fixed get.lienage and remove.lineage bug with confidence scores that are floats....

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index b6bf5cd397644ad215a8a88f269f461d04add112..93669ba7babe40f9b5889e953bf943d362cd7bbe 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -18,15 +18,23 @@
 #include "validparameter.h"
 #include "mothurout.h"
 
+
 class Command {
        
        public:
-               Command() {  m = MothurOut::getInstance();  }
+               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;
+               bool calledHelp;
+       
+               map<string, vector<string> >::iterator itTypes;
 };
 
 #endif