changing command name classify.shared to classifyrf.shared

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 7855ddedd11f05b8e8c628e2d5c49c82be646a9b..7d1af2551c7a6717c1d3ea807af0e56de0fc218e 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;
@@ -303,6 +307,14 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
                                        
                                        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"; }
                                }
+                
+                //check for blank file
+                if (ableToOpen != 1) {
+                    if (m->isBlank(container[parameter])) {
+                        m->mothurOut("[ERROR]: " + container[parameter] + " is blank, aborting."); m->mothurOutEndLine(); return "not found"; 
+                    }
+                }
+                    
                        }
                }else { return "not found"; }