// 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 LIKESETTINGS
#define LIKESETTINGS


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

#include <map>
#include "basic_bull.hpp"
#include "models.hpp"
#include "mth_exception.hpp"


namespace bull {
class LikeSettingException :public MTHException {public: LikeSettingException(const char *p) : MTHException(p) {}
};

/*		The purpose of these the settings classes is to provide an interface
	with the program and allow checking that all of the user selections are legal without allocating memory 
	to do the likelihood calculations.	Essentially these are the classes that would be directly affected
	by a lset command.	Once a LScore (or search) are started.	These classes are used to set up the appropriate data
	partitions, parameter alteration information, and the like attributes for the tree and nodes
	LSettings constructor should be called right after the data is read into the file.	
	IMPORTANT -- after being constructed all the taxa names are added to IncludedTaxa, the arguments should be the start and end of the 
	data matrix.  Thus LSettings should be warned if any taxa or data are excluded
	Right now I have it in the FinishCharactersBlock()
*/

class ModSettings{
	bool stationaryModel,useCurrentBrLen;
	double startingBrLen;
	Model *mod;
	PartModIndex ownerOfBlen,ownerOfBlenMod;//change ownerOfBlenMod to vector to allow relaxed clock starting points (multiple modifiers with one model)
	int blenSetting,blenModSetting,numBrLenMod;
	bool hasBrLenMod;
	public :
	ModSettings(Model *);
	void SetUseCurrentBrLen(bool);
	Model *GetModel();
	bool StationaryModel();
	PartModIndex GetBrLenOwner()	{return ownerOfBlen;}
	PartModIndex GetBrLenModOwner() {return ownerOfBlenMod;}
	int GetBLenSetting()	{ return blenSetting;}
	int GetBLenModSetting() { return blenModSetting;}
	bool HasBrLenMod()	{return hasBrLenMod;}
	int GetNumBrLenMod()	{return numBrLenMod;}
};

class PartSettings{
	friend class LikePartSettings;
	public :
	bool AligningSeqs;
	typedef pair<int,int> segment;
	vector<segment> segmentsInPartition;
	
	PartSettings(int start,int end);
	int GetNSegments();
	pair<int,int> GetSegment(int i);
	bool DoingAlignment();
	int GetRawDataSize();
};

class LikePartSettings{
	public :
	int nmodels;
	vector<ModSettings *> modSettings;
	int ModelMixingSetting;
	FreqParamGroup *ModelMixingStartingVals;
	
	LikePartSettings(PartSettings*);
	void SetUseCurrentBrLen(bool);
	int GetNModels();
	Model *GetModel(int i);
	bool AllStationaryModels();
	int GetModelMixingParamSettings()	{return ModelMixingSetting;}
	double GetStartingFreqnOfThisModel(int j);
	PartModIndex GetBrLenOwner(int j)	{assert(j < nmodels);
		return modSettings[j]->GetBrLenOwner();
		}
	PartModIndex GetBrLenModOwner(int j)	{assert(j < nmodels);
		return modSettings[j]->GetBrLenModOwner();
		}
	int GetBLenSetting(int i)	{return modSettings[i]->GetBLenSetting();}
	int GetBLenModSetting(int i)	{return modSettings[i]->GetBLenModSetting();}
	bool HasBrLenMod(int j) {return modSettings[j]->HasBrLenMod();}
	int GetNumBrLenMod(int m)	{return modSettings[m]->GetNumBrLenMod();}
};

class DataSettings {
	friend class LikeSettings;
	friend class ParsSettings;
	protected :
	int nDataPartitions;
	vector<std::string> IncludedTaxa;
	bool userInputBrLen;
	public:
	vector<PartSettings *> dataPartSettings;
	int GetNDataPartitions();
	int GetRawDataSize(int i);
	bool TreatGapsAsFifth() {return false;}
	void CopyAPartitionsRawData(short *destination,map<std::string,EncodedChars *>&rawData,int num,int taxnum);
	int GetNIncludedTaxa()	{return IncludedTaxa.size();}
	bool DoingAlignment();
	bool DoingAlignment(int i);
	std::string GetNameOfNthIncludedTaxon(int i)	{return IncludedTaxa[i];}
	void AddTaxon(std::string i)	{IncludedTaxa.push_back(i);}
};

class LikeSettings {
	bool summingOverAllAncStates;
	public:
	bool optimizingBrLens;
	bool maximize;//true if ML false if just scoring one instantiation of parameters
	int maxPasses;//max number of smoothing passes for each of the parameters sets
	double delta;// smallest change in likelihood score that will keep optimization going
	DataSettings *sharedDataSettings;
	
	bool useRSBranchLengths;//Rogers Swofford approximation
	bool sumOverAncStates;// whether using Felsensteins pruning vs calculating the like of one reconstruction
	public:
	vector<LikePartSettings *> partSettings;

	LikeSettings(DataSettings *);//see note above
	void SetUseCurrentBrLen(bool);
	int GetNModelsInPart(int i);
	Model *GetModel(int i,int j);
	bool SummingOverAllAncStates();
	bool AllStationaryModels();
	int GetModelMixingParamSettings(int i)	{return partSettings[i]->GetModelMixingParamSettings();}
	double GetStartingFreqnOfThisModel(int i,int j) {return partSettings[i]->GetStartingFreqnOfThisModel(j);}
	int GetNSetsOfBranchLengths();
	PartModIndex GetOwnerOfNthSetOfBrLengths(int ownint);
	PartModIndex GetOwnerOfBrLens(int p,int	 m);
	int GetNSetsOfBranchLengthModifiers();
	PartModIndex GetOwnerOfNthSetOfBrLengthModifiers(int ownint);
	PartModIndex GetOwnerOfBrLenModifiers(int p,int	 m);
	int GetBLenSetting(int p,int m)		{return partSettings[p]->GetBLenSetting(m);}
	int GetBLenModSetting(int p,int m)	{return partSettings[p]->GetBLenModSetting(m);}
	bool HasBrLenMod(int p,int m)	{return partSettings[p]->HasBrLenMod(m);}
	int GetNumBrLenMod(int p,int m) {return partSettings[p]->GetNumBrLenMod(m);}
};

class ParsSettings {
	ParsSettings(DataSettings *);//see note above
	
};

} // namespace bull

#endif