X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.h;h=e92569d6f27defcf14b0e6d2527bf9d743bd0988;hb=1b4b18b3e6fa1436b7cc6dcb14c749ac1ae1bdd8;hp=5c5a7ac474ecc0ce7308672e1a606c0052643caa;hpb=92f998cc7debc4bf3e8594848586b8153d96db16;p=mothur.git

diff --git a/classify.h b/classify.h
index 5c5a7ac..e92569d 100644
--- a/classify.h
+++ b/classify.h
@@ -26,13 +26,12 @@ 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);
+	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:
 
@@ -46,8 +45,10 @@ protected:
 	string taxFile, templateFile, simpleTax;
 	vector<string> names;
 	
-	void readTaxonomy(string);
+	int readTaxonomy(string);
 	vector<string> parseTax(string);
+	MothurOut* m;
+	
 };
 
 /**************************************************************************************************/