Provide methods to compute substitution mappings. More...

#include <Bpp/Phyl/Mapping/SubstitutionMappingTools.h>

Public Member Functions
	SubstitutionMappingTools ()

virtual	~SubstitutionMappingTools ()

Static Public Member Functions
static ProbabilisticSubstitutionMapping *	computeSubstitutionVectors (const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true) throw (Exception)
	Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation. More...

static ProbabilisticSubstitutionMapping *	computeSubstitutionVectors (const DRTreeLikelihood &drtl, const std::vector< int > &nodeIds, SubstitutionCount &substitutionCount, bool verbose=true) throw (Exception)
	Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation. More...

static ProbabilisticSubstitutionMapping *	computeSubstitutionVectors (const DRTreeLikelihood &drtl, const SubstitutionModelSet &modelSet, const std::vector< int > &nodeIds, SubstitutionCount &substitutionCount, bool verbose=true) throw (Exception)

static ProbabilisticSubstitutionMapping *	computeSubstitutionVectorsNoAveraging (const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true) throw (Exception)
	Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation. More...

static ProbabilisticSubstitutionMapping *	computeSubstitutionVectorsNoAveragingMarginal (const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true) throw (Exception)
	Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation. More...

static ProbabilisticSubstitutionMapping *	computeSubstitutionVectorsMarginal (const DRTreeLikelihood &drtl, SubstitutionCount &substitutionCount, bool verbose=true) throw (Exception)
	Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation. More...

static ProbabilisticSubstitutionMapping *	computeOneJumpProbabilityVectors (const DRTreeLikelihood &drtl, bool verbose=true) throw (Exception)
	This method computes for each site and for each branch the probability that at least one jump occurred. More...

static void	writeToStream (const ProbabilisticSubstitutionMapping &substitutions, const SiteContainer &sites, size_t type, std::ostream &out) throw (IOException)
	Write the substitutions vectors to a stream. More...

static void	readFromStream (std::istream &in, ProbabilisticSubstitutionMapping &substitutions, size_t type) throw (IOException)
	Read the substitutions vectors from a stream. More...

static std::vector< double >	computeTotalSubstitutionVectorForSite (const SubstitutionMapping &smap, size_t siteIndex)
	Sum all type of substitutions for each branch of a given position (specified by its index). More...

static double	computeNormForSite (const SubstitutionMapping &smap, size_t siteIndex)
	Compute the norm of a substitution vector for a given position (specified by its index). More...

static std::vector< double >	computeSumForBranch (const SubstitutionMapping &smap, size_t branchIndex)
	Sum all substitutions for each type of a given branch (specified by its index). More...

static std::vector< double >	computeSumForSite (const SubstitutionMapping &smap, size_t siteIndex)
	Sum all substitutions for each type of a given site (specified by its index). More...

static std::vector< std::vector< double > >	getCountsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)
	Returns the counts on each branch. More...

static std::vector< std::vector< double > >	getCountsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModelSet &modelSet, const SubstitutionRegister &reg, double threshold=-1, bool verbose=true)

static std::vector< std::vector< double > >	getNormalizationsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModel *nullModel, const SubstitutionRegister &reg, bool verbose=true)
	Returns the normalization factors due to the null model on each branch, for each register. More...

static std::vector< std::vector< double > >	getNormalizationsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, const SubstitutionModelSet *nullModelSet, const SubstitutionRegister &reg, bool verbose=true)
	Returns the normalization factors due to the set of null models on each branch, for each register. More...

static std::vector< std::vector< double > >	getNormalizedCountsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel model, SubstitutionModel nullModel, const SubstitutionRegister &reg, bool verbose=true)
	Returns the counts normalized by a null model. More...

static std::vector< std::vector< double > >	getNormalizedCountsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModelSet modelSet, SubstitutionModelSet nullModelSet, const SubstitutionRegister &reg, bool verbose=true)
	Returns the counts normalized by a null model set. More...

static std::vector< std::vector< double > >	getRelativeCountsPerBranch (DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg, bool stationarity=true, double threshold=-1)
	Returns the counts relative to the frequency of the states in case of non-stationarity. More...

static void	outputTotalCountsPerBranchPerSite (std::string &filename, DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg)
	Output the sum of the counts par branch per site, in a file. More...

static void	outputIndividualCountsPerBranchPerSite (const std::string &filenamePrefix, DRTreeLikelihood &drtl, const std::vector< int > &ids, SubstitutionModel *model, const SubstitutionRegister &reg)
	Output individual counts par branch per site, in files. More...

