X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=8d0e507a8f35bc7d9ee8664765194c546d736c1b;hb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;hp=5142ca22eabb2d6a3121e6dc2701cb4a04fe9f1f;hpb=5a3592c6478d5d786ec20e4bee71854ad92fdb8c;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 5142ca2..8d0e507 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -11,7 +11,7 @@
 #include "engine.hpp"
 #include "globaldata.hpp"
 
-using namespace std;
+/**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
 
@@ -20,19 +20,19 @@ int main(int argc, char *argv[]){
 		//srand(54321);
 		srand( (unsigned)time( NULL ) );
 
-		Engine* dotur;
+		Engine* mothur;
 		bool bail = 0;
 
 		if(argc>1){
-			dotur = new BatchEngine(argv[1]);
+			mothur = new BatchEngine(argv[0], argv[1]);
 		}
 		else{
-			dotur = new InteractEngine();		
+			mothur = new InteractEngine(argv[0]);		
 		}
 
-		while(bail == 0)		{	bail = dotur->getInput();			}
+		while(bail == 0)		{	bail = mothur->getInput();			}
 	
-		delete dotur;
+		delete mothur;
 	
 		return 0;
 	}
@@ -46,3 +46,5 @@ int main(int argc, char *argv[]){
 	}
 }
 
+/**************************************************************************************************/
+