Utilitary methods to compute site patterns. More...

#include <Bpp/Phyl/PatternTools.h>

Static Public Member Functions
template<class N , class E , class I >
static std::unique_ptr< AlignmentDataInterface >	getSequenceSubset (const AlignmentDataInterface &sequenceSet, const std::shared_ptr< N > node, const AssociationTreeGraphImplObserver< N, E, I > &tree)
	Extract the sequences corresponding to a given subtree. More...

template<class N , class E , class I >
static std::unique_ptr< SiteContainerInterface >	getSequenceSubset (const SiteContainerInterface &sequenceSet, const std::shared_ptr< N > node, const AssociationTreeGraphImplObserver< N, E, I > &tree)
	Extract the sequences corresponding to a given subtree. More...

template<class N , class E , class I >
static std::unique_ptr< ProbabilisticSiteContainerInterface >	getSequenceSubset (const ProbabilisticSiteContainerInterface &sequenceSet, const std::shared_ptr< N > node, const AssociationTreeGraphImplObserver< N, E, I > &tree)
	Extract the sequences corresponding to a given subtree. More...

static std::unique_ptr< AlignmentDataInterface >	getSequenceSubset (const AlignmentDataInterface &sequenceSet, const Node &node)
	Extract the sequences corresponding to a given subtree. More...

static std::unique_ptr< SiteContainerInterface >	getSequenceSubset (const SiteContainerInterface &sequenceSet, const Node &node)
	Extract the sequences corresponding to a given subtree. More...

static std::unique_ptr< ProbabilisticSiteContainerInterface >	getSequenceSubset (const ProbabilisticSiteContainerInterface &sequenceSet, const Node &node)
	Extract the sequences corresponding to a given subtree. More...

static std::unique_ptr< AlignmentDataInterface >	getSequenceSubset (const AlignmentDataInterface &sequenceSet, const std::vector< std::string > &names)
	Extract the sequences corresponding to a given set of names. More...

static std::unique_ptr< SiteContainerInterface >	getSequenceSubset (const SiteContainerInterface &sequenceSet, const std::vector< std::string > &names)
	Extract the sequences in a SiteContainer corresponding to a given set of names. More...

static std::unique_ptr< ProbabilisticSiteContainerInterface >	getSequenceSubset (const ProbabilisticSiteContainerInterface &sequenceSet, const std::vector< std::string > &names)
	Extract the sequences in a ProbabilisticSiteContainer corresponding to a given set of names. More...

static std::unique_ptr< AlignmentDataInterface >	shrinkSiteSet (const AlignmentDataInterface &siteSet)
	Compress a site container by removing duplicated sites. More...

static std::unique_ptr< SiteContainerInterface >	shrinkSiteSet (const SiteContainerInterface &siteSet)
	Compress a site container by removing duplicated sites. More...

static std::unique_ptr< ProbabilisticSiteContainerInterface >	shrinkSiteSet (const ProbabilisticSiteContainerInterface &siteSet)
	Compress a site container by removing duplicated sites. More...

static Vint	getIndexes (const AlignmentDataInterface &sequences1, const AlignmentDataInterface &sequences2)
	Look for the occurrence of each site in sequences1 in sequences2 and send the position of the first occurrence, or -1 if not found. More...

Detailed Description

Utilitary methods to compute site patterns.

These methods are mainly designed to save computation in likelihood and parsimony methods.

Definition at line 31 of file PatternTools.h.

Member Function Documentation

◆ getIndexes()

Vint PatternTools::getIndexes	(	const AlignmentDataInterface &	sequences1,
		const AlignmentDataInterface &	sequences2
	)

static

Look for the occurrence of each site in sequences1 in sequences2 and send the position of the first occurrence, or -1 if not found.

Parameters

sequences1	First container.
sequences2	Second container.

Returns: A vector of positions.

Definition at line 263 of file PatternTools.cpp.

References bpp::SiteTools::areSymbolListsIdentical(), and bpp::TemplateAlignmentDataInterface< class >::getNumberOfSites().

◆ getSequenceSubset() [1/9]

std::unique_ptr< AlignmentDataInterface > PatternTools::getSequenceSubset	(	const AlignmentDataInterface &	sequenceSet,
		const Node &	node
	)

static

Extract the sequences corresponding to a given subtree.

Parameters

sequenceSet	The container to look in.
node	The root node of the subtree to check.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 20 of file PatternTools.cpp.

