Merge remote-tracking branch 'origin/master'

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 1150e53735481aea3377ec81f78c0d2544f324e6..542f8d346447322aea63491e092b97632449bd62 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -188,7 +188,11 @@ SharedCommand::SharedCommand(string option)  {
              countfile = validParameter.validFile(parameters, "count", true);
              if (countfile == "not open") { countfile = ""; abort = true; }    
              else if (countfile == "not found") { countfile = ""; }
-             else {  m->setCountTableFile(countfile); }
+             else {  
+                 m->setCountTableFile(countfile); 
+                 CountTable temp;
+                 if (!temp.testGroups(countfile)) { m->mothurOut("[ERROR]: Your count file does not have group info, aborting."); m->mothurOutEndLine(); abort=true; }
+             }
                         
             if ((biomfile == "") && (listfile == "")) { 
                                //is there are current file available for either of these?
@@ -825,7 +829,7 @@ 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 +1087,12 @@ 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]); }
                        }
                }