5  *  bayesian.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 11/3/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "classify.h"
  15
  16 /**************************************************************************************************/
  17
  18 class Bayesian : public Classify {
  19
  20 public:
  21         Bayesian(string, string, string, int, int, int, int);
  22         ~Bayesian();
  23
  24         string getTaxonomy(Sequence*);
  25
  26 private:
  27         vector< vector<float> > wordGenusProb;  //vector of maps from genus to probability
  28                                                                                 //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
  29
  30         vector<int> genusTotals;
  31         vector<int> genusNodes;  //indexes in phyloTree where genus' are located
  32
  33         int kmerSize, numKmers, confidenceThreshold, iters;
  34
  35         string bootstrapResults(vector<int>, int, int);
  36         int getMostProbableTaxonomy(vector<int>);
  37         void readProbFile(ifstream&, ifstream&, string, string);
  38         bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
  39
  40 };
  41
  42 /**************************************************************************************************/
  43
  44 #endif
  45