X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bayesian.h;h=405fee3679df7b94ae8f392f62c27886e0b11e36;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=1cf5145132eab009b9d807f69de655fc26d59a40;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/bayesian.h b/bayesian.h
index 1cf5145..405fee3 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, 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();
 	
 };