X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.h;h=d4082fe9c82a7aeeb41aeaad62f016d0ec588d4d;hb=03853e0d0006e46e164fc1668865248f1bdbc166;hp=fedfa0ce8d372420baba40964010fd46004fb716;hpb=9b884118e97081d743c7b001216567f9b9131258;p=mothur.git

diff --git a/weighted.h b/weighted.h
index fedfa0c..d4082fe 100644
--- a/weighted.h
+++ b/weighted.h
@@ -12,26 +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*);
+		
 		EstOutput getValues(Tree*, string, string);
+		EstOutput getValues(Tree*, int, string);
 		
 	private:
-		GlobalData* globaldata;
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+
 		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;
 		
-		vector<double> getBranchLengthSums(Tree*);
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
+		double getLengthToRoot(Tree*, int, string, string);
 };
 
 /***********************************************************************/