The PolymorphismSequenceContainer class. More...

#include <Bpp/PopGen/PolymorphismSequenceContainer.h>

Inheritance diagram for bpp::PolymorphismSequenceContainer:

Collaboration diagram for bpp::PolymorphismSequenceContainer:

Public Member Functions
	PolymorphismSequenceContainer (const Alphabet *alpha)
	Build a new empty PolymorphismSequenceContainer. More...

	PolymorphismSequenceContainer (size_t size, const Alphabet *alpha)
	Build a new empty PolymorphismSequenceContainer of given size. More...

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

	PolymorphismSequenceContainer (const OrderedSequenceContainer &sc)
	Build a PolymorphismSequenceContainer by copying data from an OrderedSequenceContainer. More...

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

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

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

Sequence *	removeSequence (size_t index)
	Remove a sequence by index and return a pointer to this removed sequence. More...

Sequence *	removeSequence (const std::string &name)
	Remove a sequence by name and return a pointer to this removed sequence. More...

void	deleteSequence (size_t index)
	Delete a sequence by index. More...

void	deleteSequence (const std::string &name)
	Delete a sequence by name. More...

void	addSequenceWithFrequency (const Sequence &sequence, unsigned int frequency, bool checkName=true)
	Add a sequence to the container. More...

void	addSequenceWithFrequency (const Sequence &sequence, size_t sequenceIndex, unsigned int frequency, bool checkName=true)

void	addSequence (const Sequence &sequence, bool checkName=true)

void	addSequence (const Sequence &sequence, size_t sequenceIndex, bool checkName=true)

void	clear ()
	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...

SiteContainer *	toSiteContainer () const
	convert the container to a site container, with sequences dulicated according to their respective frequencies. More...

void	setSequence (const std::string &name, const Sequence &sequence, bool checkName)

void	setSequence (size_t sequenceIndex, const Sequence &sequence, bool checkName)

std::string	toString (const std::string &name) const

virtual std::string	toString (size_t sequenceIndex) const

virtual std::string	toString (size_t sequenceIndex) const =0

virtual std::string	toString (size_t sequenceIndex) const

virtual std::string	toString (size_t sequenceIndex) const =0

const Comments &	getComments (const std::string &name) const

const Comments &	getComments () const

virtual const Comments &	getComments (size_t sequenceIndex) const

virtual const Comments &	getComments (size_t sequenceIndex) const =0

virtual const Comments &	getComments (size_t sequenceIndex) const

virtual const Comments &	getComments (size_t sequenceIndex) const =0

void	setComments (const std::string &name, const Comments &comments)

void	setComments (const Comments &comments)

void	setComments (size_t sequenceIndex, const Comments &comments)

virtual void	setComments (const std::string &name, const Comments &comments)=0

virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0

void	setComments (size_t sequenceIndex, const Comments &comments)

virtual void	setComments (const std::string &name, const Comments &comments)=0

virtual void	setComments (size_t sequenceIndex, const Comments &comments)=0

virtual const Alphabet *	getAlphabet () const=0

const Alphabet *	getAlphabet () const

const Alphabet *	getAlphabet () const

virtual double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const =0

double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const

double	getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const

double	getStateValueAt (size_t siteIndex, const std::string &sequenceName, int state) const

double	getStateValueAt (size_t siteIndex, size_t sequenceIndex, int state) const

virtual const Comments &	getGeneralComments () const=0

const Comments &	getGeneralComments () const

const Comments &	getGeneralComments () const

virtual void	setGeneralComments (const Comments &comments)=0

void	setGeneralComments (const Comments &comments)

void	setGeneralComments (const Comments &comments)

virtual void	deleteGeneralComments ()=0

void	deleteGeneralComments ()

void	deleteGeneralComments ()

void	clearComments ()

const CruxSymbolListSite &	getSymbolListSite (size_t siteIndex) const

CruxSymbolListSite &	getSymbolListSite (size_t siteIndex)

size_t	getSize () const

size_t	getSize () const

const std::shared_ptr< Site >	getObject (size_t objectIndex) const

std::shared_ptr< Site >	getObject (size_t objectIndex)

const std::shared_ptr< Sequence >	getObject (size_t objectIndex) const

std::shared_ptr< Sequence >	getObject (size_t objectIndex)

const std::shared_ptr< Sequence >	getObject (const std::string &name) const

std::shared_ptr< Sequence >	getObject (const std::string &name)

void	addObject (std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false)

virtual void	addObject (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false)

void	addObject (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false)

virtual void	addObject (std::shared_ptr< T > object, size_t objectIndex, const std::string &name, bool check=false)=0

