fixing bugs while testing

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 4b263b491c59c0cd14abaf0d4553ffa20fdd26f6..7855ddedd11f05b8e8c628e2d5c49c82be646a9b 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -291,6 +291,18 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
                                        m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
                                        return "not open"; 
                                }
+                               
+                               //check phylip file to make sure its really phylip and not column
+                               if ((it->first == "phylip") && (ableToOpen != 1)) {
+                                       ifstream inPhylip;
+                                       m->openInputFile(it->second, inPhylip);
+                                                                               
+                                       string numTest, name;
+                                       inPhylip >> numTest >> name;
+                                       inPhylip.close();
+                                       
+                                       if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, aborting."); m->mothurOutEndLine(); return "not found"; }
+                               }
                        }
                }else { return "not found"; }