X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unweighted.h;h=b136b007b517e56645be544ee6556f83a45de649;hb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e;hp=b24ad22a318624d8953b3f2e742fdc3e7c80d2ea;hpb=5a3592c6478d5d786ec20e4bee71854ad92fdb8c;p=mothur.git

diff --git a/unweighted.h b/unweighted.h
index b24ad22..b136b00 100644
--- a/unweighted.h
+++ b/unweighted.h
@@ -12,27 +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*, string, string) { return data; };
+		EstOutput getValues(Tree*, int, string);
+		EstOutput getValues(Tree*, string, string, int, string);
 		
 	private:
-		GlobalData* globaldata;
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+		
 		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, 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