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);
  22         ~Bayesian() {};
  23
  24         string getTaxonomy(Sequence*);
  25         //map<string, int> getConfidenceScores() { return taxConfidenceScore; }
  26
  27 private:
  28         //map<string, vector<double> > taxonomyProbability;     //probability of a word being in a given taxonomy.
  29                                                                                                         //taxonomyProbability[bacteria;][0] = probabtility that a sequence within bacteria; would contain kmer 0;
  30                                                                                                         //taxonomyProbability[bacteria;][1] = probabtility that a sequence within bacteria; would contain kmer 1...
  31
  32         vector< vector<float> > wordGenusProb;  //vector of maps from genus to probability
  33                                                                                                 //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
  34
  35         vector<int> genusTotals;
  36         vector<int> genusNodes;  //indexes in phyloTree where genus' are located
  37
  38         int kmerSize, numKmers, confidenceThreshold;
  39
  40         string bootstrapResults(vector<int>, int, int);
  41         int getMostProbableTaxonomy(vector<int>);
  42         void readProbFile(ifstream&, ifstream&);
  43         //map<string, int> parseTaxMap(string);
  44
  45 };
  46
  47 /**************************************************************************************************/
  48
  49 #endif
  50