// 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(BULLCMDLINE_H)
#define BULLCMDLINE_H

#include <ostream>

#define THREETAXONHACK

#if defined HAVE_CONFIG_H && HAVE_CONFIG_H
#	include <config.h>
#endif 
#if defined HAVE_UNISTD_H && HAVE_UNISTD_H
#	include <unistd.h>
#elif defined HAVE_SYS_TYPES_H && HAVE_SYS_TYPES_H
#	include <sys/types.h>
#endif



#include "basic_bull.hpp"
#include "bull_io.hpp"
#include "bull_listener.hpp"
#include "bull_parsers.hpp"
#include "char_encoding.hpp"
#include "my_nexus.hpp"
#include "encoded_chars.hpp"
#include "util.hpp"
#include "tree.hpp"
#include "ssrf_codon_sub_mod.hpp"
#include "settings.hpp"


#define COMMAND_MAXLEN	255

namespace bull {
class NoSuchTree : public MTHException { public :
	NoSuchTree() : MTHException() {}
	NoSuchTree(const char *c) :MTHException(c) { }
	};

class NoModel : public MTHException { public :
	NoModel() : MTHException() {}
	NoModel(const char *c) :MTHException(c) { }
	};

class BullKernel;
class Bull:  public NexusBlock, public Nexus, public BullListener
{
	public:
		Bull();
		virtual ~Bull();
		void OutputComment( std::string s );
		void ExitingBlock( std::string blockName );
		void EnteringBlock( std::string blockName );
		void HandleNextCommand();
		void NexusError(const std::string& msg, std::istream::pos_type pos, long line, long col );
		void PreprocessNextCommand();
		void ExecuteStarting() {}
		void ExecuteStopping() {}
		void Report(std::ostream& out );
		void Run(char *);
		void SkipBlock(NexusToken &, const std::string & blockName) const;
		void SkippingBlock(const std::string & blockName) const;
		void SkippingCommand( std::string commandName );

	protected:
		void deleteNexusBlocks();
		void FactoryDefaults();
		void FinishTaxaBlock();
		void FinishTreesBlock();

		bool FileExists( const char* fn );
		Tree *FindTreeFromName(std::string);
		std::string GetFileName( NexusToken& token );
		long GetLongInteger( NexusToken& token );
		double	GetDouble( NexusToken& token );
		EncodingType Bull::InterpretOutputType(NexusToken &token);
		void RequireTokenAndAdvance(NexusToken & token, const char *expected, const char *cmd);
		void RequireSemicolon(NexusToken & token, const char *cmd) const;
		void ThrowNoSemicolon(NexusToken & token, const char *cmd) const;

		void HandleEndblock( NexusToken& token );
		void HandleExecute( NexusToken& token );
		void HandleExecuteBullBlocksInFile( NexusToken& tok );
		void HandleLog( NexusToken& token );
		void HandleGetTrees(NexusToken& token );
		void HandleCodLikeStartVal(NexusToken& token);
		void HandleSimulate(NexusToken& token );

		
		void ParseGetTrees(GetTreesOpts *, NexusToken& ttoken) const;
		void ParseCodLikeStartValCommand(CodLikeStartOpts *, NexusToken& ttoken) const;
		SimulateOpts ParseSimulateCommand(NexusToken& token) const;
		
		void ResetBlocks();
		void Read( NexusToken& token );
		void Reset();
		void TryAdvancedCommands(NexusToken &token);
		void WriteSimulations(int num,Tree *t,std::string outpfn,std::string paupblockfn,int outputEncodingType,int totRepNum,long seedAtBeg,int simCondNum,bool autoPaup=false);


		mutable BullIO ioObject;
		bool quit_now;
		char next_command[COMMAND_MAXLEN+1]; // used to store the command that is being parsed.

		TreesBlock * trees_block; ///most recent NexusBlock with tree descriptions
		TaxaBlock * taxa_block;
		BullKernel * kernel;		
};

} //namespace bull 


#endif