X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.h;h=0ccfab55ad9500f46f33d74e1c1c19f95ec525ba;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=e3bf3a8fc240648e4a38f48ced539845d3648706;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/unweighted.h b/unweighted.h
index e3bf3a8..0ccfab5 100644
--- a/unweighted.h
+++ b/unweighted.h
@@ -19,21 +19,34 @@
 class Unweighted : public TreeCalculator  {
 	
 	public:
-		Unweighted(TreeMap* t) : tmap(t) {};
+		Unweighted(TreeMap* t, bool r) : tmap(t), includeRoot(r) {};
 		~Unweighted() {};
-		EstOutput getValues(Tree*);
+		EstOutput getValues(Tree*, int, string);
+		EstOutput getValues(Tree*, string, string, int, string);
 		
 	private:
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+		
 		GlobalData* globaldata;
 		EstOutput data;
-		vector<int> penalty;
 		TreeMap* tmap;
-		bool inUsersGroups(string);
-
+		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>);
 };
 
 /***********************************************************************/
 
-
-
-#endif
\ No newline at end of file
+#endif