Provide methods to compute reward mappings. More...

#include <Bpp/Phyl/Legacy/Mapping/RewardMappingTools.h>

Public Member Functions
	LegacyRewardMappingTools ()

virtual	~LegacyRewardMappingTools ()

Static Public Member Functions
static std::unique_ptr< LegacyProbabilisticRewardMapping >	computeRewardVectors (std::shared_ptr< const DRTreeLikelihoodInterface > drtl, const std::vector< int > &nodeIds, std::shared_ptr< Reward > reward, bool verbose=true)
	Compute the reward vectors for a particular dataset using the double-recursive likelihood computation. More...

static void	writeToStream (const LegacyProbabilisticRewardMapping &rewards, const SiteContainerInterface &sites, std::ostream &out)
	Write the reward vectors to a stream. More...

static void	readFromStream (std::istream &in, LegacyProbabilisticRewardMapping &rewards)
	Read the reward vectors from a stream. More...

static double	computeSumForBranch (const LegacyRewardMappingInterface &smap, size_t branchIndex)
	Sum all rewards of a given branch (specified by its index). More...

static double	computeSumForSite (const LegacyRewardMappingInterface &smap, size_t siteIndex)
	Sum all substitutions for each type of a given site (specified by its index). More...

Detailed Description

Provide methods to compute reward mappings.

For now, 4 methods are implemented, and provide reward mappings.

See: Minin, V.N. and Suchard, M.A., Fast, accurate and simulation-free stochastic mapping Philosophical Transactions of the Royal Society B 2008 363:3985-95.

Author: Laurent Guéguen

Definition at line 27 of file RewardMappingTools.h.

Constructor & Destructor Documentation

◆ LegacyRewardMappingTools()

bpp::LegacyRewardMappingTools::LegacyRewardMappingTools ( )

inline

Definition at line 30 of file RewardMappingTools.h.

◆ ~LegacyRewardMappingTools()

virtual bpp::LegacyRewardMappingTools::~LegacyRewardMappingTools ( )

inlinevirtual

Definition at line 31 of file RewardMappingTools.h.

Member Function Documentation

◆ computeRewardVectors()

std::unique_ptr< LegacyProbabilisticRewardMapping > LegacyRewardMappingTools::computeRewardVectors	(	std::shared_ptr< const DRTreeLikelihoodInterface >	drtl,
		const std::vector< int > &	nodeIds,
		std::shared_ptr< Reward >	reward,
		bool	verbose = `true`
	)

static

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

Parameters

drtl	A DRTreeLikelihood object.
nodeIds	The Ids of the nodes the reward vectors are computed on.
reward	The Reward to use.
verbose	Print info to screen.

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

Exceptions

Exception If the likelihood object is not initialized.

Definition at line 23 of file RewardMappingTools.cpp.

References bpp::VectorTools::contains(), bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeTemplate< N >::getNodes(), bpp::Node::getNumberOfSons(), bpp::TreeTemplate< N >::getRootId(), bpp::Node::getSon(), bpp::Node::hasFather(), and bpp::ApplicationTools::message.

Referenced by bpp::LegacySubstitutionMappingTools::computeCountsPerSitePerBranchPerType(), bpp::LegacySubstitutionMappingTools::computeCountsPerSitePerType(), and bpp::LegacySubstitutionMappingTools::getNormalizationsPerBranch().

◆ computeSumForBranch()

double LegacyRewardMappingTools::computeSumForBranch	(	const LegacyRewardMappingInterface &	smap,
		size_t	branchIndex
	)

static

Sum all rewards of a given branch (specified by its index).

Parameters

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

Returns: A vector will all rewards summed.

Definition at line 382 of file RewardMappingTools.cpp.

References bpp::LegacyMappingInterface::getNumberOfSites().

◆ computeSumForSite()

double LegacyRewardMappingTools::computeSumForSite	(	const LegacyRewardMappingInterface &	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 395 of file RewardMappingTools.cpp.

References bpp::LegacyMappingInterface::getNumberOfBranches().

◆ readFromStream()

void LegacyRewardMappingTools::readFromStream	(	std::istream &	in,
		LegacyProbabilisticRewardMapping &	rewards
	)

static

Read the reward vectors from a stream.

Parameters

in	The input stream where to read the vectors.
rewards	The mapping object to fill.

Exceptions

IOException If an input error happens.

Definition at line 341 of file RewardMappingTools.cpp.

References bpp::LegacyAbstractMapping::getNodeIndex(), bpp::DataTable::read(), bpp::LegacyProbabilisticRewardMapping::setNumberOfSites(), bpp::LegacyAbstractMapping::setSitePosition(), bpp::TextTools::toDouble(), bpp::TextTools::toInt(), and bpp::Exception::what().

◆ writeToStream()

void LegacyRewardMappingTools::writeToStream	(	const LegacyProbabilisticRewardMapping &	rewards,
		const SiteContainerInterface &	sites,
		std::ostream &	out
	)

static

Write the reward vectors to a stream.

Parameters

rewards	The reward vectors to write.
sites	The dataset associated to the vectors (needed to know the position of each site in the dataset).
out	The output stream where to write the vectors.

Exceptions

IOException If an output error happens.

Definition at line 313 of file RewardMappingTools.cpp.

References bpp::Site::getCoordinate(), bpp::Node::getDistanceToFather(), bpp::Node::getId(), bpp::LegacyAbstractMapping::getNode(), bpp::LegacyAbstractMapping::getNumberOfBranches(), bpp::LegacyAbstractMapping::getNumberOfSites(), and TemplateSiteContainerInterface< Site, Sequence, std::string >::site().

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

Bpp/Phyl/Legacy/Mapping/RewardMappingTools.h
Bpp/Phyl/Legacy/Mapping/RewardMappingTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ LegacyRewardMappingTools()

◆ ~LegacyRewardMappingTools()

Member Function Documentation

◆ computeRewardVectors()

◆ computeSumForBranch()

◆ computeSumForSite()

◆ readFromStream()

◆ writeToStream()