changing command name classify.shared to classifyrf.shared

[mothur.git] / bayesian.h

diff --git a/bayesian.h b/bayesian.h
index cbe949ff311edc776d507530fcc5b5a3f327b73e..405fee3679df7b94ae8f392f62c27886e0b11e36 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() {};
+       Bayesian(string, string, string, int, int, int, int, bool, bool);
+       ~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
+       
+       vector<diffPair> WordPairDiffArr; 
+       
+       int kmerSize, numKmers, confidenceThreshold, iters;
+       
+       string bootstrapResults(vector<int>, int, int);
+       int getMostProbableTaxonomy(vector<int>);
+       void readProbFile(ifstream&, ifstream&, string, string);
+       bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
+       bool isReversed(vector<int>&);
+       vector<int> createWordIndexArr(Sequence*);
+       int generateWordPairDiffArr();
        
 };