line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index 7990d1790586b5980fb31ada11f85b540572858f..d42406e46022bfa717e288ecf9fa05df2a3a8185 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -12,11 +12,12 @@
  
 
 
-#include <vector>
-#include <set>
-#include <string>
-
-using namespace std;
+#include "mothur.h"
+#include "globaldata.hpp"
+#include "commandoptionparser.hpp"
+#include "command.hpp"
+#include "commandfactory.hpp"
+#include "errorchecking.h"
 
 class GlobalData;
 
@@ -35,7 +36,7 @@ protected:
 
 class BatchEngine : public Engine {
 public:
-       BatchEngine(string);
+       BatchEngine(string, string);
        ~BatchEngine();
        virtual bool getInput();
        int openedBatch;
@@ -49,7 +50,7 @@ private:
 
 class InteractEngine : public Engine {
 public:
-       InteractEngine();
+       InteractEngine(string);
        ~InteractEngine();
        virtual bool getInput();
 private: