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);
24 string getTaxonomy(Sequence*);
25 //map<string, int> getConfidenceScores() { return taxConfidenceScore; }
28 //map<string, vector<double> > taxonomyProbability; //probability of a word being in a given taxonomy.
29 //taxonomyProbability[bacteria;][0] = probabtility that a sequence within bacteria; would contain kmer 0;
30 //taxonomyProbability[bacteria;][1] = probabtility that a sequence within bacteria; would contain kmer 1...
32 vector< vector<float> > wordGenusProb; //vector of maps from genus to probability
33 //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
35 vector<int> genusTotals;
36 vector<int> genusNodes; //indexes in phyloTree where genus' are located
38 int kmerSize, numKmers, confidenceThreshold;
40 string bootstrapResults(vector<int>, int, int);
41 int getMostProbableTaxonomy(vector<int>);
42 void readProbFile(ifstream&, ifstream&);
43 //map<string, int> parseTaxMap(string);
47 /**************************************************************************************************/