virtual void	addObject (std::shared_ptr< T > object, const std::string &name, bool checkName=false)

void	addObject (std::shared_ptr< T > object, const std::string &name, bool checkName=false)

void	addObject (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false)

void	addObject (std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false)

void	addObject (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false)

void	insertObject (std::shared_ptr< Site > object, size_t objectIndex)

virtual void	insertObject (std::shared_ptr< T > object, size_t objectIndex)

void	insertObject (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name)

virtual void	insertObject (std::shared_ptr< T > object, size_t objectIndex, const std::string &name)=0

void	insertObject (std::shared_ptr< T > object, size_t objectIndex)

void	insertObject (std::shared_ptr< Site > object, size_t objectIndex)

void	insertObject (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name)

bool	isAvailablePosition (size_t objectIndex) const

bool	isAvailablePosition (size_t objectIndex) const

std::shared_ptr< Site >	removeObject (size_t objectIndex)

std::shared_ptr< Sequence >	removeObject (size_t objectIndex)

std::shared_ptr< Sequence >	removeObject (const std::string &name)

std::shared_ptr< Site >	deleteObject (size_t objectIndex)

virtual std::shared_ptr< T >	deleteObject (const std::string &name)

std::shared_ptr< Sequence >	deleteObject (size_t objectIndex)

void	deleteObjects (size_t objectIndex, size_t length)

void	deleteObjects (size_t objectIndex, size_t length)

void	appendObject (std::shared_ptr< Site > object)

virtual void	appendObject (std::shared_ptr< T > object)

void	appendObject (std::shared_ptr< Sequence > object, const std::string &name, bool check=true)

void	appendObject (std::shared_ptr< T > object)

void	appendObject (std::shared_ptr< Site > object)

void	appendObject (std::shared_ptr< Sequence > object, const std::string &name, bool check=true)

void	setSize (size_t size)

void	setSize (size_t size)

size_t	getNumberOfObjects () const

size_t	getObjectPosition (const std::string &name) const

std::string	getObjectName (size_t objectIndex) const

bool	hasObject (const std::string &name) const

std::vector< std::string >	getObjectsNames () const

void	setObjectsNames (const std::vector< std::string > &names)

void	setObjectName (size_t pos, const std::string &name)

void	changeName (const std::string &okey, const std::string &nkey)

const Site &	getSite (size_t siteIndex) const

Site &	getSite (size_t siteIndex)

const Site &	getSite (size_t siteIndex) const

Site &	getSite (size_t siteIndex)

void	setSite (size_t siteIndex, const Site &site, bool checkPosition=true)

void	setSite (size_t siteIndex, const Site &site, bool checkPosition=true)

std::shared_ptr< Site >	deleteSite (size_t siteIndex)

std::shared_ptr< Site >	deleteSite (size_t siteIndex)

void	addSite (const Site &site, bool checkPosition=true)

void	addSite (const Site &site, int position, bool checkPosition=true)

void	addSite (const Site &site, size_t siteIndex, bool checkPosition=true)

void	addSite (const Site &site, size_t siteIndex, int position, bool checkPosition=true)

void	addSite (const Site &site, bool checkPosition=true)

void	addSite (const Site &site, int position, bool checkPosition=true)

void	addSite (const Site &site, size_t siteIndex, bool checkPosition=true)

void	addSite (const Site &site, size_t siteIndex, int position, bool checkPosition=true)

void	deleteSites (size_t siteIndex, size_t length)

void	deleteSites (size_t siteIndex, size_t length)

size_t	getNumberOfSites () const

size_t	getNumberOfSites () const

void	reindexSites ()

void	reindexSites ()

Vint	getSitePositions () const

Vint	getSitePositions () const

void	setSitePositions (Vint vPositions)

void	setSitePositions (Vint vPositions)

const Sequence &	getSequence (size_t sequenceIndex) const

const Sequence &	getSequence (const std::string &name) const

const Sequence &	getSequence (size_t sequenceIndex) const

const Sequence &	getSequence (const std::string &name) const

bool	hasSequence (const std::string &name) const

bool	hasSequence (const std::string &name) const

size_t	getSequencePosition (const std::string &name) const

size_t	getSequencePosition (const std::string &name) const

size_t	getNumberOfSequences () const

size_t	getNumberOfSequences () const

std::vector< std::string >	getSequencesNames () const

std::vector< std::string >	getSequencesNames () const

void	setSequencesNames (const std::vector< std::string > &names, bool checkNames=true)

void	setSequencesNames (const std::vector< std::string > &names, bool checkNames=true)

