The PolymorphismSequenceContainer class. More...

#include <Bpp/PopGen/PolymorphismSequenceContainer.h>

Inheritance diagram for bpp::PolymorphismSequenceContainer:

Collaboration diagram for bpp::PolymorphismSequenceContainer:

Public Member Functions
	PolymorphismSequenceContainer (std::shared_ptr< const Alphabet > alpha)
	Build a new empty PolymorphismSequenceContainer. More...

	PolymorphismSequenceContainer (size_t size, std::shared_ptr< const Alphabet > alpha)
	Build a new empty PolymorphismSequenceContainer of given size. More...

	PolymorphismSequenceContainer (const std::vector< std::string > &names, std::shared_ptr< const Alphabet > alpha)
	Build a new empty PolymorphismSequenceContainer with given sequence names. More...

	PolymorphismSequenceContainer (const SequenceContainerInterface &sc)
	Build a PolymorphismSequenceContainer by copying data from a SequenceContainer. More...

	PolymorphismSequenceContainer (const SequenceContainerInterface &sc, bool count)
	Build a PolymorphismSequenceContainer by copying data from a SequenceContainer. More...

	PolymorphismSequenceContainer (const PolymorphismSequenceContainer &psc)
	Copy constructor. More...

PolymorphismSequenceContainer &	operator= (const PolymorphismSequenceContainer &psc)
	Operator= : copy operator. More...

virtual	~PolymorphismSequenceContainer ()
	Destroy a PolymorphismSequenceContainer. More...

PolymorphismSequenceContainer *	clone () const override
	Clone a PolymorphismSequenceContainer. More...

std::unique_ptr< Sequence >	removeSequence (size_t sequencePosition) override

std::unique_ptr< Sequence >	removeSequence (const std::string &sequenceKey) override

void	deleteSequence (size_t sequencePosition) override

void	deleteSequence (const std::string &sequenceKey) override

void	addSequenceWithFrequency (const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence, unsigned int frequency)
	Add a sequence to the container. More...

void	insertSequenceWithFrequency (size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey, unsigned int frequency)

void	addSequence (const std::string &sequenceKey, std::unique_ptr< Sequence > &sequence) override

void	insertSequence (size_t sequencePosition, std::unique_ptr< Sequence > &sequence, const std::string &sequenceKey) override

void	clear () override
	Clear the container of all its sequences. More...

size_t	getGroupId (size_t index) const
	Get the group identifier of the sequence. More...

size_t	getGroupId (const std::string &name) const
	Get the group identifier of a sequence. More...

std::set< size_t >	getAllGroupsIds () const
	Get all the groups identifiers. More...

void	setGroupId (size_t index, size_t group_id)
	Set the group identifier of a sequence. More...

void	setGroupId (const std::string &name, size_t group_id)
	Set the group identifier of a sequence. More...

size_t	getNumberOfGroups () const
	Get the number of groups. More...

bool	hasOutgroup () const

bool	isIngroupMember (size_t index) const
	Tell if the sequence is ingroup by index. More...

bool	isIngroupMember (const std::string &name) const
	Tell if a sequence is ingroup by name. More...

void	setAsIngroupMember (size_t index)
	Set a sequence as ingroup member by index. More...

void	setAsIngroupMember (const std::string &name)
	Set a sequence as ingroup member by name. More...

void	setAsOutgroupMember (size_t index)
	Set a sequence as outgroup member by index. More...

void	setAsOutgroupMember (const std::string &name)
	Set a sequence as outgroup member by name. More...

void	setSequenceCount (size_t index, unsigned int count)
	Set the count of a sequence by index. More...

void	setSequenceCount (const std::string &name, unsigned int count)
	Set the count of a sequence by name. More...

void	incrementSequenceCount (size_t index)
	Add 1 to the sequence count. More...

void	incrementSequenceCount (const std::string &name)
	Add 1 to the sequence count. More...

void	decrementSequenceCount (size_t index)
	Removz 1 to the sequence count. More...

void	decrementSequenceCount (const std::string &name)
	Remove 1 to the sequence count. More...

unsigned int	getSequenceCount (size_t index) const
	Get the count of a sequence by index. More...

unsigned int	getSequenceCount (const std::string &name) const
	Get the count of a sequence by name. More...

std::unique_ptr< SiteContainerInterface >	toSiteContainer () const
	convert the container to a site container, with sequences dulicated according to their respective frequencies. More...

