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 7990d1790586b5980fb31ada11f85b540572858f..603ff0a1c65fa528439b7a8f456991ae600c26ef 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -12,11 +12,11 @@
  
 
 
-#include <vector>
-#include <set>
-#include <string>
-
-using namespace std;
+#include "mothur.h"
+#include "globaldata.hpp"
+#include "commandoptionparser.hpp"
+#include "command.hpp"
+#include "commandfactory.hpp"
 
 class GlobalData;
 
@@ -35,7 +35,7 @@ protected:
 
 class BatchEngine : public Engine {
 public:
-       BatchEngine(string);
+       BatchEngine(string, string);
        ~BatchEngine();
        virtual bool getInput();
        int openedBatch;
@@ -49,7 +49,7 @@ private:
 
 class InteractEngine : public Engine {
 public:
-       InteractEngine();
+       InteractEngine(string);
        ~InteractEngine();
        virtual bool getInput();
 private:
@@ -57,4 +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