8 * Created by westcott on 11/3/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
14 /* This class is a parent to bayesian, knn. */
17 #include "database.hpp"
18 #include "phylotree.h"
24 /**************************************************************************************************/
30 virtual ~Classify(){};
31 virtual string getTaxonomy(Sequence*) = 0;
32 virtual string getSimpleTax() { return simpleTax; }
33 virtual bool getFlipped() { return flipped; }
34 virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float);
35 virtual void setDistName(string s) {} //for knn, so if distance method is selected with knn you can create the smallest distance file in the right place.
39 map<string, string> taxonomy; //name maps to taxonomy
40 //map<string, int> genusCount; //maps genus to count - in essence a list of how many seqs are in each taxonomy
41 map<string, int>::iterator itTax;
42 map<string, string>::iterator it;
46 string taxFile, templateFile, simpleTax;
51 int readTaxonomy(string);
52 vector<string> parseTax(string);
57 /**************************************************************************************************/