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

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index 3aabf13de009dac3205d00c130d734d98de88dda..0e7721a1ba1a51566eaab52b909604a50d5a70eb 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -17,20 +17,25 @@
 #include "commandoptionparser.hpp"
 #include "command.hpp"
 #include "commandfactory.hpp"
+#include "mothurout.h"
 
 class GlobalData;
 
 class Engine {
 public:
-       Engine() {  cFactory = new CommandFactory();    }
-       virtual ~Engine(){  delete cFactory;  }
+       Engine(); 
+       virtual ~Engine(){}
        virtual bool getInput() = 0;
        virtual string getCommand();
-       vector<string> getOptions() {   return options;         }
-       virtual void terminateCommand(int);
+       virtual string getOutputDir()                   {       return cFactory->getOutputDir();        }
+       virtual string getLogFileName()                 {       return cFactory->getLogfileName();      }
+       virtual bool getAppend()                                {       return cFactory->getAppend();           }
+
+       vector<string> getOptions()             {       return options;         }
 protected:
        vector<string> options;
        CommandFactory* cFactory;
+       MothurOut* mout;
 };
 
 
@@ -44,6 +49,7 @@ public:
 private:
        GlobalData* globaldata;
        ifstream inputBatchFile;
+       string getNextCommand(ifstream&);
 
 };