// 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.
 

#include "like_attribute_sets.hpp"

using namespace bull;

SetOfLikeAttr::SetOfLikeAttr(int i)
{	assert(i>0);
	nparts=i;
	likeAttribs=new LikeAttr**[nparts];
	nmods=new int[nparts];
	for (int j=0;j < nparts;j++)
		{likeAttribs[j]=NULL;
		nmods[j]=0;
		}
	nmodparts=0;
}
SetOfTreeSimAttr::SetOfTreeSimAttr(int i)
{	assert(i>0);
	nparts=i;
	simAttribs=new TreeSimAttr**[nparts];
	nmods=new int[nparts];
	for (int j=0;j < nparts;j++)
		{simAttribs[j]=NULL;
		nmods[j]=0;
		}
	nmodparts=0;
	nChar=new int[i];
	modelMixingParam=new FreqParamGroup *[i];
}
	

SetOfTreeSimAttr::~SetOfTreeSimAttr()
{	delete [] modelMixingParam;//partitions responsible for deleting the acutal parameters
	delete [] nChar;
	assert(nmods && simAttribs);
	for (int i=0;i < nparts;i++)
		{
		assert(simAttribs[i]);
		for (int j=0;j < nmods[i];j++)
			{assert(simAttribs[i][j]);
			delete simAttribs[i][j];
			}
		delete [] simAttribs[i];
		}
	delete	[]simAttribs;
	delete nmods;
}

void SetOfTreeSimAttr::SetNumModsInPart(int partnum,int modnum)
{	nmodparts+=(modnum-nmods[partnum]);
	for (int i=0;i < nmods[partnum];i++)
		delete simAttribs[partnum][i];
	delete [] simAttribs[partnum];
	nmods[partnum]=modnum;
	simAttribs[partnum]=new TreeSimAttr*[modnum];
	for (int i=0;i < modnum;i++)
		*(simAttribs[partnum]+i)=NULL;
}

void SetOfTreeSimAttr::AddAtt(int p,int m,TreeSimAttr *tsa)
{	assert(p < nparts);
	assert(m < nmods[p]);
	delete simAttribs[p][m];
	simAttribs[p][m]=tsa;
}

void SetOfTreeSimAttr::PrintModel(std::ostream &usrstream)
{	for (int np=0;np < nparts;np++)
		for (int nm=0;nm < nmods[np];nm++)
			simAttribs[np][nm]->GetModel()->PrintPAUPLsetCommand();
}


SetOfLikeAttr::~SetOfLikeAttr()
{	assert(nmods && likeAttribs);
	for (int i=0;i < nparts;i++)
		{
		assert(likeAttribs[i]);
		for (int j=0;j < nmods[i];j++)
			{assert(likeAttribs[i][j]);
			delete likeAttribs[i][j];
			}
		delete [] likeAttribs[i];
		}
	delete	[]likeAttribs;
	delete [] nmods;
	
}

void SetOfTreeSimAttr::InitializeModelMixingParams()
{	for (int i=0;i < nparts;i++)
		if (nmods[i]>1)
			{assert(modelMixingParam && modelMixingParam[i]);
			modelMixingParam[i]->Initialize();
			}
}

void SetOfTreeSimAttr::InitializeLikeAttrStatics(int partnum,int modn)
{	LikeAttr::currNChar=GetNCharInEachDataSet(partnum);
	LikeAttr::currNStates=GetNStates(partnum,modn);
	LikeAttr::currModelDirty=true;//TEMPORARY
}			
void SetOfLikeAttr::SetNumModsInPart(int partnum,int modnum)
{	nmodparts+=(modnum-nmods[partnum]);
	for (int i=0;i < nmods[partnum];i++)
		delete likeAttribs[partnum][i];
	delete [] likeAttribs[partnum];
	nmods[partnum]=modnum;
	likeAttribs[partnum]=new LikeAttr*[modnum];
	for (int i=0;i < modnum;i++)
		*(likeAttribs[partnum]+i)=NULL;
}

void SetOfLikeAttr::AddLikeAtt(int p,int m,LikeAttr *la)
{	assert(p < nparts);
	assert(m < nmods[p]);
	delete likeAttribs[p][m];
	likeAttribs[p][m]=la;
}