reworked amova / homova / anosim

[mothur.git] / engine.hpp

diff --git a/engine.hpp b/engine.hpp
index 74687d2398c84a532b0ba6c68e17ed8cff1f7cf0..d5846ba65fc287a6b7de3e7f5f6cfaa57a7f5951 100644 (file)
--- a/engine.hpp
+++ b/engine.hpp
@@ -27,12 +27,16 @@ public:
        virtual ~Engine(){}
        virtual bool getInput() = 0;
        virtual string getCommand();
-       virtual string getOutputDir()   {       return cFactory->getOutputDir();  }
+       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;
+       string findMothursPath();
 };
 
 
@@ -46,6 +50,7 @@ public:
 private:
        GlobalData* globaldata;
        ifstream inputBatchFile;
+       string getNextCommand(ifstream&);
 
 };