// 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 BASICBULLDEFS
#define BASICBULLDEFS

#include <vector>

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

namespace bull {

#ifdef ALLOWMULTIHITS
	const unsigned N_MUT_PARAMS = 10;
	const unsigned MULTI_HIT_PARAM_INDEX = 9;
#else 
	const unsigned N_MUT_PARAMS = 9;
#endif

extern const double DEFAULT_START_EDGE_LEN;
extern const double BULL_SMALL_DBL;
extern const double BULL_BIG_DBL;

enum GenCode {MITO , NUCLEAR};
enum Criterion {MAX_LIKE, PARSIMONY , BAYESIAN};
enum AnalysisMode {INFERENCE, SIMULATION};

typedef std::vector<double> DblVector;
typedef std::vector<DblVector> DblMatrix;
#define CONDENSE_MATRICES 1



} // namespace bull




#endif