// 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 __NEXUS_H
#define __NEXUS_H

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

class Nexus;

//
// NexusBlock class
//
class NexusBlock
{
	friend class Nexus;

protected:
	bool isEmpty;
	Nexus* nexus;
	NexusBlock* next;
	std::string id;

	virtual void Read( NexusToken& token ) = 0;
	virtual void Reset() = 0;

public:
	mutable std::string errormsg;

	NexusBlock();
	virtual ~NexusBlock();
	
	void SetNexus( Nexus* nxsptr );

	std::string GetID();
	bool IsEmpty();

   virtual int CharLabelToNumber( std::string s );
   virtual int TaxonLabelToNumber( std::string s );

	virtual void SkippingCommand( std::string commandName );
	virtual void Report(std::ostream& out ) = 0;
};

//
// Nexus class
//
class Nexus
{

protected:
	NexusBlock* blockList;

public:
	Nexus();
	virtual ~Nexus();

	bool BlockListEmpty();
	void Add( NexusBlock* newBlock );
	void Detach( NexusBlock* newBlock );
	void Execute( NexusToken& token );

	virtual void DebugReportBlock( NexusBlock& nexusBlock );
	
	char* NCLNameAndVersion();
	char* NCLCopyrightNotice();
	char* NCLHomePageURL();

	// hooks implemented as pure virtual functions
	virtual void ExecuteStarting() = 0;
	virtual void ExecuteStopping() = 0;
	virtual void EnteringBlock( std::string blockName ) = 0;
	virtual void OutputComment( std::string comment ) = 0;
	virtual void NexusError(const std::string& msg, std::istream::pos_type pos, long line, long col ) = 0;
	virtual void SkippingBlock(const std::string & blockName ) const = 0;
};

#endif