X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.h;h=b136b007b517e56645be544ee6556f83a45de649;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=f41326115020013fb2e59df755bff1e961001c8d;hpb=a98eb683e17d8e49583bf2d215ab7562a4cdca75;p=mothur.git

diff --git a/unweighted.h b/unweighted.h
index f413261..b136b00 100644
--- a/unweighted.h
+++ b/unweighted.h
@@ -12,14 +12,14 @@
  */
 
 #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*, int, string);
 		EstOutput getValues(Tree*, string, string, int, string);
@@ -32,17 +32,17 @@ class Unweighted : public TreeCalculator  {
 		};
 		vector<linePair> lines;
 		
-		GlobalData* globaldata;
 		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);
-
+		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>);
 };
 
 /***********************************************************************/