Detailed Description

Provide methods to compute substitution mappings.

For now, only 4 methods are implemented, and provide probabilistic substitution mappings.

See: Dutheil J, Pupko T, Jean-Marie A, Galtier N. A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol. 2005 Sep;22(9):1919-28. Epub 2005 Jun 8.

Author: Julien Dutheil

Definition at line 62 of file SubstitutionMappingTools.h.

Constructor & Destructor Documentation

◆ SubstitutionMappingTools()

bpp::SubstitutionMappingTools::SubstitutionMappingTools ( )

inline

Definition at line 65 of file SubstitutionMappingTools.h.

◆ ~SubstitutionMappingTools()

virtual bpp::SubstitutionMappingTools::~SubstitutionMappingTools ( )

inlinevirtual

Definition at line 66 of file SubstitutionMappingTools.h.

Member Function Documentation

◆ computeNormForSite()

double SubstitutionMappingTools::computeNormForSite	(	const SubstitutionMapping &	smap,
		size_t	siteIndex
	)

static

Compute the norm of a substitution vector for a given position (specified by its index).

The norm is computed as: $N_i = \sqrt{\left(\sum_l {\left(\sum_t n_{l, i, t}\right)}^2\right)}$ , where $n_{l, i, t}$ is the number of substitutions of type t on site i on branch l, obtained using the () operator for the SubstitutionMapping object.

Parameters

smap	The substitution map to use.
siteIndex	The index of the substitution vector for which the norm should be computed.

Returns: The norm of the substitution vector.

Definition at line 1350 of file SubstitutionMappingTools.cpp.

References bpp::Mapping::getNumberOfBranches(), and bpp::SubstitutionMapping::getNumberOfSubstitutionTypes().

◆ computeOneJumpProbabilityVectors()

static ProbabilisticSubstitutionMapping* bpp::SubstitutionMappingTools::computeOneJumpProbabilityVectors	(	const DRTreeLikelihood &	drtl,
		bool	verbose = `true`
	)
throw	(	Exception
	)

inlinestatic

This method computes for each site and for each branch the probability that at least one jump occurred.

Here 'jump' refer to a change in the model state. Depending on the model, this might not be the same as a substitution (an alphabet state change).

Definition at line 192 of file SubstitutionMappingTools.h.

References computeSubstitutionVectors().

◆ computeSubstitutionVectors() [1/3]

static ProbabilisticSubstitutionMapping* bpp::SubstitutionMappingTools::computeSubstitutionVectors	(	const DRTreeLikelihood &	drtl,
		SubstitutionCount &	substitutionCount,
		bool	verbose = `true`
	)
throw	(	Exception
	)

inlinestatic

Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation.

Parameters

drtl	A DRTreeLikelihood object.
substitutionCount	The SubstitutionCount to use.
verbose	Print info to screen.

Returns: A vector of substitutions vectors (one for each site).

Exceptions

Exception If the likelihood object is not initialized.

Definition at line 79 of file SubstitutionMappingTools.h.

Referenced by computeOneJumpProbabilityVectors(), getCountsPerBranch(), outputIndividualCountsPerBranchPerSite(), and outputTotalCountsPerBranchPerSite().

◆ computeSubstitutionVectors() [2/3]

ProbabilisticSubstitutionMapping * SubstitutionMappingTools::computeSubstitutionVectors	(	const DRTreeLikelihood &	drtl,
		const std::vector< int > &	nodeIds,
		SubstitutionCount &	substitutionCount,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation.

Parameters

drtl	A DRTreeLikelihood object.
nodeIds	The Ids of the nodes the substitutions are counted on. If empty, count substitutions on all nodes.
substitutionCount	The SubstitutionCount to use.
verbose	Print info to screen.

Returns: A vector of substitutions vectors (one for each site).

Exceptions

Exception If the likelihood object is not initialized.

