X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;fp=validparameter.cpp;h=7855ddedd11f05b8e8c628e2d5c49c82be646a9b;hb=10c8178dc5e3f96ef8e92a986f1eddd13e622173;hp=4b263b491c59c0cd14abaf0d4553ffa20fdd26f6;hpb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index 4b263b4..7855dde 100644
--- 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"; }