X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.h;h=4e0354782e5063e2a52268e88a1412b40db3c28e;hb=d71a31a60542608595ce1278cc4a3398479cec7f;hp=a8978732af92688dfddc2ede9d1d5c13c636ea06;hpb=7a2154809d332281cf4006943a9bd94b8208c837;p=mothur.git diff --git a/classify.h b/classify.h index a897873..4e03547 100644 --- a/classify.h +++ b/classify.h @@ -26,13 +26,13 @@ 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 getConfidenceScores() { return taxConfidenceScore; } - //virtual vector 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: @@ -45,10 +45,13 @@ protected: string taxFile, templateFile, simpleTax; vector names; - //map taxConfidenceScore; + int threadID; + bool flip, flipped; - void readTaxonomy(string); + int readTaxonomy(string); vector parseTax(string); + MothurOut* m; + }; /**************************************************************************************************/