added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 4b263b491c59c0cd14abaf0d4553ffa20fdd26f6..3e1f3498ca0be8f0f010bd038273f3ea70f89d3c 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -221,6 +221,10 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
                if(it != container.end()){ //no parameter given
 
                        if(isFile == true) {
+                               
+                               int pos = (it->second).find(".tx.");
+                               if (pos != string::npos) { m->sharedHeaderMode = "tax"; }
+                               else { m->sharedHeaderMode = "otu"; }
                        
                        #ifdef USE_MPI  
                                int pid, processors;
@@ -291,6 +295,18 @@ 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"; }