8 * Created by westcott on 11/3/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
16 /**************************************************************************************************/
18 class Bayesian : public Classify {
21 Bayesian(string, string, string, int, int, int, int, bool, bool);
24 string getTaxonomy(Sequence*);
27 vector< vector<float> > wordGenusProb; //vector of maps from genus to probability
28 //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
30 vector<int> genusTotals;
31 vector<int> genusNodes; //indexes in phyloTree where genus' are located
33 vector<diffPair> WordPairDiffArr;
35 int kmerSize, numKmers, confidenceThreshold, iters;
37 string bootstrapResults(vector<int>, int, int);
38 int getMostProbableTaxonomy(vector<int>);
39 void readProbFile(ifstream&, ifstream&, string, string);
40 bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
41 bool isReversed(vector<int>&);
42 vector<int> createWordIndexArr(Sequence*);
43 int generateWordPairDiffArr();
47 /**************************************************************************************************/