added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index a35b616e6cce63d541684e057a76248481af29ca..603ff0a1c65fa528439b7a8f456991ae600c26ef 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -17,10 +17,6 @@
 #include "commandoptionparser.hpp"
 #include "command.hpp"
 #include "commandfactory.hpp"
-#include "errorchecking.h"
-
-
-using namespace std;
 
 class GlobalData;
 
@@ -39,7 +35,7 @@ protected:
 
 class BatchEngine : public Engine {
 public:
-       BatchEngine(string);
+       BatchEngine(string, string);
        ~BatchEngine();
        virtual bool getInput();
        int openedBatch;
@@ -53,7 +49,7 @@ private:
 
 class InteractEngine : public Engine {
 public:
-       InteractEngine();
+       InteractEngine(string);
        ~InteractEngine();
        virtual bool getInput();
 private:
@@ -61,4 +57,18 @@ private:
 };
 
 
+class ScriptEngine : public Engine {
+public:
+       ScriptEngine(string, string);
+       ~ScriptEngine();
+       virtual bool getInput();
+       int openedBatch;
+private:
+       GlobalData* globaldata;
+       string listOfCommands;
+       string getNextCommand(string&);
+
+};
+
+
 #endif