X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.h;h=d4082fe9c82a7aeeb41aeaad62f016d0ec588d4d;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=11cd26b2d9642cb2679a0f3dfc06d930c15127f0;hpb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;p=mothur.git

diff --git a/weighted.h b/weighted.h
index 11cd26b..d4082fe 100644
--- a/weighted.h
+++ b/weighted.h
@@ -12,14 +12,14 @@
  */
 
 #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);
@@ -33,17 +33,16 @@ class Weighted : public TreeCalculator  {
 		};
 		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); 
-		EstOutput createProcesses(Tree*, vector< vector<string> >);
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
 		double getLengthToRoot(Tree*, int, string, string);
 };