added trim.seqs command

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 8c55240965b5481bae5a551488c6e3ac957ee494..8d0e507a8f35bc7d9ee8664765194c546d736c1b 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -11,7 +11,7 @@
 #include "engine.hpp"
 #include "globaldata.hpp"
 
-using namespace std;
+/**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
 
@@ -24,10 +24,10 @@ int main(int argc, char *argv[]){
                bool bail = 0;
 
                if(argc>1){
-                       mothur = new BatchEngine(argv[1]);
+                       mothur = new BatchEngine(argv[0], argv[1]);
                }
                else{
-                       mothur = new InteractEngine();          
+                       mothur = new InteractEngine(argv[0]);           
                }
 
                while(bail == 0)                {       bail = mothur->getInput();                      }
@@ -46,3 +46,5 @@ int main(int argc, char *argv[]){
        }
 }
 
+/**************************************************************************************************/
+