VectorSiteContainer *	createEmptyContainer () const

VectorSiteContainer *	createEmptyContainer () const

int &	valueAt (const std::string &sequenceName, size_t elementIndex)

const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const

int &	valueAt (size_t sequenceIndex, size_t elementIndex)

const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const

int &	valueAt (const std::string &sequenceName, size_t elementIndex)

const int &	valueAt (const std::string &sequenceName, size_t elementIndex) const

int &	valueAt (size_t sequenceIndex, size_t elementIndex)

const int &	valueAt (size_t sequenceIndex, size_t elementIndex) const

int &	operator() (const std::string &sequenceName, size_t elementIndex)

const int &	operator() (const std::string &sequenceName, size_t elementIndex) const

int &	operator() (size_t sequenceIndex, size_t elementIndex)

const int &	operator() (size_t sequenceIndex, size_t elementIndex) const

double	operator() (size_t siteIndex, const std::string &sequenceName, int state) const

double	operator() (size_t siteIndex, size_t sequenceIndex, int state) const

int &	operator() (const std::string &sequenceName, size_t elementIndex)

const int &	operator() (const std::string &sequenceName, size_t elementIndex) const

int &	operator() (size_t sequenceIndex, size_t elementIndex)

const int &	operator() (size_t sequenceIndex, size_t elementIndex) const

double	operator() (size_t siteIndex, const std::string &sequenceName, int state) const

double	operator() (size_t siteIndex, size_t sequenceIndex, int state) const

virtual const std::string &	getName (size_t sequenceIndex) const

virtual const std::string &	getName (size_t sequenceIndex) const

Protected Member Functions
void	realloc (size_t n)

std::shared_ptr< Site >	getObject_ (size_t objectIndex) const

std::shared_ptr< T >	getObject_ (size_t objectIndex) const

void	addObject_ (std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false) const

void	addObject_ (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false) const

void	addObject_ (std::shared_ptr< T > object, const std::string &name, bool checkName=false) const

void	addObject_ (std::shared_ptr< T > object, size_t objectIndex, bool checkPosition=false) const

void	addObject_ (std::shared_ptr< Site > object, size_t objectIndex, bool checkPosition=false) const

void	addObject_ (std::shared_ptr< Sequence > object, size_t objectIndex, const std::string &name, bool check=false) const

Protected Attributes
const Alphabet *	alphabet_

Comments	comments_

std::vector< std::shared_ptr< Site > >	positions_

std::vector< std::shared_ptr< T > >	positions_

Private Attributes
std::vector< bool >	ingroup_

std::vector< unsigned int >	count_

std::vector< size_t >	group_

std::vector< std::string >	vNames_

std::map< std::string, size_t >	mNames_

std::map< std::string, std::shared_ptr< T > >	mObjects_

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 102 of file PolymorphismSequenceContainer.h.

Constructor & Destructor Documentation

◆ PolymorphismSequenceContainer() [1/8]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const Alphabet * alpha )

Build a new empty PolymorphismSequenceContainer.

Definition at line 51 of file PolymorphismSequenceContainer.cpp.

Referenced by clone().

◆ PolymorphismSequenceContainer() [2/8]

PolymorphismSequenceContainer::PolymorphismSequenceContainer	(	size_t	size,
		const Alphabet *	alpha
	)

Build a new empty PolymorphismSequenceContainer of given size.

Definition at line 59 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [3/8]

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

Build a new empty PolymorphismSequenceContainer with given sequence names.

Definition at line 67 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [4/8]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const OrderedSequenceContainer & sc )

Build a PolymorphismSequenceContainer by copying data from an OrderedSequenceContainer.

Parameters

sc	Sequence container to convert.

Definition at line 75 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [5/8]

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

Build a PolymorphismSequenceContainer by copying data from an OrderedSequenceContainer.

Note: In case of count = false, the constructor with 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 83 of file PolymorphismSequenceContainer.cpp.

References addSequenceWithFrequency(), bpp::SequenceTools::areSequencesIdentical(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::OrderedSequenceContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getSequence(), bpp::OrderedSequenceContainer::getSequence(), group_, incrementSequenceCount(), and ingroup_.

◆ PolymorphismSequenceContainer() [6/8]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const SiteContainer & sc )

Build a PolymorphismSequenceContainer by copying data from a SiteContainer.

Parameters

sc	Sequence container to convert.

Definition at line 113 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [7/8]

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

Build a PolymorphismSequenceContainer by copying data from a SiteContainer.

Note: In case of count = false, the constructor with 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 121 of file PolymorphismSequenceContainer.cpp.

