X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedutilities.h;h=df7e8d3091d811285f15cb49402053ec09a4f535;hp=f4e46311a973ae8ab10a23b7f49481f72deb8cc3;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d

diff --git a/sharedutilities.h b/sharedutilities.h
index f4e4631..df7e8d3 100644
--- a/sharedutilities.h
+++ b/sharedutilities.h
@@ -10,6 +10,7 @@
  */
 
 #include "mothur.h"
+#include "mothurout.h"
 
 class SharedRAbundVector;
 class SharedOrderVector;
@@ -18,22 +19,23 @@ class SharedOrderVector;
 
 class SharedUtil {
 	public:
-		SharedUtil() {};
+		SharedUtil() { m = MothurOut::getInstance(); }
 		~SharedUtil() {};
 		
 		void getSharedVectors(vector<string>, vector<SharedRAbundVector*>&, SharedOrderVector*);
+		void getSharedVectorswithReplacement(vector<string>, vector<SharedRAbundVector*>&, SharedOrderVector*);
+		void setGroups(vector<string>&, vector<string>&);  //globaldata->Groups, your tree or group map
 		void setGroups(vector<string>&, vector<string>&, string);  //globaldata->Groups, your tree or group map, mode
 		void setGroups(vector<string>&, vector<string>&, string&, int&, string);  //globaldata->Groups, your tree or group map, allgroups, numGroups, mode
 		void getCombos(vector<string>&, vector<string>, int&); //groupcomb, globaldata->Groups, numcomb
 		void updateGroupIndex(vector<string>&, map<string, int>&); //globaldata->Groups, groupmap->groupIndex
+		bool isValidGroup(string, vector<string>);
 		
 	private:
-	
-		bool isValidGroup(string, vector<string>);
+		MothurOut* m;
+		
 };
 
 /**************************************************************************************************/
 
-
-
-#endif
\ No newline at end of file
+#endif