changing command name classify.shared to classifyrf.shared

[mothur.git] / bayesian.h

diff --git a/bayesian.h b/bayesian.h
index 0020962f4276c9deb2129a27b2d69974783aab82..405fee3679df7b94ae8f392f62c27886e0b11e36 100644 (file)
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,30 +18,29 @@
 class Bayesian : public Classify {
        
 public:
-       Bayesian(string, string, string, int, int, bool);
-       ~Bayesian() {};
+       Bayesian(string, string, string, int, int, int, int, bool, bool);
+       ~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;
+                                                                               //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;
-       bool probs;
+       vector<diffPair> WordPairDiffArr; 
+       
+       int kmerSize, numKmers, confidenceThreshold, iters;
        
        string bootstrapResults(vector<int>, int, int);
        int getMostProbableTaxonomy(vector<int>);
-       void readProbFile(ifstream&, ifstream&);
-       //map<string, int> parseTaxMap(string);
+       void readProbFile(ifstream&, ifstream&, string, string);
+       bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
+       bool isReversed(vector<int>&);
+       vector<int> createWordIndexArr(Sequence*);
+       int generateWordPairDiffArr();
        
 };