// 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 __NEXUSDEFS_H
#define __NEXUSDEFS_H



#include <string>
#include <vector>
#include <set>
#include <map>

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


typedef std::vector<bool> BoolVect;
typedef std::vector<int> IntVect;
typedef std::vector<std::string> LabelList;
typedef std::set< int, std::less<int> > IntSet;
typedef std::map< int, LabelList, std::less<int> > LabelListBag;
typedef std::map< std::string, std::string, std::less<std::string> > AssocList;
typedef std::map< std::string, IntSet, std::less<std::string> > IntSetMap;
typedef std::vector<LabelList> AllelesVect;

#endif