added pipeline commands which involved change to command factory and command class...

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index 27355dddd933834108371d18cf66c27c4a29763b..97701aa0017ccaf821546f06e40df41cad6233e5 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -16,11 +16,21 @@
 #include "mothur.h"
 #include "optionparser.h"
 #include "validparameter.h"
+#include "mothurout.h"
 
 class Command {
+       
        public:
+               Command() {  m = MothurOut::getInstance();  }
+               virtual vector<string> getValidParameters() = 0;
+               virtual vector<string> getRequiredParameters() = 0; //adding "or" as the last element indicates one of the previous is needed
+               virtual vector<string> getRequiredFiles() = 0; //adding "or" as the last element indicates one of the previous is needed
+               virtual map<string, vector<string> > getOutputFiles() = 0; //file type to names
                virtual int execute() = 0;
                virtual void help() = 0;
+               virtual ~Command() { }
+       protected:
+               MothurOut* m;
 };
 
 #endif