X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=command.hpp;h=22f118164eb04e7d22c0438e3e42c56b79ed0f3d;hb=110ed3a070bf6b602cccef89c8626cce033315d3;hp=f65f6cc0fb14ab1d892dbcc5df567c086ca183c9;hpb=5e031adc86a1fc125c4abb3d4048f209d52f9b6d;p=mothur.git

diff --git a/command.hpp b/command.hpp
index f65f6cc..22f1181 100644
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -17,22 +17,36 @@
 #include "optionparser.h"
 #include "validparameter.h"
 #include "mothurout.h"
+#include "commandparameter.h"
+
 
 class Command {
 	
 	public:
-		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
+		Command() {  m = MothurOut::getInstance();   } 
+		
+		//needed by gui
+		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
+		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:
 		MothurOut* m;
-		
 		bool calledHelp;
+			
+		map<string, vector<string> > outputTypes;
+		vector<CommandParameter> parameters;
 	
 		map<string, vector<string> >::iterator itTypes;
 };