8 * Created by westcott on 11/3/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
14 /* This class is a parent to phylotyp, bayesian, knn. */
17 #include "database.hpp"
18 #include "doTaxonomy.h"
24 /**************************************************************************************************/
29 Classify(string, string, string, int, int, int, int, int);
30 Classify(){ delete phyloTree; }
32 virtual ~Classify(){};
33 virtual string getTaxonomy(Sequence*) = 0;
34 //virtual map<string, int> getConfidenceScores() { return taxConfidenceScore; }
35 //virtual vector<string> parseTax(string);
36 virtual string getSimpleTax() { return simpleTax; }
40 map<string, string> taxonomy; //name maps to taxonomy
41 //map<string, int> genusCount; //maps genus to count - in essence a list of how many seqs are in each taxonomy
42 map<string, int>::iterator itTax;
43 map<string, string>::iterator it;
47 string taxFile, templateFile, simpleTax;
49 //map<string, int> taxConfidenceScore;
51 void readTaxonomy(string);
52 vector<string> parseTax(string);
55 /**************************************************************************************************/