fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index fd80ad1e9fc786fece31e00525476c453c6c2344..22f118164eb04e7d22c0438e3e42c56b79ed0f3d 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -29,6 +29,8 @@ class Command {
                virtual string getCommandName() = 0;
                virtual string getCommandCategory() = 0;
                virtual string getHelpString() = 0;
+               virtual string getCitation() = 0;
+               virtual string getDescription() = 0;
                
                virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
                virtual vector<string> setParameters() = 0; //to fill parameters
@@ -36,6 +38,7 @@ class Command {
        
                virtual int execute() = 0;
                virtual void help() = 0;
+               void citation() { m->mothurOutEndLine(); m->mothurOut(getCitation()); m->mothurOutEndLine(); }
                virtual ~Command() { }
        
        protected: