X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=command.hpp;h=6a1a4deea6c1df252a627fa827bb33a8f49b439c;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=2d1981aa4cca8d7e608e3708750fc079600d1265;hpb=f6c7165727bc17a5fbbcbb774d75ccffeb7f3da5;p=mothur.git

diff --git a/command.hpp b/command.hpp
index 2d1981a..6a1a4de 100644
--- a/command.hpp
+++ b/command.hpp
@@ -17,23 +17,35 @@
 #include "optionparser.h"
 #include "validparameter.h"
 #include "mothurout.h"
-#include "currentfile.h"
+#include "commandparameter.h"
+
 
 class Command {
 	
 	public:
-		Command() {  m = MothurOut::getInstance(); currentFiles = CurrentFile::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 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->mothurOut(getCitation()); }
 		virtual ~Command() { }
+	
 	protected:
 		MothurOut* m;
-		CurrentFile* currentFiles;
 		bool calledHelp;
+			
+		map<string, vector<string> > outputTypes;
+		vector<CommandParameter> parameters;
 	
 		map<string, vector<string> >::iterator itTypes;
 };