X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.hpp;h=0e7721a1ba1a51566eaab52b909604a50d5a70eb;hb=a250de2144fa57c7f18152251bf726303522119b;hp=df4e08d879103c95e2959130eda2d19296f0a0f3;hpb=a5afca18544555fba2d9c3670ad1f8574916b0a0;p=mothur.git

diff --git a/engine.hpp b/engine.hpp
index df4e08d..0e7721a 100644
--- a/engine.hpp
+++ b/engine.hpp
@@ -17,6 +17,7 @@
 #include "commandoptionparser.hpp"
 #include "command.hpp"
 #include "commandfactory.hpp"
+#include "mothurout.h"
 
 class GlobalData;
 
@@ -26,11 +27,15 @@ public:
 	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&);
 
 };