Utilitary function to manipulate PolymorphismSequenceContainer. More...

#include <Bpp/PopGen/PolymorphismSequenceContainerTools.h>

Public Member Functions
	~PolymorphismSequenceContainerTools ()

Static Public Member Functions
static PolymorphismSequenceContainer *	read (const std::string &path, const Alphabet *alpha)
	Read a Mase+ file and return a PolymorphismSequenceContainer. Toggle Sequence when selection tag begin with OUTGROUP (see Polymorphix) More...

static PolymorphismSequenceContainer *	extractIngroup (const PolymorphismSequenceContainer &psc)
	Extract ingroup sequences from a PolymorphismSequenceContainer and create a new one. More...

static PolymorphismSequenceContainer *	extractOutgroup (const PolymorphismSequenceContainer &psc)
	Extract outgroup sequences from a PolymorphismSequenceContainer and create a new one. More...

static PolymorphismSequenceContainer *	extractGroup (const PolymorphismSequenceContainer &psc, size_t group_id)
	Extract a special group from the PolymorphismSequenceContainer. More...

static PolymorphismSequenceContainer *	getSelectedSequences (const PolymorphismSequenceContainer &psc, const SequenceSelection &ss)
	Extract selected sequences. More...

static PolymorphismSequenceContainer *	sample (const PolymorphismSequenceContainer &psc, size_t n, bool replace=true)
	Get a random set of sequences. More...

static PolymorphismSequenceContainer *	getSitesWithoutGaps (const PolymorphismSequenceContainer &psc)
	Retrieves sites without gaps from PolymorphismSequenceContainer. More...

static size_t	getNumberOfNonGapSites (const PolymorphismSequenceContainer &psc, bool ingroup)
	Return number of sites without gaps in a PolymorphismSequenceContainer. More...

static size_t	getNumberOfCompleteSites (const PolymorphismSequenceContainer &psc, bool ingroup)
	Return number of completely resolved sites in a PolymorphismSequenceContainer. More...

static PolymorphismSequenceContainer *	getCompleteSites (const PolymorphismSequenceContainer &psc)
	Retrieves complete sites from a PolymorphismSequenceContainer. More...

static PolymorphismSequenceContainer *	excludeFlankingGap (const PolymorphismSequenceContainer &psc)
	exclude flanking sites with gap but keep gap sites within the alignment More...

static PolymorphismSequenceContainer *	getSelectedSites (const PolymorphismSequenceContainer &psc, const std::string &setName, bool phase)
	Get a PolymorphismSequenceContainer corresponding to a site selection annotated in the mase comments. More...

static PolymorphismSequenceContainer *	getNonCodingSites (const PolymorphismSequenceContainer &psc, const std::string &setName)
	Retrieve non-coding sites defined in the mase file header. More...

static PolymorphismSequenceContainer *	getOnePosition (const PolymorphismSequenceContainer &psc, const std::string &setName, size_t pos)
	Retrieve sites at one codon position (1,2,3) More...

static PolymorphismSequenceContainer *	getIntrons (const PolymorphismSequenceContainer &psc, const std::string &setName, const GeneticCode *gCode)
	Retrieve intron sites. More...

static PolymorphismSequenceContainer *	get5Prime (const PolymorphismSequenceContainer &psc, const std::string &setName)
	Retrieve 5' sites. More...

static PolymorphismSequenceContainer *	get3Prime (const PolymorphismSequenceContainer &psc, const std::string &setName, const GeneticCode *gCode)
	Retrieve 3' sites. More...

static std::string	getIngroupSpeciesName (const PolymorphismSequenceContainer &psc)
	Get the species name of the ingroup. More...

static PolymorphismSequenceContainer *	getSynonymousSites (const PolymorphismSequenceContainer &psc, const GeneticCode &gCode)
	Retrieve synonymous codon sites. More...

static PolymorphismSequenceContainer *	getNonSynonymousSites (const PolymorphismSequenceContainer &psc, const GeneticCode &gCode)
	Retrieve non-synonymous codon sites. More...

Detailed Description

Utilitary function to manipulate PolymorphismSequenceContainer.

