X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=command.hpp;h=22f118164eb04e7d22c0438e3e42c56b79ed0f3d;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=6d734e00b5dd1ef8cc3a4239a8c0b10ad18f8acc;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/command.hpp b/command.hpp
index 6d734e0..22f1181 100644
--- a/command.hpp
+++ b/command.hpp
@@ -1,6 +1,6 @@
 #ifndef COMMAND_HPP
 #define COMMAND_HPP
-
+//test2
 /*
  *  command.h
  *  
@@ -10,17 +10,45 @@
  *
  */
 
-/*This class is a parent to all the command classes.  It has one pure int execute(). */
+/*This class is a parent to all the command classes.  */
 
-using namespace std;
 
-#include <iostream>
-#include <fstream>
+#include "mothur.h"
+#include "optionparser.h"
+#include "validparameter.h"
+#include "mothurout.h"
+#include "commandparameter.h"
 
 
 class Command {
+	
 	public:
+		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