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// $Id: siteSpecificRate.h 3428 2008-01-30 12:30:46Z cohenofi $
#ifndef ___SITE_SPECIFIC_RATE_GL_
#define ___SITE_SPECIFIC_RATE_GL_
#include "definitions.h"
#include "tree.h"
#include "sequenceContainer.h"
#include "stochasticProcess.h"
#include "computePijComponent.h"
//#include "likelihoodComputationGL.h"
// the function returns the total log-likelihood of the rates.
// it is used for computing the rates, when there is one tree common to
// all positions and 1 stochastic process common to all position.
namespace siteSpecificRateGL {
MDOUBLE computeML_siteSpecificRate(Vdouble & ratesV,
Vdouble & likelihoodsV,
const sequenceContainer& sd,
const stochasticProcess& sp,
const tree& et,
const MDOUBLE maxRate=20.0f,
const MDOUBLE tol=0.0001f);
// this function is the same as the one above, but here, each site can have its
//own tree, or its own stochastic process.
//etVec: a vector of possible trees.
//spVec: a vector of possible stochastic processes.
//treeAttributesVec: defines which tree is assigned to a specific position.
//NOTE: the possible attributes are 1,2..., so that the tree for position i
//is etVec[treeAttributesVec[i]-1]
//The same is true for the stochastic process atributes vector.
MDOUBLE computeML_siteSpecificRate(Vdouble & ratesV,
Vdouble & likelihoodsV,
const Vint& spAttributesVec,
const Vint& treeAttributesVec,
const vector<tree> & etVec,
const vector<const stochasticProcess *> & spVec,
const sequenceContainer& sc,
const MDOUBLE maxRate,
const MDOUBLE tol);
// this function is the same as the one above, but here,
// there are only tree attributes.
MDOUBLE computeML_siteSpecificRate(Vdouble & ratesV,
Vdouble & likelihoodsV,
const Vint& treeAttributesVec,
const vector<tree> & etVec,
const stochasticProcess& sp,
const sequenceContainer& sc,
const MDOUBLE maxRate,
const MDOUBLE tol);
// this function is the same as the one above, but here,
// there are only stochastic process attributes.
MDOUBLE computeML_siteSpecificRate(Vdouble & ratesV,
Vdouble & likelihoodsV,
const Vint& spAttributesVec,
const tree & et,
const vector<const stochasticProcess* > & spVec,
const sequenceContainer& sc,
const MDOUBLE maxRate,
const MDOUBLE tol);
void computeML_siteSpecificRate(int pos,
const sequenceContainer& sc,
const stochasticProcess& sp,
const tree &et,
MDOUBLE& bestRate,
MDOUBLE& posL,
const MDOUBLE maxRate,
const MDOUBLE tol);
// BAYESIAN PART
// 1 sequence container, 1 tree, 1 position
void computeEB_EXP_siteSpecificRate(int pos,
const sequenceContainer& sc,
const stochasticProcess& sp,
const computePijGam& cpg,
const tree &et,
MDOUBLE& bestRate,
MDOUBLE & stdRate,
MDOUBLE & lowerConf,
MDOUBLE & upperConf,
const MDOUBLE alphaConf,
VVdouble* LpostPerCat=NULL,
Vdouble* pLforMissingDataPerCat=NULL);
// 1 stochastic process, 1 tree, all positions
void computeEB_EXP_siteSpecificRate(Vdouble & ratesV,
Vdouble & stdV,
Vdouble & lowerBoundV,
Vdouble & upperBoundV,
const sequenceContainer& sc,
const stochasticProcess& sp,
const tree& et,
const MDOUBLE alphaConf,
VVdouble* LpostPerCat=NULL,
Vdouble* pLforMissingDataPerCat=NULL);
// many stochastic process, many tree, all positions
void computeEB_EXP_siteSpecificRate(Vdouble & ratesV,
Vdouble & stdV,
Vdouble & lowerBoundV,
Vdouble & upperBoundV,
const Vint& spAttributesVec,
const Vint& treeAttributesVec,
const sequenceContainer& sc,
const vector<tree> & etVec,
const vector<const stochasticProcess *> & spVec,
const MDOUBLE alphaConf);
// many stochastic process, 1 tree, all positions
void computeEB_EXP_siteSpecificRate(Vdouble & ratesV,
Vdouble & stdV,
Vdouble & lowerBoundV,
Vdouble & upperBoundV,
const Vint& spAttributesVec,
const sequenceContainer& sc,
const tree & et,
const vector<const stochasticProcess *> & spVec,
const MDOUBLE alphaConf);
// 1 stochastic process, many tree, all positions
void computeEB_EXP_siteSpecificRate(Vdouble & ratesV,
Vdouble & stdV,
Vdouble & lowerBoundV,
Vdouble & upperBoundV,
const Vint& treeAttributesVec,
const sequenceContainer& sc,
const vector<tree> & etVec,
const stochasticProcess & sp,
const MDOUBLE alphaConf);
};
#endif
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