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

virtual const Comments &	getComments () const=0

const Comments &	getComments () const override

virtual void	setComments (const Comments &comments)=0

void	setComments (const Comments &comments) override

virtual void	clearComments ()=0

void	clearComments () override

const SiteType &	site (size_t sitePosition) const override

const SiteType &	site (size_t sitePosition) const override

void	setSite (size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override

void	setSite (size_t sitePosition, std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override

std::unique_ptr< SiteType >	removeSite (size_t sitePosition) override

std::unique_ptr< SiteType >	removeSite (size_t sitePosition) override

void	deleteSite (size_t sitePosition) override

void	deleteSite (size_t sitePosition) override

void	addSite (std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override

void	addSite (std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate=true) override

void	addSite (std::unique_ptr< SiteType > &site, bool checkCoordinate=true) override

void	addSite (std::unique_ptr< SiteType > &site, size_t sitePosition, bool checkCoordinate=true) override

void	deleteSites (size_t sitePosition, size_t length) override

void	deleteSites (size_t sitePosition, size_t length) override

size_t	getNumberOfSites () const override

size_t	getNumberOfSites () const override

void	reindexSites () override

void	reindexSites () override

Vint	getSiteCoordinates () const override

Vint	getSiteCoordinates () const override

void	setSiteCoordinates (const Vint &vCoordinates) override

void	setSiteCoordinates (const Vint &vCoordinates) override

bool	hasSequence (const std::string &sequenceKey) const override

bool	hasSequence (const std::string &sequenceKey) const override

size_t	getSequencePosition (const std::string &sequenceKey) const override

size_t	getSequencePosition (const std::string &sequenceKey) const override

const SequenceType &	sequence (const std::string &sequenceKey) const override

const SequenceType &	sequence (size_t sequencePosition) const override

const SequenceType &	sequence (const std::string &sequenceKey) const override

const SequenceType &	sequence (size_t sequencePosition) const override

size_t	getNumberOfSequences () const override

size_t	getNumberOfSequences () const override

std::vector< std::string >	getSequenceKeys () const override

std::vector< std::string >	getSequenceKeys () const override

void	setSequenceKeys (const std::vector< std::string > &sequenceKeys) override

void	setSequenceKeys (const std::vector< std::string > &sequenceKeys) override

const std::string &	sequenceKey (size_t sequencePosition) const override

const std::string &	sequenceKey (size_t sequencePosition) const override

std::vector< std::string >	getSequenceNames () const override

std::vector< std::string >	getSequenceNames () const override

void	setSequenceNames (const std::vector< std::string > &names, bool updateKeys) override

void	setSequenceNames (const std::vector< std::string > &names, bool updateKeys) override

std::vector< Comments >	getSequenceComments () const override

std::vector< Comments >	getSequenceComments () const override

TemplateVectorSiteContainer< SiteType, SequenceType > *	createEmptyContainer () const override

TemplateVectorSiteContainer< SiteType, SequenceType > *	createEmptyContainer () const override

const SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t sitePosition) const override

SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t sitePosition) override

const SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t sitePosition) const override

SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t sitePosition) override

const SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t sitePosition) const override

SequenceType::ElementType &	valueAt (const std::string &sequenceKey, size_t sitePosition) override

const SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t sitePosition) const override

