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