X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=command.hpp;h=04285feff832088547c64a0f43da9c70dd7b1db5;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=97701aa0017ccaf821546f06e40df41cad6233e5;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/command.hpp b/command.hpp
index 97701aa..04285fe 100644
--- a/command.hpp
+++ b/command.hpp
@@ -17,20 +17,38 @@
 #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;
 };
 
 #endif