X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=validparameter.cpp;h=7d1af2551c7a6717c1d3ea807af0e56de0fc218e;hp=4b263b491c59c0cd14abaf0d4553ffa20fdd26f6;hb=615301e57c25e241356a9c2380648d117709458d;hpb=df41d90a9611eab75d0516e2654ed8580f8df24c

diff --git a/validparameter.cpp b/validparameter.cpp
index 4b263b4..7d1af25 100644
--- 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 +295,26 @@ 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"; }
+				}
+                
+                //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"; }