Definition at line 63 of file SubstitutionMappingTools.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeLikelihood::ConstBranchModelDescription::getModel(), bpp::TreeLikelihood::ConstBranchModelDescription::getNewSiteIterator(), bpp::TreeTemplate< N >::getNodes(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::TreeLikelihood::ConstBranchModelIterator::hasNext(), and bpp::TreeLikelihood::ConstBranchModelIterator::next().

◆ computeSubstitutionVectors() [3/3]

ProbabilisticSubstitutionMapping * SubstitutionMappingTools::computeSubstitutionVectors	(	const DRTreeLikelihood &	drtl,
		const SubstitutionModelSet &	modelSet,
		const std::vector< int > &	nodeIds,
		SubstitutionCount &	substitutionCount,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Definition at line 373 of file SubstitutionMappingTools.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeLikelihood::ConstBranchModelDescription::getNewSiteIterator(), bpp::TreeTemplate< N >::getNodes(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::TreeLikelihood::ConstBranchModelIterator::hasNext(), and bpp::TreeLikelihood::ConstBranchModelIterator::next().

◆ computeSubstitutionVectorsMarginal()

ProbabilisticSubstitutionMapping * SubstitutionMappingTools::computeSubstitutionVectorsMarginal	(	const DRTreeLikelihood &	drtl,
		SubstitutionCount &	substitutionCount,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation.

The marginal probability is used for weighting, i.e. the product of probabilities for the pair.

This function is mainly for testing purpose (see Dutheil et al. 2005). For practical use, consider using the 'getSubstitutionVectors' method instead.

Parameters

drtl	A DRTreeLikelihood object.
substitutionCount	The substitutionsCount to use.
verbose	Print info to screen.

Returns: A vector of substitutions vectors (one for each site).

Exceptions

Exception If the likelihood object is not initialized.

Definition at line 1113 of file SubstitutionMappingTools.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeLikelihood::ConstBranchModelDescription::getModel(), bpp::TreeLikelihood::ConstBranchModelDescription::getNewSiteIterator(), bpp::TreeTemplate< N >::getNodes(), and bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate().

◆ computeSubstitutionVectorsNoAveraging()

ProbabilisticSubstitutionMapping * SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging	(	const DRTreeLikelihood &	drtl,
		SubstitutionCount &	substitutionCount,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation.

In this method, substitution counts are computed using the pair of ancestral states with maximum likelihood. This is a kind of joint-pair ancestral reconstruction, as in Galtier and Boursot (1998). This reconstruction possibly takes into account several rate classes, and substitution counts are averaged over all rate classes, weighted by their conditional likelihood.

This function is mainly for testing purpose (see Dutheil et al. 2005). For practical use, consider using the 'getSubstitutionVectors' method instead.

Parameters

drtl	A DRTreeLikelihood object.
substitutionCount	The substitutionsCount to use.
verbose	Print info to screen.

Returns: A vector of substitutions vectors (one for each site).

Exceptions

Exception If the likelihood object is not initialized.

Definition at line 685 of file SubstitutionMappingTools.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeLikelihood::ConstBranchModelDescription::getModel(), bpp::TreeLikelihood::ConstBranchModelDescription::getNewSiteIterator(), bpp::TreeTemplate< N >::getNodes(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::TreeLikelihood::ConstBranchModelIterator::hasNext(), and bpp::TreeLikelihood::ConstBranchModelIterator::next().

◆ computeSubstitutionVectorsNoAveragingMarginal()

ProbabilisticSubstitutionMapping * SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal	(	const DRTreeLikelihood &	drtl,
		SubstitutionCount &	substitutionCount,
		bool	verbose = `true`
	)
throw	(	Exception
	)

static

Compute the substitutions vectors for a particular dataset using the double-recursive likelihood computation.

In this method, all ancestral states are estimated using marginal likelihoods, putatively intregated over several rate classes. For each branch, the number of substitution given marginal states is used. This method, used with a SimpleSubstitutionCount objet is equivalent to Tufféry and Darlu's (2000) computation of substitution vectors.

Use with another substitution count objet is in most cases irrelevent.

Parameters

drtl	A DRTreeLikelihood object.
substitutionCount	The substitutionsCount to use.
verbose	Print info to screen.

Returns: A vector of substitutions vectors (one for each site).

