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, bool, bool);
  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         vector<diffPair> WordPairDiffArr;
  34
  35         int kmerSize, numKmers, confidenceThreshold, iters;
  36
  37         string bootstrapResults(vector<int>, int, int);
  38         int getMostProbableTaxonomy(vector<int>);
  39         void readProbFile(ifstream&, ifstream&, string, string);
  40         bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
  41         bool isReversed(vector<int>&);
  42         vector<int> createWordIndexArr(Sequence*);
  43         int generateWordPairDiffArr();
  44
  45 };
  46
  47 /**************************************************************************************************/
  48
  49 #endif
  50