added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index fd80ad1e9fc786fece31e00525476c453c6c2344..f5e09042234f1c39ac8010f859e6f69708871dc3 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -29,13 +29,17 @@ 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 string getOutputFileNameTag(string, string) = 0;  //we may not know the complete filename, because some commands use info from the file to create the output file name (ie label). but we do the ending tag which should be enough to find the output file name from a list. Allows for optional passing of the inputFileName for the commands that require its extension.
                virtual vector<string> setParameters() = 0; //to fill parameters
                virtual vector<CommandParameter> getParameters() { return parameters; }
        
                virtual int execute() = 0;
                virtual void help() = 0;
+               void citation() { m->mothurOutEndLine(); m->mothurOut(getCitation()); m->mothurOutEndLine(); }
                virtual ~Command() { }
        
        protected: