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#ifndef ___LIKELIHOOD_COMPUTATION_GL
#define ___LIKELIHOOD_COMPUTATION_GL
#include "definitions.h"
#include "computePijComponent.h"
#include "sequenceContainer.h"
#include "suffStatComponent.h"
#include "unObservableData.h"
#include "computeUpAlg.h"
namespace likelihoodComputationGL {
MDOUBLE getTreeLikelihoodAllPosAlphTheSame(const tree& tr,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& spVVec,
const distribution * distGain, const distribution * distLoss,
const Vdouble * const weights,
unObservableData *unObservableData_p =NULL);
void fillPijAndUp(const tree& tr,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& spVVec,
const distribution * distGain, const distribution * distLoss,
vector<computePijGam>& pi_vec,
vector<suffStatGlobalGam>& ssc_vec,
vector<computeUpAlg>& cup_vec);
MDOUBLE getProbOfPosUpIsFilledSelectionGam(const int pos,const tree& tr,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& spVVec, // only needed for sp.freq(let)
const suffStatGlobalGamPos& cup,
const distribution * distGain, const distribution * distLoss);
MDOUBLE getTreeLikelihoodFromUp2(const tree& tr,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& spVVec,// only needed for sp.freq(let)
const suffStatGlobalGam& cup,
const distribution * distGain, const distribution * distLoss,
const Vdouble * weights,
unObservableData *unObservableData_p,
Vdouble* posLike =NULL);
MDOUBLE getTreeLikelihoodFromUp2(const tree& tr,
const sequenceContainer& sc,
const vector<vector<stochasticProcess*> >& spVVec,// only needed for sp.freq(let)
const vector<suffStatGlobalGam>& cup_vec,
const distribution * distGain, const distribution * distLoss,
const Vdouble * weights,
unObservableData *unObservableData_p,
Vdouble* posLike =NULL);
// Error
//MDOUBLE getTreeLikelihoodAllPosAlphTheSameNoComputeUp(const tree& tr,
// const sequenceContainer& sc,
// const vector<vector<stochasticProcess*> >& spVVec,
// const distribution * distGain, const distribution * distLoss,
// unObservableData *unObservableData_p);
///********************************************************************************************
//un-obervable data
//*********************************************************************************************/
//// used to fill the likelihood for the unobservable for each category
// doubleRep getLofPos(const int pos,
// const tree& tr,
// const sequenceContainer& sc,
// const computePijGam& pi,
// const stochasticProcess& sp,
// Vdouble& likePerCat); // all the likdelhoodsPerCat and rateProb are filled
//// likelihood computation - full data (1)
// MDOUBLE getTreeLikelihoodAllPosAlphTheSame(const tree& tr,
// const sequenceContainer& sc,
// const stochasticProcess& sp,
// const Vdouble * const weights,
// Vdouble *pLforMissingDataPerCat=NULL);
//// likelihood computation - per pos (1.1)
// doubleRep getLofPos(const int pos, // this function is used
// const tree& tr, // when gamma, and the br-len
// const sequenceContainer& sc, // are the same for all pos.
// const computePijGam& pi,
// const stochasticProcess& sp,
// Vdouble *pLforMissingDataPerCat=NULL);
//// likelihood computation - per pos, per cat (1.1.1)
// doubleRep getLofPos(const int pos, // this function is used
// const tree& tr, // when the br-len
// const sequenceContainer& sc, // are the same for all
// const computePijHom& pi, // positions.
// const stochasticProcess& sp);
//
// Vdouble getLofPosPerCat(const int pos, // used when the likelihood given each category is needed, not only the sum
// const tree& tr,
// const sequenceContainer& sc,
// const computePijGam& pi,
// const stochasticProcess& sp);
};
#endif
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