X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.h;h=bf0e0d4f90198ef353c2c1899414f699454c8a7e;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=8955ef7a2253ec5a1f2985d09198431a66a8db2c;hpb=692e0c1f69a78b568dc85cbdcea9fb6c189e2e6c;p=mothur.git

diff --git a/parsimony.h b/parsimony.h
index 8955ef7..bf0e0d4 100644
--- a/parsimony.h
+++ b/parsimony.h
@@ -12,25 +12,33 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Parsimony : public TreeCalculator  {
 	
 	public:
-		Parsimony(TreeMap* t) : tmap(t) {};
+		Parsimony() {};
 		~Parsimony() {};
-		EstOutput getValues(Tree*);
+		EstOutput getValues(Tree*, 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;
-		bool inUsersGroups(string);
-		map<string, int>::iterator it;
+		int processors;
+		string outputDir;
+	
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
 };
 
 /***********************************************************************/
-#endif
\ No newline at end of file
+
+#endif