added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index e6e790d1687f27a7607555c176bd7b1ebcd44363..39801063110e6ca91a3f9029caf5c7b6eb8d6e91 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -1083,8 +1083,12 @@ int SharedCommand::ListGroupSameSeqs(vector<string>& groupMapsSeqs, SharedListVe
                        for (int j = 0; j < listNames.size(); j++) {
                                int num = groupNamesSeqs.count(listNames[j]);
                                
-                               if (num == 0) { error = 1; m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your groupfile. Please correct."); m->mothurOutEndLine(); }
-                               else { groupNamesSeqs.erase(listNames[j]); }
+                               if (num == 0) { 
+                    error = 1; 
+                    if (groupfile != "") { 
+                        m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your groupfile. Please correct."); m->mothurOutEndLine();   } 
+                    else{ m->mothurOut("[ERROR]: " + listNames[j] + " is in your listfile and not in your count file. Please correct."); m->mothurOutEndLine();        }
+                }else { groupNamesSeqs.erase(listNames[j]); }
                        }
                }