X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bayesian.h;h=405fee3679df7b94ae8f392f62c27886e0b11e36;hp=012def96d8d2d04c8c258963668e261f125a9871;hb=615301e57c25e241356a9c2380648d117709458d;hpb=050220fe7822cc660615972a0054cf4a83eefbe4

diff --git a/bayesian.h b/bayesian.h
index 012def9..405fee3 100644
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,24 +18,29 @@
 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*);
 	
 private:
 	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;
+										//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
 	
+	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();
 	
 };