X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.h;h=e751d2e79d19f17a2dd3a9af34ea11be95586ef4;hb=731d19a6eaf81768ed35e4be25fbac5686a2a7a0;hp=f27df8c9495d36ea9b98f74b521316af95271a0f;hpb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;p=mothur.git

diff --git a/unweighted.h b/unweighted.h
index f27df8c..e751d2e 100644
--- a/unweighted.h
+++ b/unweighted.h
@@ -19,10 +19,10 @@
 class Unweighted : public TreeCalculator  {
 	
 	public:
-		Unweighted(TreeMap* t) : tmap(t) {};
+		Unweighted(TreeMap* t, bool r) : tmap(t), includeRoot(r) {};
 		~Unweighted() {};
 		EstOutput getValues(Tree*, int, string);
-		EstOutput getValues(Tree*, string, string);
+		EstOutput getValues(Tree*, string, string, int, string);
 		
 	private:
 		struct linePair {
@@ -30,18 +30,20 @@ class Unweighted : public TreeCalculator  {
 			int num;
 			linePair(int i, int j) : start(i), num(j) {}
 		};
-		vector<linePair*> lines;
+		vector<linePair> lines;
 		
-		GlobalData* globaldata;
-		Tree* copyTree;
 		EstOutput data;
 		TreeMap* tmap;
 		int processors;
 		string outputDir;
+		map< vector<string>, set<int> > rootForGrouping;  //maps a grouping combo to the roots 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, bool); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, bool);
+		int getRoot(Tree*, int, vector<string>);
 };
 
 /***********************************************************************/