Author: Sylvain Gaillard

Definition at line 71 of file PolymorphismSequenceContainerTools.h.

Constructor & Destructor Documentation

◆ ~PolymorphismSequenceContainerTools()

PolymorphismSequenceContainerTools::~PolymorphismSequenceContainerTools ( )

Definition at line 48 of file PolymorphismSequenceContainerTools.cpp.

Member Function Documentation

◆ excludeFlankingGap()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::excludeFlankingGap ( const PolymorphismSequenceContainer & psc )

static

exclude flanking sites with gap but keep gap sites within the alignment

Parameters

psc	a PolymorphismSequenceContainer reference

Definition at line 320 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::clone(), bpp::VectorSiteContainer::deleteSite(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::VectorSiteContainer::getSite(), and bpp::SiteTools::hasGap().

◆ extractGroup()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::extractGroup	(	const PolymorphismSequenceContainer &	psc,
		size_t	group_id
	)

static

Extract a special group from the PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference.
group_id	the group identifier as an size_t.

Exceptions

GroupNotFoundException if group_id is not found.

Definition at line 151 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::clone(), bpp::PolymorphismSequenceContainer::deleteSequence(), bpp::PolymorphismSequenceContainer::getGroupId(), and bpp::VectorSiteContainer::getNumberOfSequences().

◆ extractIngroup()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::extractIngroup ( const PolymorphismSequenceContainer & psc )

static

Extract ingroup sequences from a PolymorphismSequenceContainer and create a new one.

Parameters

psc	a PolymorphismSequenceContainer reference

Exceptions

Exception if there is no ingroup sequence

Definition at line 105 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::clone(), bpp::PolymorphismSequenceContainer::deleteSequence(), bpp::VectorSiteContainer::getNumberOfSequences(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ extractOutgroup()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::extractOutgroup ( const PolymorphismSequenceContainer & psc )

static

Extract outgroup sequences from a PolymorphismSequenceContainer and create a new one.

Parameters

psc	a PolymorphismSequenceContainer reference

Exceptions

Exception if there is no outgroup sequence

Definition at line 128 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::clone(), bpp::PolymorphismSequenceContainer::deleteSequence(), bpp::VectorSiteContainer::getNumberOfSequences(), and bpp::PolymorphismSequenceContainer::isIngroupMember().

◆ get3Prime()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::get3Prime	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		const GeneticCode *	gCode
	)

static

Retrieve 3' sites.

Parameters

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection
gCode	The genetic code to use

Definition at line 530 of file PolymorphismSequenceContainerTools.cpp.

References bpp::CodonAlphabet::getCodon(), bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::VectorSiteContainer::getSite(), bpp::MaseTools::getSiteSet(), bpp::GeneticCode::getSourceAlphabet(), bpp::Site::getValue(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::GeneticCode::isStop(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ get5Prime()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::get5Prime	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName
	)

static

Retrieve 5' sites.

Parameters

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection

Definition at line 492 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::MaseTools::getPhase(), bpp::SiteContainerTools::getSelectedSites(), bpp::VectorSiteContainer::getSite(), bpp::MaseTools::getSiteSet(), bpp::Site::getValue(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ getCompleteSites()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getCompleteSites ( const PolymorphismSequenceContainer & psc )

static

Retrieves complete sites from a PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference

Definition at line 295 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::addSite(), bpp::VectorSiteContainer::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::VectorSiteContainer::getSequencesNames(), bpp::CompleteSiteContainerIterator::hasMoreSites(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::CompleteSiteContainerIterator::nextSite(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), bpp::PolymorphismSequenceContainer::setGroupId(), bpp::PolymorphismSequenceContainer::setSequenceCount(), and bpp::VectorSiteContainer::setSequencesNames().

◆ getIngroupSpeciesName()

string PolymorphismSequenceContainerTools::getIngroupSpeciesName ( const PolymorphismSequenceContainer & psc )

static

Get the species name of the ingroup.

Parameters

psc	a PolymorphismSequenceContainer.

Definition at line 570 of file PolymorphismSequenceContainerTools.cpp.

References bpp::MaseTools::getAvailableSequenceSelections(), bpp::VectorSiteContainer::getGeneralComments(), and bpp::StringTokenizer::getToken().

