X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.hpp;h=5311da9e1e3aafb3c447b2e51ec411cb29c79d14;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=d4ec3b65a5cdd428c44967ed66ea454d7bc5b2f8;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/engine.hpp b/engine.hpp
index d4ec3b6..5311da9 100644
--- a/engine.hpp
+++ b/engine.hpp
@@ -13,25 +13,27 @@
 
 
 #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;
+	string findMothursPath();
 };
 
 
@@ -43,8 +45,8 @@ public:
 	virtual bool getInput();
 	int openedBatch;
 private:
-	GlobalData* globaldata;
 	ifstream inputBatchFile;
+	string getNextCommand(ifstream&);
 
 };
 
@@ -56,8 +58,6 @@ public:
 	~InteractEngine();
 	virtual bool getInput();
 private:
-	GlobalData* globaldata;
-	vector<string> previousInputs; //this is used to make the arrow keys work
 	
 };
 
@@ -69,7 +69,6 @@ public:
 	virtual bool getInput();
 	int openedBatch;
 private:
-	GlobalData* globaldata;
 	string listOfCommands;
 	string getNextCommand(string&);