X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bayesian.h;h=405fee3679df7b94ae8f392f62c27886e0b11e36;hp=7100bf33b00c3fa85bd0c928c00daf82647f851a;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=f27b66ce6415eb14c434f9850019c7cf140e023e

diff --git a/bayesian.h b/bayesian.h
index 7100bf3..405fee3 100644
--- a/bayesian.h
+++ b/bayesian.h
@@ -18,29 +18,29 @@
 class Bayesian : public Classify {
 	
 public:
-	Bayesian(string, string, string, int, int, int);
-	~Bayesian() {};
+	Bayesian(string, string, string, int, int, int, int, bool, bool);
+	~Bayesian();
 	
 	string getTaxonomy(Sequence*);
-	//map<string, int> getConfidenceScores() { return taxConfidenceScore; }
 	
 private:
-	//map<string, vector<double> > taxonomyProbability;	//probability of a word being in a given taxonomy. 
-													//taxonomyProbability[bacteria;][0] = probabtility that a sequence within bacteria; would contain kmer 0;
-													//taxonomyProbability[bacteria;][1] = probabtility that a sequence within bacteria; would contain kmer 1...
-	
 	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&);
-	//map<string, int> parseTaxMap(string);
+	void readProbFile(ifstream&, ifstream&, string, string);
+	bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
+	bool isReversed(vector<int>&);
+	vector<int> createWordIndexArr(Sequence*);
+	int generateWordPairDiffArr();
 	
 };