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) throw (Exception)
	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) throw (Exception)
	Extract ingroup sequences from a PolymorphismSequenceContainer and create a new one. More...

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

static PolymorphismSequenceContainer *	extractGroup (const PolymorphismSequenceContainer &psc, size_t group_id) throw (Exception)
	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) throw (Exception)
	Return number of sites without gaps in a PolymorphismSequenceContainer. More...

static size_t	getNumberOfCompleteSites (const PolymorphismSequenceContainer &psc, bool ingroup) throw (Exception)
	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...

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 46 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 318 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::clone().

◆ extractGroup()

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

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 149 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::deleteSequence().

◆ extractIngroup()

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

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 103 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::deleteSequence().

◆ extractOutgroup()

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

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 126 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::deleteSequence().

◆ 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 528 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::isIngroupMember(), 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 490 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), 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 293 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), bpp::PolymorphismSequenceContainer::setGroupId(), and bpp::PolymorphismSequenceContainer::setSequenceCount().

◆ getIngroupSpeciesName()

string PolymorphismSequenceContainerTools::getIngroupSpeciesName ( const PolymorphismSequenceContainer & psc )

static

Get the species name of the ingroup.

Parameters

psc	a PolymorphismSequenceContainer.

Definition at line 568 of file PolymorphismSequenceContainerTools.cpp.

◆ 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 433 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::isIngroupMember(), 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 364 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

◆ getNumberOfCompleteSites()

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

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 263 of file PolymorphismSequenceContainerTools.cpp.

◆ getNumberOfNonGapSites()

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

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 233 of file PolymorphismSequenceContainerTools.cpp.

◆ 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 392 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), 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 172 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::addSequenceWithFrequency(), bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::getSequenceCount(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), 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 335 of file PolymorphismSequenceContainerTools.cpp.

References bpp::PolymorphismSequenceContainer::getGroupId(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().