X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.h;h=b136b007b517e56645be544ee6556f83a45de649;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=d39b5e7e71f97a543e92cac087cebbe3d9b41b43;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/unweighted.h b/unweighted.h
index d39b5e7..b136b00 100644
--- a/unweighted.h
+++ b/unweighted.h
@@ -12,26 +12,39 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Unweighted : public TreeCalculator  {
 	
 	public:
-		Unweighted(TreeMap* t) : tmap(t) {};
+        Unweighted(bool r) : 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;
+		
 		EstOutput data;
-		vector<int> penalty;
-		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, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, bool, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, bool, CountTable*);
+		int getRoot(Tree*, int, vector<string>);
 };
 
 /***********************************************************************/
 
-
-
-#endif
\ No newline at end of file
+#endif