added modify names parameter to set.dir

[mothur.git] / bayesian.h

diff --git a/bayesian.h b/bayesian.h
index a1f693bb8f815dd0a6cb1d6155e9c032caf6fcea..405fee3679df7b94ae8f392f62c27886e0b11e36 100644 (file)
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,7 +18,7 @@
 class Bayesian : public Classify {
        
 public:
-       Bayesian(string, string, string, int, int, int);
+       Bayesian(string, string, string, int, int, int, int, bool, bool);
        ~Bayesian();
        
        string getTaxonomy(Sequence*);
@@ -30,12 +30,17 @@ private:
        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();
        
 };