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 0020962f4276c9deb2129a27b2d69974783aab82..70757be9ecf2a4c6791fd0fec7c9f74ab8a13501 100644 (file)
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,30 +18,23 @@
 class Bayesian : public Classify {
        
 public:
-       Bayesian(string, string, string, int, int, bool);
+       Bayesian(string, string, string, int, 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;
-       bool probs;
+       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);
        
 };