X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classify.h;h=7b4c1022fef35aacbc33824d99ede551e55b187c;hp=bd9f34bc7eb3f51b6b360ce4b4f18251f194e155;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=4a2d841cb97fb02351022efe9d7068b1dc212bf9

diff --git a/classify.h b/classify.h
index bd9f34b..7b4c102 100644
--- a/classify.h
+++ b/classify.h
@@ -17,10 +17,8 @@
 #include "database.hpp"
 #include "phylotree.h"
 
-
 class Sequence;
 
-
 /**************************************************************************************************/
 
 class Classify {
@@ -30,12 +28,13 @@ public:
 	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.
 	
 protected:
 
 	map<string, string> taxonomy;  //name maps to taxonomy
-	//map<string, int> genusCount;  //maps genus to count - in essence a list of how many seqs are in each taxonomy
 	map<string, int>::iterator itTax;
 	map<string, string>::iterator it;
 	Database* database;
@@ -43,9 +42,12 @@ protected:
 	
 	string taxFile, templateFile, simpleTax;
 	vector<string> names;
+	int threadID, numLevels, numTaxa;
+	bool flip, flipped, shortcuts;
 	
 	int readTaxonomy(string);
 	vector<string> parseTax(string);
+    double getLogExpSum(vector<double>, int&);
 	MothurOut* m;
 	
 };