added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index 0e7721a1ba1a51566eaab52b909604a50d5a70eb..5311da9e1e3aafb3c447b2e51ec411cb29c79d14 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -13,14 +13,11 @@
 
 
 #include "mothur.h"
-#include "globaldata.hpp"
 #include "commandoptionparser.hpp"
 #include "command.hpp"
 #include "commandfactory.hpp"
 #include "mothurout.h"
 
-class GlobalData;
-
 class Engine {
 public:
        Engine(); 
@@ -36,6 +33,7 @@ protected:
        vector<string> options;
        CommandFactory* cFactory;
        MothurOut* mout;
+       string findMothursPath();
 };
 
 
@@ -47,7 +45,6 @@ public:
        virtual bool getInput();
        int openedBatch;
 private:
-       GlobalData* globaldata;
        ifstream inputBatchFile;
        string getNextCommand(ifstream&);
 
@@ -61,7 +58,7 @@ public:
        ~InteractEngine();
        virtual bool getInput();
 private:
-       GlobalData* globaldata;
+       
 };
 
 
@@ -72,7 +69,6 @@ public:
        virtual bool getInput();
        int openedBatch;
 private:
-       GlobalData* globaldata;
        string listOfCommands;
        string getNextCommand(string&);