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

//	  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.
 

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

//	  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.
 

#ifndef MYNEXUS_H
#define MYNEXUS_H

#include <iostream>
#include <fstream>

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


#include "nexus_defs.hpp"
#include "nexus_token.hpp"
#include "nexus.hpp"
#include "taxa_block.hpp"
#include "trees_block.hpp"
#include "xbull.hpp"

 
class MyNexus : public Nexus
{	struct NoDataFile { };
	public:
		 std::ofstream outf;
		 Nexus *parentNexus;

		MyNexus(Nexus *pb)	{
						parentNexus=pb;
						}
		
		
		bool FileExists( char* fn );

		void ExecuteStarting() {parentNexus->ExecuteStarting();}
		void ExecuteStopping() {parentNexus->ExecuteStarting();}
		void OutputComment( std::string s ) {
			parentNexus->OutputComment(s);
			}
		void EnteringBlock( std::string blockName ) {
			parentNexus->EnteringBlock(blockName);
		}
		
		void SkippingBlock(const std::string & blockName ) const {
			parentNexus->SkippingBlock(blockName);
		}
		
		void DebugReportBlock( NexusBlock& nexusBlock ) {
		 parentNexus->DebugReportBlock(nexusBlock);
		}

		void NexusError(const std::string& msg, std::istream::pos_type pos, long line, long col ) {
			parentNexus->NexusError(msg, pos, line, col);
		}
};


#endif