X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.hpp;h=d5846ba65fc287a6b7de3e7f5f6cfaa57a7f5951;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=276d29267a298dd7c2f52c9b550b3d9b37c555a0;hpb=36a8526766106bce1412e530e99f9c699dd59105;p=mothur.git

diff --git a/engine.hpp b/engine.hpp
index 276d292..d5846ba 100644
--- a/engine.hpp
+++ b/engine.hpp
@@ -17,22 +17,26 @@
 #include "commandoptionparser.hpp"
 #include "command.hpp"
 #include "commandfactory.hpp"
-#include "errorchecking.h"
-
-
-using namespace std;
+#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;
+	string findMothursPath();
 };
 
 
@@ -46,6 +50,7 @@ public:
 private:
 	GlobalData* globaldata;
 	ifstream inputBatchFile;
+	string getNextCommand(ifstream&);
 
 };
 
@@ -61,4 +66,18 @@ private:
 };
 
 
+class ScriptEngine : public Engine {
+public:
+	ScriptEngine(string, string);
+	~ScriptEngine();
+	virtual bool getInput();
+	int openedBatch;
+private:
+	GlobalData* globaldata;
+	string listOfCommands;
+	string getNextCommand(string&);
+
+};
+
+
 #endif