SequenceType::ElementType &	valueAt (size_t sequencePosition, size_t sitePosition) override

double	getStateValueAt (size_t sitePosition, const std::string &sequenceKey, int state) const override

double	getStateValueAt (size_t sitePosition, size_t sequencePosition, int state) const override

double	getStateValueAt (size_t sitePosition, const std::string &sequenceKey, int state) const override

double	getStateValueAt (size_t sitePosition, size_t sequencePosition, int state) const override

double	operator() (size_t sitePosition, const std::string &sequenceKey, int state) const override

double	operator() (size_t sitePosition, size_t sequencePosition, int state) const override

double	operator() (size_t sitePosition, const std::string &sequenceKey, int state) const override

double	operator() (size_t sitePosition, size_t sequencePosition, int state) const override

void	setSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequence) override

void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequence) override

void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequence, const std::string &sequenceKey) override

void	setSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequence) override

void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequence) override

void	setSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequence, const std::string &sequenceKey) override

void	addSequence (const std::string &sequenceKey, std::unique_ptr< SequenceType > &sequence) override

void	insertSequence (size_t sequencePosition, std::unique_ptr< SequenceType > &sequence, const std::string &sequenceKey) override

Protected Member Functions
SiteType &	site_ (size_t sitePosition)

void	realloc_ (size_t n)

Protected Attributes
VectorPositionedContainer< SiteType >	siteContainer_

VectorMappedContainer< SequenceType >	sequenceContainer_

std::vector< std::string >	sequenceNames_

std::vector< Comments >	sequenceComments_

std::shared_ptr< const Alphabet >	alphabet_

Comments	comments_

Private Attributes
std::vector< bool >	ingroup_

std::vector< unsigned int >	count_

std::vector< size_t >	group_

Detailed Description

The PolymorphismSequenceContainer class.

This is a VectorSiteContainer with effectif for each sequence. It also has flag for ingroup and outgroup.

Author: Sylvain Gaillard

Definition at line 66 of file PolymorphismSequenceContainer.h.

Constructor & Destructor Documentation

◆ PolymorphismSequenceContainer() [1/6]

bpp::PolymorphismSequenceContainer::PolymorphismSequenceContainer ( std::shared_ptr< const Alphabet > alpha )

inline

Build a new empty PolymorphismSequenceContainer.

Definition at line 79 of file PolymorphismSequenceContainer.h.

Referenced by clone().

◆ PolymorphismSequenceContainer() [2/6]

bpp::PolymorphismSequenceContainer::PolymorphismSequenceContainer	(	size_t	size,
		std::shared_ptr< const Alphabet >	alpha
	)

inline

Build a new empty PolymorphismSequenceContainer of given size.

Definition at line 89 of file PolymorphismSequenceContainer.h.

◆ PolymorphismSequenceContainer() [3/6]

bpp::PolymorphismSequenceContainer::PolymorphismSequenceContainer	(	const std::vector< std::string > &	names,
		std::shared_ptr< const Alphabet >	alpha
	)

inline

Build a new empty PolymorphismSequenceContainer with given sequence names.

Definition at line 99 of file PolymorphismSequenceContainer.h.

◆ PolymorphismSequenceContainer() [4/6]

bpp::PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const SequenceContainerInterface & sc )

inline

Build a PolymorphismSequenceContainer by copying data from a SequenceContainer.

Parameters

sc	Sequence container to convert.

Definition at line 111 of file PolymorphismSequenceContainer.h.

◆ PolymorphismSequenceContainer() [5/6]

PolymorphismSequenceContainer::PolymorphismSequenceContainer	(	const SequenceContainerInterface &	sc,
		bool	count
	)

Build a PolymorphismSequenceContainer by copying data from a SequenceContainer.

Note: In case of count = false, the constructor without additional argument will be more efficient.

Parameters

sc	Sequence container to convert.
count	Tell if identical sequences should be collapsed and counted. If not (the historical behavior), sequences are duplicated and stored with a frequency of 1.

Definition at line 14 of file PolymorphismSequenceContainer.cpp.

References addSequenceWithFrequency(), bpp::SequenceTools::areSequencesIdentical(), bpp::Sequence::clone(), bpp::TemplateSequenceContainerInterface< class, class >::getNumberOfSequences(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), group_, incrementSequenceCount(), ingroup_, bpp::TemplateSequenceContainerInterface< class, class >::sequence(), and bpp::TemplateVectorSiteContainer< class, class >::sequence().

◆ PolymorphismSequenceContainer() [6/6]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const PolymorphismSequenceContainer & psc )

Copy constructor.

Definition at line 51 of file PolymorphismSequenceContainer.cpp.

