added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
index a2401dde6c10feaa4f83c6f3f7a65b8ff885dafd..4e0354782e5063e2a52268e88a1412b40db3c28e 100644 (file)
--- a/classify.h
+++ b/classify.h
@@ -27,13 +27,12 @@ class Classify {
 
 public:
        Classify();
-       
-       virtual ~Classify(){  delete phyloTree; if (database != NULL) {  delete database; } };
+       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:
 
@@ -46,6 +45,8 @@ protected:
        
        string taxFile, templateFile, simpleTax;
        vector<string> names;
+       int threadID;
+       bool flip, flipped;
        
        int readTaxonomy(string);
        vector<string> parseTax(string);