// 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 SETSOFLIKEATTRIBUTES
#define SETSOFLIKEATTRIBUTES


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

#include "like_attributes.hpp"
#include "part_mod_index.hpp"
namespace bull {

class SetOfLikeAttr
{
	public:
		
		SetOfLikeAttr(int i);	
		~SetOfLikeAttr();	
		Model *GetModel(int p,int m) {return likeAttribs[p][m]->GetModel();}
		void SetNumModsInPart(int partnum,int modnum);
		void AddLikeAtt(int p,int m,LikeAttr *);
		int GetNParts() {return nparts;}
		int GetNModels(int i) {return nmods[i];}
		LikeAttr *GetLikeAtt(int p,int m)	{return likeAttribs[p][m];}
		SetOfLikeAttr *Copy();

	protected:
		int nmodparts; // number of partiotions+models
		int nparts;// number of partitions
		int *nmods;
		LikeAttr*** likeAttribs;

};

class SetOfTreeSimAttr
{
	public:
		int maxReps,nparts,*nmods,*nChar;

		SetOfTreeSimAttr(int i);
		~SetOfTreeSimAttr();
		
		void SetNumModsInPart(int partnum,int modnum);
		void AddAtt(int p,int m,TreeSimAttr *tsa);
		int GetNParts() {return nparts;}
		int GetNModels(int i) {return nmods[i];}
		Model *GetModel(int p,int m) {return simAttribs[p][m]->GetModel();}
		TreeSimAttr *GetSimAtt(int p,int m) {return simAttribs[p][m];}
		
		void SetModelMixingParam(int i,FreqParamGroup *mmp) {
			assert(modelMixingParam && i < nparts);
			modelMixingParam[i]=mmp;
			}
		void InitializeModelMixingParams();
		void InitializeLikeAttrStatics(int partnum,int modn);
		int GetNCharInSimAttr(int p,int m) //should be NCharInEachDataSet * maxReps
			{return simAttribs[p][m]->GetNChar();}
		int GetNCharInEachDataSet(int p)	{return nChar[p];}
		void SetNCharInEachDataSet(int p,int nc) {
			nChar[p]=nc;
		}
	
		int GetNStates(int p,int m) {
			return simAttribs[p][m]->GetNStates();
		}
		void PrintModel(std::ostream &usrstream);
		bool GetOwnsBrLengths(bull::PartModIndex pmi)	{
			return simAttribs[pmi.partNum][pmi.modNum]->GetOwnsBrLen();
		}

	protected:
		int nmodparts;//number of partitions+models, and number of partitions
		TreeSimAttr*** simAttribs;
		FreqParamGroup **modelMixingParam;	

	friend class Tree;
};
} // namespace bull
#endif