References count_, getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), getSequenceCount(), group_, ingroup_, and isIngroupMember().

◆ ~PolymorphismSequenceContainer()

PolymorphismSequenceContainer::~PolymorphismSequenceContainer ( )

virtual

Destroy a PolymorphismSequenceContainer.

Class destructor:

Definition at line 88 of file PolymorphismSequenceContainer.cpp.

References clear().

Member Function Documentation

◆ addSequence()

void bpp::PolymorphismSequenceContainer::addSequence	(	const std::string &	sequenceKey,
		std::unique_ptr< Sequence > &	sequence
	)

inlineoverride

Definition at line 193 of file PolymorphismSequenceContainer.h.

References addSequenceWithFrequency(), bpp::TemplateVectorSiteContainer< class, class >::sequence(), and bpp::TemplateVectorSiteContainer< class, class >::sequenceKey().

Referenced by bpp::SequenceStatistics::mkTable().

◆ addSequenceWithFrequency()

void bpp::PolymorphismSequenceContainer::addSequenceWithFrequency	(	const std::string &	sequenceKey,
		std::unique_ptr< Sequence > &	sequence,
		unsigned int	frequency
	)

inline

Add a sequence to the container.

Exceptions

AlphabetMismatchException	if the sequence's alphabet doesn't match the container's alphabet.
SequenceException	if the sequence's size doesn't match the sequence's size of the container.
SequenceException	if the sequence's name already exists in the container.

Definition at line 169 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::addSequence(), count_, group_, ingroup_, bpp::TemplateVectorSiteContainer< class, class >::sequence(), and bpp::TemplateVectorSiteContainer< class, class >::sequenceKey().

Referenced by addSequence(), and PolymorphismSequenceContainer().

◆ clear()

void bpp::PolymorphismSequenceContainer::clear ( )

inlineoverridevirtual

Clear the container of all its sequences.

Reimplemented from bpp::TemplateVectorSiteContainer< class, class >.

Definition at line 208 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::clear(), count_, group_, and ingroup_.

Referenced by ~PolymorphismSequenceContainer().

◆ clone()

PolymorphismSequenceContainer* bpp::PolymorphismSequenceContainer::clone ( ) const

inlineoverridevirtual

Clone a PolymorphismSequenceContainer.

Reimplemented from bpp::TemplateVectorSiteContainer< class, class >.

Definition at line 147 of file PolymorphismSequenceContainer.h.

References PolymorphismSequenceContainer().

◆ decrementSequenceCount() [1/2]

void PolymorphismSequenceContainer::decrementSequenceCount ( const std::string & name )

Remove 1 to the sequence count.

Exceptions

SequenceNotFoundException	if name is not found among the sequences' names.
BadIntegerException	if count < 1 ... use deleteSequence instead of setting the count to 0.

Definition at line 286 of file PolymorphismSequenceContainer.cpp.

References decrementSequenceCount(), and bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition().

◆ decrementSequenceCount() [2/2]

void PolymorphismSequenceContainer::decrementSequenceCount ( size_t index )

Removz 1 to the sequence count.

Exceptions

IndexOutOfBoundsException	if index exceeds the number of sequences in the container.
BadIntegerException	if count < 1 ... use deleteSequence instead of setting the count to 0.

Definition at line 275 of file PolymorphismSequenceContainer.cpp.

References count_, and bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences().

Referenced by decrementSequenceCount().

◆ deleteSequence() [1/2]

void PolymorphismSequenceContainer::deleteSequence ( const std::string & sequenceKey )

overridevirtual

Reimplemented from bpp::TemplateVectorSiteContainer< class, class >.

Definition at line 137 of file PolymorphismSequenceContainer.cpp.

References removeSequence().

◆ deleteSequence() [2/2]

void PolymorphismSequenceContainer::deleteSequence ( size_t sequencePosition )

overridevirtual

Reimplemented from bpp::TemplateVectorSiteContainer< class, class >.

Definition at line 123 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and removeSequence().

◆ getAllGroupsIds()

std::set< size_t > PolymorphismSequenceContainer::getAllGroupsIds ( ) const

Get all the groups identifiers.

