sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index d4ec3b65a5cdd428c44967ed66ea454d7bc5b2f8..460e245bf5312d81f5b15d70387cf9ec63d472f6 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -13,25 +13,26 @@
 
 
 #include "mothur.h"
-#include "globaldata.hpp"
 #include "commandoptionparser.hpp"
 #include "command.hpp"
 #include "commandfactory.hpp"
-
-class GlobalData;
+#include "mothurout.h"
 
 class Engine {
 public:
-       Engine() {  cFactory = new CommandFactory();    }
-       virtual ~Engine(){  delete cFactory;  }
+       Engine(); 
+       virtual ~Engine(){}
        virtual bool getInput() = 0;
-//     string getCommand()                     {       return command;         }
-       vector<string> getOptions() {   return options;         }
-       virtual void terminateCommand(int);
+       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;
 };
 
 
@@ -43,8 +44,8 @@ public:
        virtual bool getInput();
        int openedBatch;
 private:
-       GlobalData* globaldata;
        ifstream inputBatchFile;
+       string getNextCommand(ifstream&);
 
 };
 
@@ -56,8 +57,6 @@ public:
        ~InteractEngine();
        virtual bool getInput();
 private:
-       GlobalData* globaldata;
-       vector<string> previousInputs; //this is used to make the arrow keys work
        
 };
 
@@ -69,7 +68,6 @@ public:
        virtual bool getInput();
        int openedBatch;
 private:
-       GlobalData* globaldata;
        string listOfCommands;
        string getNextCommand(string&);