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[mothur.git] / bayesian.h

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+#ifndef BAYESIAN_H
+#define BAYESIAN_H
+
+/*
+ *  bayesian.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/3/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "classify.h"
+
+/**************************************************************************************************/
+
+class Bayesian : public Classify {
+       
+public:
+       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;
+       
+       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();
+       
+};
+
+/**************************************************************************************************/
+
+#endif
+