X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.h;h=4e0354782e5063e2a52268e88a1412b40db3c28e;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=f13224a14fe456d8acc0a868047145492b9e62e6;hpb=ef3f6d42fe720cd6d91419e5e32f8c04d8765010;p=mothur.git

diff --git a/classify.h b/classify.h
index f13224a..4e03547 100644
--- a/classify.h
+++ b/classify.h
@@ -15,7 +15,7 @@
 
 #include "mothur.h"
 #include "database.hpp"
-#include "doTaxonomy.h"
+#include "phylotree.h"
 
 
 class Sequence;
@@ -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<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:
 
@@ -45,10 +45,13 @@ protected:
 	
 	string taxFile, templateFile, simpleTax;
 	vector<string> names;
-	//map<string, int> taxConfidenceScore;
+	int threadID;
+	bool flip, flipped;
 	
-	void readTaxonomy(string);
+	int readTaxonomy(string);
 	vector<string> parseTax(string);
+	MothurOut* m;
+	
 };
 
 /**************************************************************************************************/