References addSequenceWithFrequency(), bpp::SequenceTools::areSequencesIdentical(), bpp::VectorSiteContainer::getNumberOfSequences(), bpp::SiteContainer::getNumberOfSequences(), bpp::VectorSiteContainer::getSequence(), bpp::SiteContainer::getSequence(), group_, incrementSequenceCount(), and ingroup_.

◆ PolymorphismSequenceContainer() [8/8]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const PolymorphismSequenceContainer & psc )

Copy constructor.

Definition at line 151 of file PolymorphismSequenceContainer.cpp.

References count_, getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), getSequenceCount(), group_, ingroup_, and isIngroupMember().

◆ ~PolymorphismSequenceContainer()

PolymorphismSequenceContainer::~PolymorphismSequenceContainer ( )

virtual

Destroy a PolymorphismSequenceContainer.

Definition at line 188 of file PolymorphismSequenceContainer.cpp.

References clear().

Member Function Documentation

◆ addSequence() [1/2]

void bpp::PolymorphismSequenceContainer::addSequence	(	const Sequence &	sequence,
		bool	checkName = `true`
	)

inlinevirtual

Reimplemented from bpp::VectorSiteContainer.

Definition at line 225 of file PolymorphismSequenceContainer.h.

References addSequenceWithFrequency().

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

◆ addSequence() [2/2]

void bpp::PolymorphismSequenceContainer::addSequence	(	const Sequence &	sequence,
		size_t	sequenceIndex,
		bool	checkName = `true`
	)

inline

Definition at line 228 of file PolymorphismSequenceContainer.h.

References addSequenceWithFrequency().

◆ addSequenceWithFrequency() [1/2]

void PolymorphismSequenceContainer::addSequenceWithFrequency	(	const Sequence &	sequence,
		size_t	sequenceIndex,
		unsigned int	frequency,
		bool	checkName = `true`
	)

Definition at line 268 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::addSequence(), count_, group_, and ingroup_.

◆ addSequenceWithFrequency() [2/2]

void PolymorphismSequenceContainer::addSequenceWithFrequency	(	const Sequence &	sequence,
		unsigned int	frequency,
		bool	checkName = `true`
	)

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 251 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::addSequence(), count_, group_, and ingroup_.

Referenced by addSequence(), bpp::DataSet::getPolymorphismSequenceContainer(), bpp::PolymorphismSequenceContainerTools::getSelectedSequences(), and PolymorphismSequenceContainer().

◆ clear()

void PolymorphismSequenceContainer::clear ( )

virtual

Clear the container of all its sequences.

Reimplemented from bpp::VectorSiteContainer.

Definition at line 285 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::clear(), count_, group_, and ingroup_.

Referenced by ~PolymorphismSequenceContainer().

◆ clone()

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

inlinevirtual

Clone a PolymorphismSequenceContainer.

Reimplemented from bpp::VectorSiteContainer.

Definition at line 181 of file PolymorphismSequenceContainer.h.

References PolymorphismSequenceContainer().

Referenced by bpp::PolymorphismSequenceContainerTools::excludeFlankingGap(), bpp::PolymorphismSequenceContainerTools::extractGroup(), bpp::PolymorphismSequenceContainerTools::extractIngroup(), and bpp::PolymorphismSequenceContainerTools::extractOutgroup().

◆ 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 504 of file PolymorphismSequenceContainer.cpp.

References decrementSequenceCount(), and bpp::VectorSiteContainer::getSequencePosition().

◆ decrementSequenceCount() [2/2]

void PolymorphismSequenceContainer::decrementSequenceCount ( size_t index )

Removz 1 to the sequence count.

Exceptions

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

Definition at line 493 of file PolymorphismSequenceContainer.cpp.

References count_, and bpp::VectorSiteContainer::getNumberOfSequences().

Referenced by decrementSequenceCount().

◆ deleteSequence() [1/2]

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

Delete a sequence by name.

Exceptions

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

Definition at line 237 of file PolymorphismSequenceContainer.cpp.

References removeSequence().

◆ deleteSequence() [2/2]

void PolymorphismSequenceContainer::deleteSequence ( size_t index )

Delete a sequence by index.

Exceptions

IndexOutOfBoundsException if index excedes the number of sequences.

Definition at line 223 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getNumberOfSequences(), and removeSequence().

Referenced by bpp::PolymorphismSequenceContainerTools::extractGroup(), bpp::PolymorphismSequenceContainerTools::extractIngroup(), and bpp::PolymorphismSequenceContainerTools::extractOutgroup().

◆ getAllGroupsIds()

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

Get all the groups identifiers.

Definition at line 318 of file PolymorphismSequenceContainer.cpp.

