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

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index fd80ad1e9fc786fece31e00525476c453c6c2344..04285feff832088547c64a0f43da9c70dd7b1db5 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -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: