X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classify.h;h=7b4c1022fef35aacbc33824d99ede551e55b187c;hp=03142353feb8af7b8488007e5367144602a45acf;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63

diff --git a/classify.h b/classify.h
index 0314235..7b4c102 100644
--- a/classify.h
+++ b/classify.h
@@ -11,34 +11,30 @@
  */
 
 
-/* This class is a parent to phylotyp, bayesian, knn.  */
+/* This class is a parent to bayesian, knn.  */
 
 #include "mothur.h"
 #include "database.hpp"
-#include "doTaxonomy.h"
-
+#include "phylotree.h"
 
 class Sequence;
 
-
 /**************************************************************************************************/
 
 class Classify {
 
 public:
-	Classify(string, string, string, int, int, int, int, int);
-	Classify(){	delete phyloTree;  }
-	
+	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:
 
 	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;
@@ -46,10 +42,14 @@ protected:
 	
 	string taxFile, templateFile, simpleTax;
 	vector<string> names;
-	//map<string, int> taxConfidenceScore;
+	int threadID, numLevels, numTaxa;
+	bool flip, flipped, shortcuts;
 	
-	void readTaxonomy(string);
+	int readTaxonomy(string);
 	vector<string> parseTax(string);
+    double getLogExpSum(vector<double>, int&);
+	MothurOut* m;
+	
 };
 
 /**************************************************************************************************/