// This file is part of BULL, a program for phylogenetic simulations
// most of the code was written by Mark T. Holder.

//	This program is for internal use by the lab of Dr. Tandy Warnow only.
//	Do not redistribute the code.  It is distributed in the hope that it will be useful,
//	but WITHOUT ANY WARRANTY; without even the implied warranty of
//	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
//
//	Some of the code is from publically available source by Paul Lewis, Ziheng Yang, 
//	John Huelsenbeck, David Swofford , and others  (as noted in the code).
//	In fact the main structure of the program was created by modifying Paul Lewis' 
//	basiccmdline.cpp from his NCL
//
//	This code was used in Mark's dissertation, some changes were made in order to 
//	get it to compile on gcc.  It is possible that this porting introduced bugs (very
//	little debugging has been done on UNIX platforms).	I would suggest checking 
//	the simulator by generating data on trees with short branches, etc.
#if !defined(BULL_IO_HPP)
#define BULL_IO_HPP

#include <fstream>
#include <string>

#if defined HAVE_CONFIG_H && HAVE_CONFIG_H
#	include <config.h>
#endif 

namespace bull {


class BullIO
{
	public:
		BullIO();
		virtual ~BullIO();

		virtual void print(const std::string &msg, bool linefeed = true ,bool flusht = true) const;
		void printMessage(bool linefeed = true , bool flusht = true) {
			this->print(this->message, linefeed, flusht);
			this->message.clear();
		}
		virtual bool userSaysOk(const std::string & mb_message, const std::string & mb_title, bool defaultVal);

		std::string message;

	protected:
		bool inf_open;
		bool logf_open;
		mutable std::ofstream logf;
};

} //namespace bull 

#endif