X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.h;h=180409ce2dbad5da67b570a7ca4a3666c61ae3b3;hb=d71a31a60542608595ce1278cc4a3398479cec7f;hp=b0d443333d230b410d6a4f64c88c2ee0b18f2a61;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/weighted.h b/weighted.h
index b0d4433..180409c 100644
--- a/weighted.h
+++ b/weighted.h
@@ -19,18 +19,34 @@
 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:
+		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, float> WScore; //a score for each group combination i.e. AB, AC, BC.
+		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, TreeMap*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, TreeMap*);
+		double getLengthToRoot(Tree*, int, string, string);
 };
 
 /***********************************************************************/
 
 
-#endif
\ No newline at end of file
+#endif