added sort parameter to get.otulist

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
index f13224a14fe456d8acc0a868047145492b9e62e6..bd9f34bc7eb3f51b6b360ce4b4f18251f194e155 100644 (file)
--- a/classify.h
+++ b/classify.h
@@ -15,7 +15,7 @@
 
 #include "mothur.h"
 #include "database.hpp"
-#include "doTaxonomy.h"
+#include "phylotree.h"
 
 
 class Sequence;
@@ -26,13 +26,11 @@ class Sequence;
 class Classify {
 
 public:
-       Classify(string, string, string, int, float, float, float, float);
-       
-       virtual ~Classify(){  delete phyloTree; delete database;  };
+       Classify();
+       virtual ~Classify(){};
        virtual string getTaxonomy(Sequence*) = 0;
-       //virtual map<string, int> getConfidenceScores() { return taxConfidenceScore; }
-       //virtual vector<string> parseTax(string);
        virtual string getSimpleTax()  { return simpleTax;      }
+       virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float);
        
 protected:
 
@@ -45,10 +43,11 @@ protected:
        
        string taxFile, templateFile, simpleTax;
        vector<string> names;
-       //map<string, int> taxConfidenceScore;
        
-       void readTaxonomy(string);
+       int readTaxonomy(string);
        vector<string> parseTax(string);
+       MothurOut* m;
+       
 };
 
 /**************************************************************************************************/