Definition at line 151 of file PolymorphismSequenceContainer.cpp.

References group_.

Referenced by bpp::DataSetTools::buildDataSet(), and getNumberOfGroups().

◆ getGroupId() [1/2]

size_t bpp::PolymorphismSequenceContainer::getGroupId ( const std::string & name ) const

inline

Get the group identifier of a sequence.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 233 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and group_.

◆ getGroupId() [2/2]

size_t bpp::PolymorphismSequenceContainer::getGroupId ( size_t index ) const

inline

Get the group identifier of the sequence.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 221 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and group_.

◆ getNumberOfGroups()

size_t bpp::PolymorphismSequenceContainer::getNumberOfGroups ( ) const

inline

Get the number of groups.

Definition at line 283 of file PolymorphismSequenceContainer.h.

References getAllGroupsIds().

◆ getSequenceCount() [1/2]

unsigned int PolymorphismSequenceContainer::getSequenceCount ( const std::string & name ) const

Get the count of a sequence by name.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 313 of file PolymorphismSequenceContainer.cpp.

References getSequenceCount(), and bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition().

◆ getSequenceCount() [2/2]

unsigned int PolymorphismSequenceContainer::getSequenceCount ( size_t index ) const

Get the count of a sequence by index.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 304 of file PolymorphismSequenceContainer.cpp.

References count_, and bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences().

Referenced by bpp::DataSetTools::buildDataSet(), bpp::PolymorphismSequenceContainerTools::getCompleteSites(), bpp::PolymorphismSequenceContainerTools::getNonSynonymousSites(), bpp::PolymorphismSequenceContainerTools::getSelectedSequences(), getSequenceCount(), bpp::PolymorphismSequenceContainerTools::getSitesWithoutGaps(), bpp::PolymorphismSequenceContainerTools::getSynonymousSites(), operator=(), PolymorphismSequenceContainer(), and toSiteContainer().

◆ hasOutgroup()

bool PolymorphismSequenceContainer::hasOutgroup ( ) const

Returns: True is the container contains at least one outgroup sequence.

Definition at line 163 of file PolymorphismSequenceContainer.cpp.

References ingroup_.

◆ incrementSequenceCount() [1/2]

void PolymorphismSequenceContainer::incrementSequenceCount ( const std::string & name )

Add 1 to the sequence count.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 261 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and incrementSequenceCount().

◆ incrementSequenceCount() [2/2]

void PolymorphismSequenceContainer::incrementSequenceCount ( size_t index )

Add 1 to the sequence count.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 252 of file PolymorphismSequenceContainer.cpp.

References count_, and bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences().

Referenced by incrementSequenceCount(), and PolymorphismSequenceContainer().

◆ insertSequence()

void bpp::PolymorphismSequenceContainer::insertSequence	(	size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence,
		const std::string &	sequenceKey
	)

inlineoverride

Definition at line 200 of file PolymorphismSequenceContainer.h.

References insertSequenceWithFrequency(), bpp::TemplateVectorSiteContainer< class, class >::sequence(), and bpp::TemplateVectorSiteContainer< class, class >::sequenceKey().

◆ insertSequenceWithFrequency()

void bpp::PolymorphismSequenceContainer::insertSequenceWithFrequency	(	size_t	sequencePosition,
		std::unique_ptr< Sequence > &	sequence,
		const std::string &	sequenceKey,
		unsigned int	frequency
	)

inline

Definition at line 181 of file PolymorphismSequenceContainer.h.

References count_, group_, ingroup_, bpp::TemplateVectorSiteContainer< class, class >::insertSequence(), bpp::TemplateVectorSiteContainer< class, class >::sequence(), and bpp::TemplateVectorSiteContainer< class, class >::sequenceKey().

Referenced by insertSequence().

◆ isIngroupMember() [1/2]

bool bpp::PolymorphismSequenceContainer::isIngroupMember ( const std::string & name ) const

inline

Tell if a sequence is ingroup by name.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 310 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and ingroup_.

◆ isIngroupMember() [2/2]

bool bpp::PolymorphismSequenceContainer::isIngroupMember ( size_t index ) const

inline

Tell if the sequence is ingroup by index.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 298 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and ingroup_.

◆ operator=()

PolymorphismSequenceContainer & PolymorphismSequenceContainer::operator= ( const PolymorphismSequenceContainer & psc )

Operator= : copy operator.

Definition at line 67 of file PolymorphismSequenceContainer.cpp.

References count_, getGroupId(), bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), getSequenceCount(), group_, ingroup_, isIngroupMember(), and bpp::TemplateVectorSiteContainer< class, class >::operator=().

◆ removeSequence() [1/2]

std::unique_ptr< Sequence > PolymorphismSequenceContainer::removeSequence ( const std::string & sequenceKey )

overridevirtual

Reimplemented from bpp::TemplateVectorSiteContainer< class, class >.

Definition at line 109 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and removeSequence().

◆ removeSequence() [2/2]

std::unique_ptr< Sequence > PolymorphismSequenceContainer::removeSequence ( size_t sequencePosition )

overridevirtual

Other methods:

Reimplemented from bpp::TemplateVectorSiteContainer< class, class >.

Definition at line 97 of file PolymorphismSequenceContainer.cpp.

References count_, bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), group_, ingroup_, and bpp::TemplateVectorSiteContainer< class, class >::removeSequence().

Referenced by deleteSequence(), and removeSequence().

◆ setAsIngroupMember() [1/2]

void PolymorphismSequenceContainer::setAsIngroupMember ( const std::string & name )

Set a sequence as ingroup member by name.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 184 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and ingroup_.

◆ setAsIngroupMember() [2/2]

void PolymorphismSequenceContainer::setAsIngroupMember ( size_t index )

Set a sequence as ingroup member by index.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 175 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and ingroup_.

◆ setAsOutgroupMember() [1/2]

void PolymorphismSequenceContainer::setAsOutgroupMember ( const std::string & name )

Set a sequence as outgroup member by name.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 208 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and ingroup_.

◆ setAsOutgroupMember() [2/2]

void PolymorphismSequenceContainer::setAsOutgroupMember ( size_t index )

Set a sequence as outgroup member by index.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 199 of file PolymorphismSequenceContainer.cpp.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and ingroup_.

Referenced by bpp::SequenceStatistics::mkTable().

◆ setGroupId() [1/2]

void bpp::PolymorphismSequenceContainer::setGroupId	(	const std::string &	name,
		size_t	group_id
	)

inline

Set the group identifier of a sequence.

Exceptions

SequenceNotFoundException if name is not found among the sequences' names.

Definition at line 268 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and group_.

◆ setGroupId() [2/2]

void bpp::PolymorphismSequenceContainer::setGroupId	(	size_t	index,
		size_t	group_id
	)

inline

Set the group identifier of a sequence.

Exceptions

IndexOutOfBoundsException if index exceeds the number of sequences in the container.

Definition at line 256 of file PolymorphismSequenceContainer.h.

References bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences(), and group_.

◆ setSequenceCount() [1/2]

void PolymorphismSequenceContainer::setSequenceCount	(	const std::string &	name,
		unsigned int	count
	)

Set the count of a sequence by name.

Exceptions

throw	SequenceNotFoundException if name is not found among the sequences' names.
BadIntegerException	if count < 1 ... use deleteSequence instead of setting the count to 0.

Definition at line 234 of file PolymorphismSequenceContainer.cpp.

References count(), bpp::TemplateVectorSiteContainer< class, class >::getSequencePosition(), and setSequenceCount().

◆ setSequenceCount() [2/2]

void PolymorphismSequenceContainer::setSequenceCount	(	size_t	index,
		unsigned int	count
	)

Set the count of a sequence by index.

Exceptions

IndexOutOfBoundsException	if index exceeds the number of sequences in the container.
BadIntegerException	if count < 1 ... use deleteSequence instead of setting the count to 0.

Definition at line 223 of file PolymorphismSequenceContainer.cpp.

References count(), count_, and bpp::TemplateVectorSiteContainer< class, class >::getNumberOfSequences().

Referenced by setSequenceCount().