// 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 __NEXUSTOKEN_H
#define __NEXUSTOKEN_H

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

// NexusToken class
//
class NexusToken
{
	std::istream&	in;
	int		   newlineType;
	std::istream::pos_type filepos;
	long	   fileline;
	long	   filecol;
	std::string token;
	std::string comment;
	char	   saved;
	bool	   atEOF;
	bool	   atEOL;
	char	   special;
	int		   labileFlags;

protected:

	void AppendToComment( char ch );
	void AppendToToken( char ch );
	char GetNextChar();
	void GetComment();
	void GetCurlyBracketedToken();
	void GetDoubleQuotedToken();
	void GetQuoted();
	void GetParentheticalToken();
	bool IsPunctuation( char ch );
	bool IsWhitespace( char ch );
	bool IsConsistentWithFirstPartOfSciNotation();
public:
	enum {
		saveCommandComments	  = 0x0001,
		parentheticalToken	  = 0x0002,
		curlyBracketedToken	  = 0x0004,
		doubleQuotedToken	  = 0x0008,
		singleCharacterToken  = 0x0010,
		newlineIsToken		  = 0x0020,
		tildeIsPunctuation	  = 0x0040,
	  useSpecialPunctuation = 0x0080
	};

   std::string errormsg;

	NexusToken(std::istream& i );
	virtual ~NexusToken();

	////////////////////////////////////////////////////////////////////////////
	/// true if the input stream is exhausted or out of commission
	bool	   AtEOF() const {
		return atEOF;
	}
	////////////////////////////////////////////////////////////////////////////
	/// true iff the last call to GetNextToken encountered the newline 
	/// AND the newlineIsToken labile flag was in effect.
	bool	   AtEOL() const {
		return atEOL;
	}
	long	   GetFileColumn() const {
		return filecol;
	}
	std::iostream::pos_type GetFilePosition() const {
		return filepos;
	}
	long	   GetFileLine() const {
		return fileline;
	}
	const std::string & GetToken() const {
		return token;
	}
	std::size_t GetTokenLength() const {
		return GetToken().length();
	}
	
	bool	   Abbreviation( std::string s );
	bool	   Begins( std::string s, bool respect_case = false );
	void	   BlanksToUnderscores();
	bool	   Equals( std::string s, bool respect_case = false );
	void	   GetNextToken();
	bool	   IsPlusMinusToken();
	bool	   IsPunctuationToken();
	bool	   IsWhitespaceToken();
	void	   ReplaceToken( const std::string s );
	void	   ResetToken();
	void	   SetSpecialPunctuationCharacter( char c );
	void	   SetLabileFlagBit( int bit );
	bool	   StoppedOn( char ch );
	void	   StripWhitespace();
	void	   Write(std::ostream& out );
	void	   Writeln(std::ostream& out );
//	MTH additions
	bool	IsInteger();
	long	GetLongEquivalent();//should be called after IsInteger returns true

	// virtual function that should be overridden in derived classes
	virtual void OutputComment( std::string& msg );
};

#endif