Exceptions

Exception If the likelihood object is not initialized.

Definition at line 982 of file SubstitutionMappingTools.cpp.

References bpp::MarginalAncestralStateReconstruction::getAllAncestralStates(), bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeLikelihood::ConstBranchModelDescription::getModel(), bpp::TreeLikelihood::ConstBranchModelDescription::getNewSiteIterator(), bpp::TreeTemplate< N >::getNodes(), bpp::TreeLikelihood::ConstBranchModelIterator::hasNext(), and bpp::TreeLikelihood::ConstBranchModelIterator::next().

◆ computeSumForBranch()

vector< double > SubstitutionMappingTools::computeSumForBranch	(	const SubstitutionMapping &	smap,
		size_t	branchIndex
	)

static

Sum all substitutions for each type of a given branch (specified by its index).

Parameters

smap	The substitution map to use.
branchIndex	The index of the substitution vector for which the counts should be computed.

Returns: A vector will all counts summed for each types of substitutions.

Definition at line 1367 of file SubstitutionMappingTools.cpp.

References bpp::Mapping::getNumberOfSites(), and bpp::SubstitutionMapping::getNumberOfSubstitutionTypes().

◆ computeSumForSite()

vector< double > SubstitutionMappingTools::computeSumForSite	(	const SubstitutionMapping &	smap,
		size_t	siteIndex
	)

static

Sum all substitutions for each type of a given site (specified by its index).

Parameters

smap	The substitution map to use.
siteIndex	The index of the substitution vector for which the counts should be computed.

Returns: A vector will all counts summed for each types of substitutions.

Definition at line 1384 of file SubstitutionMappingTools.cpp.

References bpp::Mapping::getNumberOfBranches(), and bpp::SubstitutionMapping::getNumberOfSubstitutionTypes().

◆ computeTotalSubstitutionVectorForSite()

vector< double > SubstitutionMappingTools::computeTotalSubstitutionVectorForSite	(	const SubstitutionMapping &	smap,
		size_t	siteIndex
	)

static

Sum all type of substitutions for each branch of a given position (specified by its index).

Parameters

smap	The substitution map to use.
siteIndex	The index of the substitution vector for which the counts should be computed.

Returns: A vector will all counts for all types of substitutions summed.

Definition at line 1332 of file SubstitutionMappingTools.cpp.

References bpp::Mapping::getNumberOfBranches(), and bpp::SubstitutionMapping::getNumberOfSubstitutionTypes().

Referenced by outputTotalCountsPerBranchPerSite().

◆ getCountsPerBranch() [1/2]

vector< vector< double > > SubstitutionMappingTools::getCountsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		SubstitutionModel *	model,
		const SubstitutionRegister &	reg,
		double	threshold = `-1`,
		bool	verbose = `true`
	)

static

Returns the counts on each branch.

Parameters

drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
model	The model on which the SubstitutionCount is built
reg	the Substitution Register
threshold	value above which counts are considered saturated (default: -1 means no threshold).
verbose	Display progress messages.

Returns: A vector of substitutions vectors (one per branch per type).

Definition at line 1400 of file SubstitutionMappingTools.cpp.

References bpp::SubstitutionRegister::clone(), computeSubstitutionVectors(), bpp::AbstractMapping::getNodeIndex(), bpp::AbstractMapping::getNumberOfSites(), and bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes().

◆ getCountsPerBranch() [2/2]

vector< vector< double > > SubstitutionMappingTools::getCountsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		const SubstitutionModelSet &	modelSet,
		const SubstitutionRegister &	reg,
		double	threshold = `-1`,
		bool	verbose = `true`
	)

static

Definition at line 1482 of file SubstitutionMappingTools.cpp.

References bpp::SubstitutionRegister::clone(), computeSubstitutionVectors(), bpp::SubstitutionModelSet::getModel(), bpp::AbstractMapping::getNodeIndex(), bpp::AbstractMapping::getNumberOfSites(), and bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes().

◆ getNormalizationsPerBranch() [1/2]

vector< vector< double > > SubstitutionMappingTools::getNormalizationsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		const SubstitutionModel *	nullModel,
		const SubstitutionRegister &	reg,
		bool	verbose = `true`
	)

static

Returns the normalization factors due to the null model on each branch, for each register.

