fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index 6a1a4deea6c1df252a627fa827bb33a8f49b439c..f5e09042234f1c39ac8010f859e6f69708871dc3 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -30,14 +30,16 @@ class Command {
                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->mothurOut(getCitation()); }
+               void citation() { m->mothurOutEndLine(); m->mothurOut(getCitation()); m->mothurOutEndLine(); }
                virtual ~Command() { }
        
        protected: