changed the daughterLevels in classifiers summary file to reflect the classifications...

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index c04cd4ed69306116f7eb72e64bf5fd2e01d92015..0e7721a1ba1a51566eaab52b909604a50d5a70eb 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -13,33 +13,43 @@
 
 
 #include "mothur.h"
-
-using namespace std;
+#include "globaldata.hpp"
+#include "commandoptionparser.hpp"
+#include "command.hpp"
+#include "commandfactory.hpp"
+#include "mothurout.h"
 
 class GlobalData;
 
 class Engine {
 public:
-       virtual ~Engine(){};
+       Engine(); 
+       virtual ~Engine(){}
        virtual bool getInput() = 0;
-//     string getCommand()                     {       return command;         }
-       vector<string> getOptions() {   return options;         }
+       virtual string getCommand();
+       virtual string getOutputDir()                   {       return cFactory->getOutputDir();        }
+       virtual string getLogFileName()                 {       return cFactory->getLogfileName();      }
+       virtual bool getAppend()                                {       return cFactory->getAppend();           }
+
+       vector<string> getOptions()             {       return options;         }
 protected:
-//     string command;
        vector<string> options;
+       CommandFactory* cFactory;
+       MothurOut* mout;
 };
 
 
 
 class BatchEngine : public Engine {
 public:
-       BatchEngine(string);
+       BatchEngine(string, string);
        ~BatchEngine();
        virtual bool getInput();
        int openedBatch;
 private:
        GlobalData* globaldata;
        ifstream inputBatchFile;
+       string getNextCommand(ifstream&);
 
 };
 
@@ -47,7 +57,7 @@ private:
 
 class InteractEngine : public Engine {
 public:
-       InteractEngine();
+       InteractEngine(string);
        ~InteractEngine();
        virtual bool getInput();
 private:
@@ -55,4 +65,18 @@ private:
 };
 
 
+class ScriptEngine : public Engine {
+public:
+       ScriptEngine(string, string);
+       ~ScriptEngine();
+       virtual bool getInput();
+       int openedBatch;
+private:
+       GlobalData* globaldata;
+       string listOfCommands;
+       string getNextCommand(string&);
+
+};
+
+
 #endif