added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
index 03142353feb8af7b8488007e5367144602a45acf..5c5a7ac474ecc0ce7308672e1a606c0052643caa 100644 (file)
--- a/classify.h
+++ b/classify.h
@@ -11,11 +11,11 @@
  */
 
 
-/* This class is a parent to phylotyp, bayesian, knn.  */
+/* This class is a parent to bayesian, knn.  */
 
 #include "mothur.h"
 #include "database.hpp"
-#include "doTaxonomy.h"
+#include "phylotree.h"
 
 
 class Sequence;
@@ -26,10 +26,9 @@ class Sequence;
 class Classify {
 
 public:
-       Classify(string, string, string, int, int, int, int, int);
-       Classify(){     delete phyloTree;  }
+       Classify(string, string, string, int, float, float, float, float);
        
-       virtual ~Classify(){};
+       virtual ~Classify(){  delete phyloTree; delete database;  };
        virtual string getTaxonomy(Sequence*) = 0;
        //virtual map<string, int> getConfidenceScores() { return taxConfidenceScore; }
        //virtual vector<string> parseTax(string);
@@ -46,7 +45,6 @@ protected:
        
        string taxFile, templateFile, simpleTax;
        vector<string> names;
-       //map<string, int> taxConfidenceScore;
        
        void readTaxonomy(string);
        vector<string> parseTax(string);