changes while testing

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 1e5fe11de39f34b30f59249895bcf393506e32f9..64f9ab6822301310e975e6bbe58736e953eed4f2 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -355,11 +355,19 @@ int RemoveGroupsCommand::execute(){
                        
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all
-                       SharedUtil* util = new SharedUtil();
                        vector<string> namesGroups = groupMap->getNamesOfGroups();
-                       util->setGroups(Groups, namesGroups);
-                       delete util;
-                       
+                       vector<string> checkedGroups;
+            for (int i = 0; i < Groups.size(); i++) {
+                if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
+                else {  m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
+            }
+            
+            if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
+                       else {
+                Groups = checkedGroups;
+                m->setGroups(Groups);
+            }
+            
                        //fill names with names of sequences that are from the groups we want to remove 
                        fillNames();