◆ getSequenceSubset() [2/9]

template<class N , class E , class I >

static std::unique_ptr<AlignmentDataInterface> bpp::PatternTools::getSequenceSubset	(	const AlignmentDataInterface &	sequenceSet,
		const std::shared_ptr< N >	node,
		const AssociationTreeGraphImplObserver< N, E, I > &	tree
	)

inlinestatic

Extract the sequences corresponding to a given subtree.

Parameters

sequenceSet	The container to look in.
node	The root node of the subtree to check.
tree	The tree owing the node.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 44 of file PatternTools.h.

Referenced by bpp::AbstractTreeParsimonyScore::init_(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), and bpp::DRHomogeneousTreeLikelihood::setData().

◆ getSequenceSubset() [3/9]

std::unique_ptr< AlignmentDataInterface > PatternTools::getSequenceSubset	(	const AlignmentDataInterface &	sequenceSet,
		const std::vector< std::string > &	names
	)

static

Extract the sequences corresponding to a given set of names.

Parameters

sequenceSet	The container to look in.
names	The names of the sequences to look for.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 115 of file PatternTools.cpp.

References bpp::TemplateAlignmentDataInterface< class >::getAlphabet().

◆ getSequenceSubset() [4/9]

std::unique_ptr< ProbabilisticSiteContainerInterface > PatternTools::getSequenceSubset	(	const ProbabilisticSiteContainerInterface &	sequenceSet,
		const Node &	node
	)

static

Extract the sequences corresponding to a given subtree.

Parameters

sequenceSet	The container to look in.
node	The root node of the subtree to check.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 78 of file PatternTools.cpp.

References bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::ApplicationTools::displayWarning(), bpp::TemplateSiteContainerInterface< class, class, class >::getAlphabet(), bpp::TreeTemplateTools::getLeaves(), bpp::TemplateSiteContainerInterface< class, class, class >::getNumberOfSites(), bpp::TemplateSiteContainerInterface< class, class, class >::getSiteCoordinates(), and bpp::TemplateSiteContainerInterface< class, class, class >::sequence().

◆ getSequenceSubset() [5/9]

template<class N , class E , class I >

static std::unique_ptr<ProbabilisticSiteContainerInterface> bpp::PatternTools::getSequenceSubset	(	const ProbabilisticSiteContainerInterface &	sequenceSet,
		const std::shared_ptr< N >	node,
		const AssociationTreeGraphImplObserver< N, E, I > &	tree
	)

inlinestatic

Extract the sequences corresponding to a given subtree.

Parameters

sequenceSet	The container to look in.
node	The root node of the subtree to check.
tree	The tree owing the node.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 122 of file PatternTools.h.

References bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::ApplicationTools::displayWarning(), bpp::TemplateSiteContainerInterface< class, class, class >::getAlphabet(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getLeavesUnderNode(), bpp::TemplateSiteContainerInterface< class, class, class >::getNumberOfSites(), bpp::TemplateSiteContainerInterface< class, class, class >::getSiteCoordinates(), and bpp::TemplateSiteContainerInterface< class, class, class >::sequence().

◆ getSequenceSubset() [6/9]

std::unique_ptr< ProbabilisticSiteContainerInterface > PatternTools::getSequenceSubset	(	const ProbabilisticSiteContainerInterface &	sequenceSet,
		const std::vector< std::string > &	names
	)

static

Extract the sequences in a ProbabilisticSiteContainer corresponding to a given set of names.

Parameters

sequenceSet	The container to look in.
names	The names of the sequences to look for.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 162 of file PatternTools.cpp.

References bpp::TemplateSiteContainerInterface< class, class, class >::getAlphabet(), bpp::TemplateSiteContainerInterface< class, class, class >::getSiteCoordinates(), bpp::TemplateSiteContainerInterface< class, class, class >::hasSequence(), and bpp::TemplateSiteContainerInterface< class, class, class >::sequence().

◆ getSequenceSubset() [7/9]

std::unique_ptr< SiteContainerInterface > PatternTools::getSequenceSubset	(	const SiteContainerInterface &	sequenceSet,
		const Node &	node
	)

static

Extract the sequences corresponding to a given subtree.

Parameters

sequenceSet	The container to look in.
node	The root node of the subtree to check.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 43 of file PatternTools.cpp.

References bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::ApplicationTools::displayWarning(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getAlphabet(), bpp::TreeTemplateTools::getLeaves(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getNumberOfSites(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getSiteCoordinates(), and TemplateSiteContainerInterface< Site, Sequence, std::string >::sequence().

◆ getSequenceSubset() [8/9]

template<class N , class E , class I >

static std::unique_ptr<SiteContainerInterface> bpp::PatternTools::getSequenceSubset	(	const SiteContainerInterface &	sequenceSet,
		const std::shared_ptr< N >	node,
		const AssociationTreeGraphImplObserver< N, E, I > &	tree
	)

inlinestatic

Extract the sequences corresponding to a given subtree.

Parameters

sequenceSet	The container to look in.
node	The root node of the subtree to check.
tree	The tree owing the node.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 76 of file PatternTools.h.

References bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::ApplicationTools::displayWarning(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getAlphabet(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getLeavesUnderNode(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getNumberOfSites(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getSiteCoordinates(), and TemplateSiteContainerInterface< Site, Sequence, std::string >::sequence().

◆ getSequenceSubset() [9/9]

std::unique_ptr< SiteContainerInterface > PatternTools::getSequenceSubset	(	const SiteContainerInterface &	sequenceSet,
		const std::vector< std::string > &	names
	)

static

Extract the sequences in a SiteContainer corresponding to a given set of names.

Parameters

sequenceSet	The container to look in.
names	The names of the sequences to look for.

Returns: A new site container with corresponding sequences.

Exceptions

Exception if an error occurred.

Definition at line 141 of file PatternTools.cpp.

References TemplateSiteContainerInterface< Site, Sequence, std::string >::getAlphabet(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getSiteCoordinates(), TemplateSiteContainerInterface< Site, Sequence, std::string >::hasSequence(), and TemplateSiteContainerInterface< Site, Sequence, std::string >::sequence().

◆ shrinkSiteSet() [1/3]

std::unique_ptr< AlignmentDataInterface > PatternTools::shrinkSiteSet ( const AlignmentDataInterface & siteSet )

static

Compress a site container by removing duplicated sites.

Parameters

siteSet The container to look in.

Returns: A new site container with unique sites.

Exceptions

Exception if an error occurred.

Definition at line 185 of file PatternTools.cpp.

◆ shrinkSiteSet() [2/3]

std::unique_ptr< ProbabilisticSiteContainerInterface > PatternTools::shrinkSiteSet ( const ProbabilisticSiteContainerInterface & siteSet )

static

Compress a site container by removing duplicated sites.

Parameters

siteSet The container to look in.

Returns: A new site container with unique sites.

Exceptions

Exception if an error occurred.

Definition at line 234 of file PatternTools.cpp.

References bpp::SiteTools::areSymbolListsIdentical(), bpp::TemplateSiteContainerInterface< class, class, class >::getAlphabet(), bpp::TemplateSiteContainerInterface< class, class, class >::getNumberOfSites(), bpp::TemplateSiteContainerInterface< class, class, class >::getSequenceNames(), and bpp::TemplateSiteContainerInterface< class, class, class >::site().

◆ shrinkSiteSet() [3/3]

std::unique_ptr< SiteContainerInterface > PatternTools::shrinkSiteSet ( const SiteContainerInterface & siteSet )

static

Compress a site container by removing duplicated sites.

Parameters

siteSet The container to look in.

Returns: A new site container with unique sites.

Exceptions

Exception if an error occurred.

Definition at line 207 of file PatternTools.cpp.

References bpp::SiteTools::areSymbolListsIdentical(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getAlphabet(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getNumberOfSites(), TemplateSiteContainerInterface< Site, Sequence, std::string >::getSequenceNames(), and TemplateSiteContainerInterface< Site, Sequence, std::string >::site().

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

Bpp/Phyl/PatternTools.h
Bpp/Phyl/PatternTools.cpp

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ getIndexes()

◆ getSequenceSubset() [1/9]

◆ getSequenceSubset() [2/9]

◆ getSequenceSubset() [3/9]

◆ getSequenceSubset() [4/9]

◆ getSequenceSubset() [5/9]

◆ getSequenceSubset() [6/9]

◆ getSequenceSubset() [7/9]

◆ getSequenceSubset() [8/9]

◆ getSequenceSubset() [9/9]

◆ shrinkSiteSet() [1/3]

◆ shrinkSiteSet() [2/3]

◆ shrinkSiteSet() [3/3]