References group_.

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

◆ getGroupId() [1/2]

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

Get the group identifier of a sequence.

Exceptions

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

Definition at line 304 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and group_.

◆ getGroupId() [2/2]

size_t PolymorphismSequenceContainer::getGroupId ( size_t index ) const

Get the group identifier of the sequence.

Exceptions

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

Definition at line 295 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getNumberOfSequences(), and group_.

◆ getNumberOfGroups()

size_t PolymorphismSequenceContainer::getNumberOfGroups ( ) const

Get the number of groups.

Definition at line 353 of file PolymorphismSequenceContainer.cpp.

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 531 of file PolymorphismSequenceContainer.cpp.

References getSequenceCount(), and bpp::VectorSiteContainer::getSequencePosition().

◆ getSequenceCount() [2/2]

unsigned int PolymorphismSequenceContainer::getSequenceCount ( size_t index ) const

Get the count of a sequence by index.

Exceptions

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

Definition at line 522 of file PolymorphismSequenceContainer.cpp.

References count_, and bpp::VectorSiteContainer::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 360 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 479 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and incrementSequenceCount().

◆ incrementSequenceCount() [2/2]

void PolymorphismSequenceContainer::incrementSequenceCount ( size_t index )

Add 1 to the sequence count.

Exceptions

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

Definition at line 470 of file PolymorphismSequenceContainer.cpp.

References count_, and bpp::VectorSiteContainer::getNumberOfSequences().

Referenced by incrementSequenceCount(), and PolymorphismSequenceContainer().

◆ isIngroupMember() [1/2]

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

Tell if a sequence is ingroup by name.

Exceptions

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

Definition at line 379 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and ingroup_.

◆ isIngroupMember() [2/2]

bool PolymorphismSequenceContainer::isIngroupMember ( size_t index ) const

Tell if the sequence is ingroup by index.

Exceptions

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

Definition at line 370 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getNumberOfSequences(), and ingroup_.

◆ operator=()

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

Operator= : copy operator.

Definition at line 167 of file PolymorphismSequenceContainer.cpp.

References count_, getGroupId(), bpp::VectorSiteContainer::getNumberOfSequences(), getSequenceCount(), group_, ingroup_, isIngroupMember(), and bpp::VectorSiteContainer::operator=().

◆ removeSequence() [1/2]

Sequence * PolymorphismSequenceContainer::removeSequence ( const std::string & name )

virtual

Remove a sequence by name and return a pointer to this removed sequence.

Exceptions

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

Reimplemented from bpp::VectorSiteContainer.

Definition at line 209 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and removeSequence().

◆ removeSequence() [2/2]

Sequence * PolymorphismSequenceContainer::removeSequence ( size_t index )

virtual

Remove a sequence by index and return a pointer to this removed sequence.

Exceptions

IndexOutOfBoundsException if index excedes the number of sequences.

Reimplemented from bpp::VectorSiteContainer.

Definition at line 197 of file PolymorphismSequenceContainer.cpp.

References count_, bpp::VectorSiteContainer::getNumberOfSequences(), group_, ingroup_, and bpp::VectorSiteContainer::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 402 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and ingroup_.

◆ setAsIngroupMember() [2/2]

void PolymorphismSequenceContainer::setAsIngroupMember ( size_t index )

Set a sequence as ingroup member by index.

Exceptions

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

Definition at line 393 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::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 426 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and ingroup_.

◆ setAsOutgroupMember() [2/2]

void PolymorphismSequenceContainer::setAsOutgroupMember ( size_t index )

Set a sequence as outgroup member by index.

Exceptions

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

Definition at line 417 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getNumberOfSequences(), and ingroup_.

◆ setGroupId() [1/2]

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

Set the group identifier of a sequence.

Exceptions

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

Definition at line 339 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::getSequencePosition(), and group_.

◆ setGroupId() [2/2]

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

Set the group identifier of a sequence.

Exceptions

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

Definition at line 330 of file PolymorphismSequenceContainer.cpp.

References bpp::VectorSiteContainer::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 452 of file PolymorphismSequenceContainer.cpp.

References count(), bpp::VectorSiteContainer::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 excedes the number of sequences in the container.
BadIntegerException	if count < 1 ... use deleteSequence instead of setting the count to 0.

Definition at line 441 of file PolymorphismSequenceContainer.cpp.

References count(), count_, and bpp::VectorSiteContainer::getNumberOfSequences().

Referenced by bpp::PolymorphismSequenceContainerTools::getCompleteSites(), bpp::PolymorphismSequenceContainerTools::getSitesWithoutGaps(), and setSequenceCount().