X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bayesian.h;h=7c884337495dbb1e0213d1171a54ca20e0eb932c;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=6e35e9f8bd485734962e55a140f2dbb134cc8110;hpb=92f998cc7debc4bf3e8594848586b8153d96db16;p=mothur.git

diff --git a/bayesian.h b/bayesian.h
index 6e35e9f..7c88433 100644
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,23 +18,29 @@
 class Bayesian : public Classify {
 	
 public:
-	Bayesian(string, string, string, int, int, int);
-	~Bayesian() {};
+	Bayesian(string, string, string, int, int, int, int, 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&);
+	void readProbFile(ifstream&, ifstream&, string, string);
+	bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
+	bool isReversed(vector<int>&);
+	vector<int> createWordIndexArr(Sequence*);
+	int generateWordPairDiffArr();
 	
 };