sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
index 03142353feb8af7b8488007e5367144602a45acf..7b4c1022fef35aacbc33824d99ede551e55b187c 100644 (file)
--- a/classify.h
+++ b/classify.h
@@ -11,34 +11,30 @@
  */
 
 
-/* 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;
 
-
 /**************************************************************************************************/
 
 class Classify {
 
 public:
-       Classify(string, string, string, int, int, int, int, int);
-       Classify(){     delete phyloTree;  }
-       
+       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 bool getFlipped()  { return flipped;    }
+       virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float);
+       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.
        
 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;
@@ -46,10 +42,14 @@ protected:
        
        string taxFile, templateFile, simpleTax;
        vector<string> names;
-       //map<string, int> taxConfidenceScore;
+       int threadID, numLevels, numTaxa;
+       bool flip, flipped, shortcuts;
        
-       void readTaxonomy(string);
+       int readTaxonomy(string);
        vector<string> parseTax(string);
+    double getLogExpSum(vector<double>, int&);
+       MothurOut* m;
+       
 };
 
 /**************************************************************************************************/