Parameters

drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
nullModel	The model on which the SubstitutionCount is built
reg	the Substitution Register
verbose	Display progress messages.

Returns: A vector of normalization vectors (one per branch per type).

Definition at line 1564 of file SubstitutionMappingTools.cpp.

References bpp::RewardMappingTools::computeRewardVectors(), bpp::SubstitutionModel::getAlphabet(), bpp::SubstitutionModel::getAlphabetStates(), bpp::TreeLikelihood::getNumberOfSites(), bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), bpp::SubstitutionRegister::getType(), bpp::SubstitutionRegister::getTypeName(), and bpp::SubstitutionModel::Qij().

◆ getNormalizationsPerBranch() [2/2]

vector< vector< double > > SubstitutionMappingTools::getNormalizationsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		const SubstitutionModelSet *	nullModelSet,
		const SubstitutionRegister &	reg,
		bool	verbose = `true`
	)

static

Returns the normalization factors due to the set of null models on each branch, for each register.

Parameters

drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
nullModelSet	The model on which the SubstitutionCount is built
reg	the Substitution Register
verbose	Display progress messages.

Returns: A vector of normalization vectors (one per branch per type).

Definition at line 1631 of file SubstitutionMappingTools.cpp.

References bpp::RewardMappingTools::computeRewardVectors(), bpp::SubstitutionModelSet::getAlphabet(), bpp::SubstitutionModel::getAlphabetStates(), bpp::SubstitutionModelSet::getModel(), bpp::AbstractMapping::getNodeIndex(), bpp::SubstitutionModelSet::getNodesWithModel(), bpp::SubstitutionModelSet::getNumberOfModels(), bpp::TreeLikelihood::getNumberOfSites(), bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), bpp::SubstitutionRegister::getType(), bpp::SubstitutionRegister::getTypeName(), and bpp::SubstitutionModel::Qij().

◆ getNormalizedCountsPerBranch() [1/2]

vector< vector< double > > SubstitutionMappingTools::getNormalizedCountsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		SubstitutionModel *	model,
		SubstitutionModel *	nullModel,
		const SubstitutionRegister &	reg,
		bool	verbose = `true`
	)

static

Returns the counts normalized by a null model.

Parameters

drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
model	The model on which the SubstitutionCount is built
nullModel	The null model used for normalization.
reg	the Substitution Register
verbose	Display progress messages.

Definition at line 1716 of file SubstitutionMappingTools.cpp.

References bpp::TreeTemplate< N >::getNode(), and bpp::TreeLikelihood::getTree().

◆ getNormalizedCountsPerBranch() [2/2]

vector< vector< double > > SubstitutionMappingTools::getNormalizedCountsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		SubstitutionModelSet *	modelSet,
		SubstitutionModelSet *	nullModelSet,
		const SubstitutionRegister &	reg,
		bool	verbose = `true`
	)

static

Returns the counts normalized by a null model set.

Parameters

drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
modelSet	The model set on which the SubstitutionCount is built
nullModelSet	The null model set used for normalization.
reg	the Substitution Register
verbose	Display progress messages.

Definition at line 1759 of file SubstitutionMappingTools.cpp.

References bpp::SubstitutionModelSet::getModel(), bpp::TreeTemplate< N >::getNode(), and bpp::TreeLikelihood::getTree().

◆ getRelativeCountsPerBranch()

vector< vector< double > > SubstitutionMappingTools::getRelativeCountsPerBranch	(	DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		SubstitutionModel *	model,
		const SubstitutionRegister &	reg,
		bool	stationarity = `true`,
		double	threshold = `-1`
	)

static

Returns the counts relative to the frequency of the states in case of non-stationarity.

Parameters

drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
model	The model on which the SubstitutionCount is built
reg	the Substitution Register
stationarity	if false, a correction is made if the SubstitutionRegister is a CategorySubstitutionRegister
threshold	value above which counts are considered saturated (default: -1 means no threshold).

Definition at line 1802 of file SubstitutionMappingTools.cpp.

