added get.otus and remove.otus commands

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index bd1a098c8d5662044552071c7c44a273214018ce..b1d818850bd974ff482bc8c88ffc4bdc0a3dc7bd 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1462,20 +1462,21 @@ bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string
                }
                
                //go through users set and make them floats
-               for(it = userLabels.begin(); it != userLabels.end(); ++it) {
+               for(it = userLabels.begin(); it != userLabels.end();) {
                        
                        float temp;
                        if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
                                convert(*it, temp);
                                orderFloat.push_back(temp);
                                userMap[*it] = temp;
+                               it++;
                        }else if (*it == "unique") { 
                                orderFloat.push_back(-1.0);
                                userMap["unique"] = -1.0;
+                               it++;
                        }else {
-                               if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
-                               userLabels.erase(*it); 
-                               it--;
+                               if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
+                               userLabels.erase(it++); 
                        }
                }
                
@@ -1491,11 +1492,11 @@ bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string
                        if (orderFloat[i] < labelFloat) {
                                smaller = true;
                                if (orderFloat[i] == -1) { 
-                                       if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
+                                       if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
                                        userLabels.erase("unique");
                                }
                                else {  
-                                       if (errorOff == "") { cout << "Your file does not include the label " << endl; }
+                                       if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
                                        string s = "";
                                        for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {  
                                                if (it2->second == orderFloat[i]) {  
@@ -1505,7 +1506,7 @@ bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string
                                                        break;
                                                }
                                        }
-                                       if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
+                                       if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
                                }
                        //since they are sorted once you find a bigger one stop looking
                        }else { break; }