reworked the classifiers summary file added groupfile option to classify.seqs, added...

[mothur.git] / bayesian.h

diff --git a/bayesian.h b/bayesian.h
index cbe949ff311edc776d507530fcc5b5a3f327b73e..70757be9ecf2a4c6791fd0fec7c9f74ab8a13501 100644 (file)
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,13 +18,23 @@
 class Bayesian : public Classify {
        
 public:
-       Bayesian(string, string, string, int, int, int, int, int);
+       Bayesian(string, string, string, int, int, int);
        ~Bayesian() {};
        
        string getTaxonomy(Sequence*);
        
-       
 private:
+       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, iters;
+       
+       string bootstrapResults(vector<int>, int, int);
+       int getMostProbableTaxonomy(vector<int>);
+       void readProbFile(ifstream&, ifstream&, string, string);
        
 };