bpp::PolymorphismSequenceContainerTools Class Reference

Utilitary function to manipulate PolymorphismSequenceContainer. More...

#include <Bpp/PopGen/PolymorphismSequenceContainerTools.h>

List of all members.

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)
static PolymorphismSequenceContainer *	extractIngroup (const PolymorphismSequenceContainer &psc) throw (Exception)
	Extract ingroup sequences from a PolymorphismSequenceContainer and create a new one.
static PolymorphismSequenceContainer *	extractOutgroup (const PolymorphismSequenceContainer &psc) throw (Exception)
	Extract outgroup sequences from a PolymorphismSequenceContainer and create a new one.
static PolymorphismSequenceContainer *	extractGroup (const PolymorphismSequenceContainer &psc, size_t group_id) throw (Exception)
	Extract a special group from the PolymorphismSequenceContainer.
static PolymorphismSequenceContainer *	getSelectedSequences (const PolymorphismSequenceContainer &psc, const SequenceSelection &ss)
	Extract selected sequences.
static PolymorphismSequenceContainer *	sample (const PolymorphismSequenceContainer &psc, size_t n, bool replace=true)
	Get a random set of sequences.
static PolymorphismSequenceContainer *	getSitesWithoutGaps (const PolymorphismSequenceContainer &psc)
	Retrieves sites without gaps from PolymorphismSequenceContainer.
static size_t	getNumberOfNonGapSites (const PolymorphismSequenceContainer &psc, bool ingroup) throw (Exception)
	Return number of sites without gaps in a PolymorphismSequenceContainer.
static size_t	getNumberOfCompleteSites (const PolymorphismSequenceContainer &psc, bool ingroup) throw (Exception)
	Return number of completely resolved sites in a PolymorphismSequenceContainer.
static PolymorphismSequenceContainer *	getCompleteSites (const PolymorphismSequenceContainer &psc)
	Retrieves complete sites from a PolymorphismSequenceContainer.
static PolymorphismSequenceContainer *	excludeFlankingGap (const PolymorphismSequenceContainer &psc)
	exclude flanking sites with gap but keep gap sites within the alignment
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.
static PolymorphismSequenceContainer *	getNonCodingSites (const PolymorphismSequenceContainer &psc, const std::string &setName)
	Retrieve non-coding sites defined in the mase file header.
static PolymorphismSequenceContainer *	getOnePosition (const PolymorphismSequenceContainer &psc, const std::string &setName, size_t pos)
	Retrieve sites at one codon position (1,2,3)
static PolymorphismSequenceContainer *	getIntrons (const PolymorphismSequenceContainer &psc, const std::string &setName, const CodonAlphabet *ca)
	Retrieve intron sites.
static PolymorphismSequenceContainer *	get5Prime (const PolymorphismSequenceContainer &psc, const std::string &setName)
	Retrieve 5' sites.
static PolymorphismSequenceContainer *	get3Prime (const PolymorphismSequenceContainer &psc, const std::string &setName, const CodonAlphabet *ca)
	Retrieve 3' sites.
static std::string	getIngroupSpeciesName (const PolymorphismSequenceContainer &psc)
	Get the species name of the ingroup.

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Detailed Description

Utilitary function to manipulate PolymorphismSequenceContainer.

Author:

Sylvain Gaillard

Definition at line 71 of file PolymorphismSequenceContainerTools.h.

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Constructor & Destructor Documentation

PolymorphismSequenceContainerTools::~PolymorphismSequenceContainerTools

(

)

Definition at line 46 of file PolymorphismSequenceContainerTools.cpp.

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Member Function Documentation

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

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().

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().

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().

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::get3Prime	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		const CodonAlphabet *	ca
	)		[static]

Retrieve 3' sites.

Parameters:

psc	a PolymorphismSequenceContainer
setName	name of the CDS site selection
ca	a codon alphabet

Definition at line 525 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::PolymorphismSequenceContainer::isIngroupMember(), bpp::CodonAlphabet::isStop(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

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 487 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().

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::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().

string PolymorphismSequenceContainerTools::getIngroupSpeciesName

(

const PolymorphismSequenceContainer &

psc

)

[static]

Get the species name of the ingroup.

Parameters:

psc	a PolymorphismSequenceContainer.

Definition at line 562 of file PolymorphismSequenceContainerTools.cpp.

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

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getIntrons	(	const PolymorphismSequenceContainer &	psc,
		const std::string &	setName,
		const CodonAlphabet *	ca
	)		[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
ca	a codon alphabet

Definition at line 433 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::Site::getValue(), bpp::PolymorphismSequenceContainer::isIngroupMember(), bpp::CodonAlphabet::isStop(), bpp::PolymorphismSequenceContainer::setAsIngroupMember(), bpp::PolymorphismSequenceContainer::setAsOutgroupMember(), and bpp::PolymorphismSequenceContainer::setGroupId().

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::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().

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.

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

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.

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

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::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().

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::addSequence(), 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().

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::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().

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::getSitesWithoutGaps

(

const PolymorphismSequenceContainer &

psc

)

[static]

Retrieves sites without gaps from PolymorphismSequenceContainer.

Parameters:

psc	a PolymorphismSequenceContainer reference

Definition at line 208 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().

PolymorphismSequenceContainer * PolymorphismSequenceContainerTools::read	(	const std::string &	path,
		const Alphabet *	alpha
	)		throw (Exception) [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 50 of file PolymorphismSequenceContainerTools.cpp.

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

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 192 of file PolymorphismSequenceContainerTools.cpp.

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

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

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