X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.h;h=d4082fe9c82a7aeeb41aeaad62f016d0ec588d4d;hb=20071b183e619c122bf9f63b4bb42722507c4e4a;hp=8a8ad8f2642c35083cba53d6d93e2210f113f7e0;hpb=f099fdc1e3a0d7b75d780a164e5bdb93496a7a1d;p=mothur.git

diff --git a/weighted.h b/weighted.h
index 8a8ad8f..d4082fe 100644
--- a/weighted.h
+++ b/weighted.h
@@ -12,39 +12,38 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Weighted : public TreeCalculator  {
 	
 	public:
-		Weighted(TreeMap* t) : tmap(t) {};
+        Weighted( bool r) : includeRoot(r) {};
 		~Weighted() {};
 		
-		EstOutput getValues(Tree*, string, string, vector<double>&);
+		EstOutput getValues(Tree*, string, string);
 		EstOutput getValues(Tree*, int, string);
 		
-		vector<double> getBranchLengthSums(Tree*);
-		
 	private:
 		struct linePair {
 			int start;
 			int num;
 			linePair(int i, int j) : start(i), num(j) {}
 		};
-		vector<linePair*> lines;
+		vector<linePair> lines;
 
-		GlobalData* globaldata;
 		EstOutput data;
-		TreeMap* tmap;
 		map<string, int>::iterator it;
 		map<string, double> WScore; //a score for each group combination i.e. AB, AC, BC.
 		int processors;
 		string outputDir;
+		map< vector<string>, set<int> > rootForGrouping;  //maps a grouping combo to the root for that combo
+		bool includeRoot;
 		
-		EstOutput driver(Tree*, vector< vector<string> >, int, int, vector<double>&); 
-		EstOutput createProcesses(Tree*, vector< vector<string> >, vector<double>&);
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
+		double getLengthToRoot(Tree*, int, string, string);
 };
 
 /***********************************************************************/