X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bayesian.h;h=405fee3679df7b94ae8f392f62c27886e0b11e36;hp=a1f693bb8f815dd0a6cb1d6155e9c032caf6fcea;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b

diff --git a/bayesian.h b/bayesian.h
index a1f693b..405fee3 100644
--- 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();
 	
 };