◆ getIntrons()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getIntrons	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		const GeneticCode *	gCode
	)

static

Retrieve intron sites.

Same as getNonCodgingSites but exclude 5' and 3' flanking regions if there are

Parameters

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection
gCode	The genetic code to use

Definition at line 435 of file PolymorphismSequenceContainerTools.cpp.

References bpp::CodonAlphabet::getCodon(), bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::MaseTools::getPhase(), bpp::SiteContainerTools::getSelectedSites(), bpp::VectorSiteContainer::getSite(), bpp::MaseTools::getSiteSet(), bpp::GeneticCode::getSourceAlphabet(), bpp::Site::getValue(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::GeneticCode::isStop(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ getNonCodingSites()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getNonCodingSites	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName
	)

static

Retrieve non-coding sites defined in the mase file header.

Be carefull: to use before excluding gap

Parameters

psc	a PolymorphismSequenceContainer reference
setName	name of the CDS site selection

Definition at line 366 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::SiteContainerTools::getSelectedSites(), bpp::MaseTools::getSiteSet(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ getNonSynonymousSites()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getNonSynonymousSites	(	const PolymorphismSequenceContainer &	psc,
		const GeneticCode &	gCode
	)

static

Retrieve non-synonymous codon sites.

Parameters

psc	a PolymorphismSequenceContainer.
gCode	The genetic code to use

Returns: A new PolymorphismSequenceContainer with only non-synonymous sites.

Definition at line 617 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::VectorSiteContainer::getSequencesNames(), bpp::VectorSiteContainer::getSite(), bpp::PolymorphismSequenceContainer::isIngroupMember(), and bpp::CodonSiteTools::isSynonymousPolymorphic().

◆ getNumberOfCompleteSites()

size_t PolymorphismSequenceContainerTools::getNumberOfCompleteSites	(	const PolymorphismSequenceContainer &	psc,
		bool	ingroup
	)

static

Return number of completely resolved sites in a PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference
ingroup	a boolean set to true if you want to take only ingroup sequences into account

Exceptions

Exception if there is no ingroup sequence

Definition at line 265 of file PolymorphismSequenceContainerTools.cpp.

References count(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::SimpleSiteContainerIterator::hasMoreSites(), bpp::SiteTools::isComplete(), and bpp::SimpleSiteContainerIterator::nextSite().

◆ getNumberOfNonGapSites()

size_t PolymorphismSequenceContainerTools::getNumberOfNonGapSites	(	const PolymorphismSequenceContainer &	psc,
		bool	ingroup
	)

static

Return number of sites without gaps in a PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference
ingroup	a boolean set to true if you want to take only ingroup sequences into account

Exceptions

Exception if there is no ingroup sequence

Definition at line 235 of file PolymorphismSequenceContainerTools.cpp.

References count(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::SiteTools::hasGap(), bpp::SimpleSiteContainerIterator::hasMoreSites(), and bpp::SimpleSiteContainerIterator::nextSite().

◆ getOnePosition()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getOnePosition	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		size_t	pos
	)

static

Retrieve sites at one codon position (1,2,3)

Be carefull: to use before excluding gap Be careful: if there is no phase information, the method catch an exception and set the phase to 1 This allows to use this method for PolymorphismSequenceContainer generated by getSelectedSequence

Parameters

psc	a PolymorphismSequenceContainer reference
setName	name of the CDS site selection
pos	position index.

Definition at line 394 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::MaseTools::getPhase(), bpp::SiteContainerTools::getSelectedSites(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ getSelectedSequences()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getSelectedSequences	(	const PolymorphismSequenceContainer &	psc,
		const SequenceSelection &	ss
	)

static

Extract selected sequences.

Parameters

psc	a PolymorphismSequenceContainer reference.
ss	a sequence selection.

Definition at line 174 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::addSequenceWithFrequency(), bpp::VectorSiteContainer::getAlphabet(), bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getSequence(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), bpp::VectorSiteContainer::setGeneralComments(), and bpp::PolymorphismSequenceContainer::setGroupId().

Referenced by sample().

