// 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.
 

// 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.
 

#ifndef __TREESBLOCK_H
#define __TREESBLOCK_H

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


//
// TreesBlock class
//
class TreesBlock : public NexusBlock
{
	public:
		TreesBlock( TaxaBlock& tb );
		~TreesBlock();
		
		int	 GetNumDefaultTree();
		int	 GetNumTrees();
		std::string GetTreeName( int i );
		std::string GetTreeDescription( int i );
		std::string GetTranslatedTreeDescription( int i );
		int	 IsDefaultTree( int i );
		int	 IsRootedTree( int i );
		void  Report(std::ostream& out );

	protected:
		void Read( NexusToken& token );
		void Reset();
	
		AssocList translateList;
		LabelList treeName;
		LabelList treeDescription;
		BoolVect rooted;
		TaxaBlock& taxa;
		int ntrees;
		int defaultTree;
	
};

#endif