finished work on classify.seqs bayesian method and various bug fixes

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
index 2926800284ce00cbb7ceb2768bfbe35f28a44a80..03142353feb8af7b8488007e5367144602a45acf 100644 (file)
--- a/classify.h
+++ b/classify.h
@@ -15,33 +15,41 @@
 
 #include "mothur.h"
 #include "database.hpp"
-
+#include "doTaxonomy.h"
 
 
 class Sequence;
 
+
 /**************************************************************************************************/
 
 class Classify {
 
 public:
        Classify(string, string, string, int, int, int, int, int);
-       Classify(){};
+       Classify(){     delete phyloTree;  }
        
        virtual ~Classify(){};
        virtual string getTaxonomy(Sequence*) = 0;
+       //virtual map<string, int> getConfidenceScores() { return taxConfidenceScore; }
+       //virtual vector<string> parseTax(string);
+       virtual string getSimpleTax()  { return simpleTax;      }
        
 protected:
 
        map<string, string> taxonomy;  //name maps to taxonomy
+       //map<string, int> genusCount;  //maps genus to count - in essence a list of how many seqs are in each taxonomy
+       map<string, int>::iterator itTax;
        map<string, string>::iterator it;
        Database* database;
+       PhyloTree* phyloTree;
        
-       string taxFile, templateFile;
+       string taxFile, templateFile, simpleTax;
        vector<string> names;
+       //map<string, int> taxConfidenceScore;
        
        void readTaxonomy(string);
-               
+       vector<string> parseTax(string);
 };
 
 /**************************************************************************************************/