References bpp::CategorySubstitutionRegister::getCategory(), bpp::CategorySubstitutionRegister::getCategoryFrom(), bpp::CategorySubstitutionRegister::getNumberOfCategories(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

◆ outputIndividualCountsPerBranchPerSite()

void SubstitutionMappingTools::outputIndividualCountsPerBranchPerSite	(	const std::string &	filenamePrefix,
		DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		SubstitutionModel *	model,
		const SubstitutionRegister &	reg
	)

static

Output individual counts par branch per site, in files.

Parameters

filenamePrefix	The filename prefix
drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
model	The model on which the SubstitutionCount is built
reg	the Substitution Register

Author: Iakov Davydov

Definition at line 1899 of file SubstitutionMappingTools.cpp.

References bpp::SubstitutionRegister::clone(), computeSubstitutionVectors(), bpp::AbstractMapping::getNodeIndex(), bpp::AbstractMapping::getNumberOfSites(), and bpp::SubstitutionRegister::getNumberOfSubstitutionTypes().

◆ outputTotalCountsPerBranchPerSite()

void SubstitutionMappingTools::outputTotalCountsPerBranchPerSite	(	std::string &	filename,
		DRTreeLikelihood &	drtl,
		const std::vector< int > &	ids,
		SubstitutionModel *	model,
		const SubstitutionRegister &	reg
	)

static

Output the sum of the counts par branch per site, in a file.

Parameters

filename	The name of the output file
drtl	A DRTreeLikelihood object.
ids	The numbers of the nodes of the tree
model	The model on which the SubstitutionCount is built
reg	the Substitution Register

Definition at line 1855 of file SubstitutionMappingTools.cpp.

References bpp::SubstitutionRegister::clone(), computeSubstitutionVectors(), computeTotalSubstitutionVectorForSite(), bpp::AbstractMapping::getNodeIndex(), and bpp::AbstractMapping::getNumberOfSites().

◆ readFromStream()

void SubstitutionMappingTools::readFromStream	(	std::istream &	in,
		ProbabilisticSubstitutionMapping &	substitutions,
		size_t	type
	)
throw	(	IOException
	)

static

Read the substitutions vectors from a stream.

Parameters

in	The input stream where to read the vectors.
substitutions	The mapping object to fill.
type	The type of substitutions that are read. Should be in supported by the substittuion count obect assiciated to the mapping, if any.

Exceptions

IOException If an input error happens.

Definition at line 1288 of file SubstitutionMappingTools.cpp.

◆ writeToStream()

void SubstitutionMappingTools::writeToStream	(	const ProbabilisticSubstitutionMapping &	substitutions,
		const SiteContainer &	sites,
		size_t	type,
		std::ostream &	out
	)
throw	(	IOException
	)

static

Write the substitutions vectors to a stream.

Parameters

substitutions	The substitutions vectors to write.
sites	The dataset associated to the vectors (needed to know the position of each site in the dataset).
type	The type of substitutions to be output. See SubstitutionCount class. Only one type of substitution can be output at a time.
out	The output stream where to write the vectors.

Exceptions

IOException If an output error happens.

Definition at line 1258 of file SubstitutionMappingTools.cpp.

The documentation for this class was generated from the following files:

Bpp/Phyl/Mapping/SubstitutionMappingTools.h
Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SubstitutionMappingTools()

◆ ~SubstitutionMappingTools()

Member Function Documentation

◆ computeNormForSite()

◆ computeOneJumpProbabilityVectors()

◆ computeSubstitutionVectors() [1/3]

◆ computeSubstitutionVectors() [2/3]

◆ computeSubstitutionVectors() [3/3]

◆ computeSubstitutionVectorsMarginal()

◆ computeSubstitutionVectorsNoAveraging()

◆ computeSubstitutionVectorsNoAveragingMarginal()

◆ computeSumForBranch()

◆ computeSumForSite()

◆ computeTotalSubstitutionVectorForSite()

◆ getCountsPerBranch() [1/2]

◆ getCountsPerBranch() [2/2]

◆ getNormalizationsPerBranch() [1/2]

◆ getNormalizationsPerBranch() [2/2]

◆ getNormalizedCountsPerBranch() [1/2]

◆ getNormalizedCountsPerBranch() [2/2]

◆ getRelativeCountsPerBranch()

◆ outputIndividualCountsPerBranchPerSite()

◆ outputTotalCountsPerBranchPerSite()

◆ readFromStream()

◆ writeToStream()