X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bayesian.h;fp=bayesian.h;h=7c884337495dbb1e0213d1171a54ca20e0eb932c;hb=16abd6271c455bd01b34ff89a2e3641bef0fa128;hp=1cf5145132eab009b9d807f69de655fc26d59a40;hpb=896a4f281982a3c2889f6ce6d73be997072aceae;p=mothur.git

diff --git a/bayesian.h b/bayesian.h
index 1cf5145..7c88433 100644
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,7 +18,7 @@
 class Bayesian : public Classify {
 	
 public:
-	Bayesian(string, string, string, int, int, int, int);
+	Bayesian(string, string, string, int, int, int, int, 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();
 	
 };