working on pam

[mothur.git] / sharedutilities.h

diff --git a/sharedutilities.h b/sharedutilities.h
index f4e46311a973ae8ab10a23b7f49481f72deb8cc3..df7e8d3091d811285f15cb49402053ec09a4f535 100644 (file)
--- 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