finished work on classify.seqs bayesian method and various bug fixes

[mothur.git] / bayesian.h

diff --git a/bayesian.h b/bayesian.h
index cbe949ff311edc776d507530fcc5b5a3f327b73e..9b93c839c9e5a4a749bf190c1bd95200fc82f272 100644 (file)
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,13 +18,29 @@
 class Bayesian : public Classify {
        
 public:
-       Bayesian(string, string, string, int, int, int, int, int);
+       Bayesian(string, string, string, int, int);
        ~Bayesian() {};
        
        string getTaxonomy(Sequence*);
-       
+       //map<string, int> getConfidenceScores() { return taxConfidenceScore; }
        
 private:
+       //map<string, vector<double> > taxonomyProbability;     //probability of a word being in a given taxonomy. 
+                                                                                                       //taxonomyProbability[bacteria;][0] = probabtility that a sequence within bacteria; would contain kmer 0;
+                                                                                                       //taxonomyProbability[bacteria;][1] = probabtility that a sequence within bacteria; would contain kmer 1...
+       
+       vector< vector<float> > wordGenusProb;  //vector of maps from genus to probability
+                                                                                               //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
+       
+       vector<int> genusTotals;
+       vector<int> genusNodes;  //indexes in phyloTree where genus' are located
+       
+       int kmerSize, numKmers, confidenceThreshold;
+       
+       string bootstrapResults(vector<int>, int, int);
+       int getMostProbableTaxonomy(vector<int>);
+       void readProbFile(ifstream&, ifstream&);
+       //map<string, int> parseTaxMap(string);
        
 };