added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 1150e53735481aea3377ec81f78c0d2544f324e6..39801063110e6ca91a3f9029caf5c7b6eb8d6e91 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -825,7 +825,7 @@ int SharedCommand::createSharedFromListGroup(string filename) {
         int error = ListGroupSameSeqs(namesSeqs, SharedList);
         
         if ((!pickedGroups) && (SharedList->getNumSeqs() != numGroupNames)) {  //if the user has not specified any groups and their files don't match exit with error
-            m->mothurOut("Your group file contains " + toString(numGroupNames) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); 
+            m->mothurOut("Your group file contains " + toString(numGroupNames) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); m->control_pressed = true;
             
             out.close(); m->mothurRemove(filename); //remove blank shared file you made
             
@@ -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]); }
                        }
                }