X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.h;h=b136b007b517e56645be544ee6556f83a45de649;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=f27df8c9495d36ea9b98f74b521316af95271a0f;hpb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;p=mothur.git

diff --git a/unweighted.h b/unweighted.h
index f27df8c..b136b00 100644
--- a/unweighted.h
+++ b/unweighted.h
@@ -12,17 +12,17 @@
  */
 
 #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);
+		EstOutput getValues(Tree*, string, string, int, string);
 		
 	private:
 		struct linePair {
@@ -30,18 +30,19 @@ 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, 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>);
 };
 
 /***********************************************************************/