// 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 __TAXABLOCK_H
#define __TAXABLOCK_H


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

//
// TaxaBlock class
//
class TaxaBlock : public NexusBlock
{
	friend class DataBlock;
	friend class AllelesBlock;
	friend class CharactersBlock;
	friend class DistancesBlock;

   // Adding a new data member? Don't forget to:
   // 1. Describe it in the class header comment at the top of "taxablock.cpp"
   // 2. Initialize it (unless it is self-initializing) in the constructor
   //	 and reinitialize it in the Reset function
   // 3. Describe the initial state in the constructor documentation
   // 4. Delete memory allocated to it in both the destructor and Reset function
   // 5. Report it in some way in the Report function

	int ntax;
	LabelList taxonLabels;

public:
   class nosuchtaxon {}; // exception potentially thrown by FindTaxon

private:
   void SetNtax( int n );

protected:
	void Read( NexusToken& token );
	void Reset();

public:
	TaxaBlock();
   virtual ~TaxaBlock();

   void	 AddTaxonLabel( std::string s );
   void	 ChangeTaxonLabel( int i, std::string s );
	int	  FindTaxon( std::string label );
   bool	 IsAlreadyDefined( std::string label );
   int	 GetMaxTaxonLabelLength();
	int	  GetNumTaxonLabels();
	std::string GetTaxonLabel( int i );
	void  Report(std::ostream& out );
};

#endif