added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / classify.h

diff --git a/classify.h b/classify.h
index e92569d6f27defcf14b0e6d2527bf9d743bd0988..6582be48d12bcaee868c3d64865a665eff073c42 100644 (file)
--- a/classify.h
+++ b/classify.h
@@ -30,6 +30,7 @@ public:
        virtual ~Classify(){};
        virtual string getTaxonomy(Sequence*) = 0;
        virtual string getSimpleTax()  { return simpleTax;      }
        virtual ~Classify(){};
        virtual string getTaxonomy(Sequence*) = 0;
        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.
        
        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.
        


@@ -44,6 +45,8 @@ protected:
        
        string taxFile, templateFile, simpleTax;
        vector<string> names;
        
        string taxFile, templateFile, simpleTax;
        vector<string> names;

+       int threadID;
+       bool flip, flipped, shortcuts;

        
        int readTaxonomy(string);
        vector<string> parseTax(string);
        
        int readTaxonomy(string);
        vector<string> parseTax(string);