◆ getSelectedSites()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getSelectedSites	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		bool	phase
	)

static

Get a PolymorphismSequenceContainer corresponding to a site selection annotated in the mase comments.

Be carefull : in the new PolymorphismSequenceContainer the mase comments are lost Information about cds positions and start codon is no more available

Parameters

psc	a PolymorphismSequenceContainer.
setName	The name of the set to retrieve.
phase	a boolean set to true if you want to take the phase into account during the extraction. It removes the useless sites.

Definition at line 337 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::deleteGeneralComments(), bpp::SiteContainer::deleteSite(), bpp::VectorSiteContainer::getGeneralComments(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::MaseTools::getPhase(), bpp::MaseTools::getSelectedSites(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ getSitesWithoutGaps()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getSitesWithoutGaps ( const PolymorphismSequenceContainer & psc )

static

Retrieves sites without gaps from PolymorphismSequenceContainer.

Parameters

psc	a PolymorphismSequenceContainer reference

Definition at line 210 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::addSite(), bpp::VectorSiteContainer::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::VectorSiteContainer::getSequencesNames(), bpp::NoGapSiteContainerIterator::hasMoreSites(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::NoGapSiteContainerIterator::nextSite(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), bpp::PolymorphismSequenceContainer::setGroupId(), bpp::PolymorphismSequenceContainer::setSequenceCount(), and bpp::VectorSiteContainer::setSequencesNames().

◆ getSynonymousSites()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getSynonymousSites	(	const PolymorphismSequenceContainer &	psc,
		const GeneticCode &	gCode
	)

static

Retrieve synonymous codon sites.

Parameters

psc	a PolymorphismSequenceContainer.
gCode	The genetic code to use

Returns: A new PolymorphismSequenceContainer with only synonymous sites.

Definition at line 592 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::getAlphabet(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getNumberOfSites(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::VectorSiteContainer::getSequencesNames(), bpp::VectorSiteContainer::getSite(), bpp::PolymorphismSequenceContainer::isIngroupMember(), and bpp::CodonSiteTools::isSynonymousPolymorphic().

◆ read()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::read	(	const std::string &	path,
		const Alphabet *	alpha
	)

static

Read a Mase+ file and return a PolymorphismSequenceContainer. Toggle Sequence when selection tag begin with OUTGROUP (see Polymorphix)

Parameters

path	Path to the Mase+ file
alpha	Sequence Alphabet

Exceptions

Exception if the file is not in the specified format

Definition at line 52 of file PolymorphismSequenceContainerTools.cpp.

References bpp::MaseTools::getAvailableSequenceSelections(), bpp::OrderedSequenceContainer::getGeneralComments(), bpp::MaseTools::getSequenceSet(), bpp::Mase::readSequences(), and bpp::PolymorphismSequenceContainer::setAsOutgroupMember().

◆ sample()

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::sample	(	const PolymorphismSequenceContainer &	psc,
		size_t	n,
		bool	replace = `true`
	)

static

Get a random set of sequences.

Parameters

psc	a PolymorphismSequenceContainer reference
n	the number of sequence to get
replace	a boolean flag true for sampling with replacement

Definition at line 194 of file PolymorphismSequenceContainerTools.cpp.

References bpp::VectorSiteContainer::getNumberOfSequences(), bpp::RandomTools::getSample(), and getSelectedSequences().

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

Bpp/PopGen/PolymorphismSequenceContainerTools.h
Bpp/PopGen/PolymorphismSequenceContainerTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ~PolymorphismSequenceContainerTools()

Member Function Documentation

◆ excludeFlankingGap()

◆ extractGroup()

◆ extractIngroup()

◆ extractOutgroup()

◆ get3Prime()

◆ get5Prime()

◆ getCompleteSites()

◆ getIngroupSpeciesName()

◆ getIntrons()

◆ getNonCodingSites()

◆ getNonSynonymousSites()

◆ getNumberOfCompleteSites()

◆ getNumberOfNonGapSites()

◆ getOnePosition()

◆ getSelectedSequences()

◆ getSelectedSites()

◆ getSitesWithoutGaps()

◆ getSynonymousSites()

◆ read()

◆ sample()