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 OrderedSequenceContainer &sc)
	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 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) throw (IndexOutOfBoundsException)
	Remove a sequence by index and return a pointer to this removed sequence. More...

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

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

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

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

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

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

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

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

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

size_t	getGroupId (const std::string &name) const throw (SequenceNotFoundException)
	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) throw (IndexOutOfBoundsException)
	Set the group identifier of a sequence. More...

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

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

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

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

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

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

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

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

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

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

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

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

void	decrementSequenceCount (size_t index) throw (IndexOutOfBoundsException, BadIntegerException)
	Removz 1 to the sequence count. More...

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

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

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

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 102 of file PolymorphismSequenceContainer.h.

Constructor & Destructor Documentation

◆ PolymorphismSequenceContainer() [1/5]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const Alphabet * alpha )

Build a new empty PolymorphismSequenceContainer.

Definition at line 49 of file PolymorphismSequenceContainer.cpp.

Referenced by clone().

◆ PolymorphismSequenceContainer() [2/5]

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

Build a new empty PolymorphismSequenceContainer of given size.

Definition at line 57 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [3/5]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const OrderedSequenceContainer & sc )

Build a PolymorphismSequenceContainer by copying data from an OrderedSequenceContainer.

Definition at line 65 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [4/5]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const SiteContainer & sc )

Build a PolymorphismSequenceContainer by copying data from a SiteContainer.

Definition at line 73 of file PolymorphismSequenceContainer.cpp.

◆ PolymorphismSequenceContainer() [5/5]

PolymorphismSequenceContainer::PolymorphismSequenceContainer ( const PolymorphismSequenceContainer & psc )

Copy constructor.

Definition at line 81 of file PolymorphismSequenceContainer.cpp.

References count_, getGroupId(), getSequenceCount(), group_, ingroup_, and isIngroupMember().

◆ ~PolymorphismSequenceContainer()

PolymorphismSequenceContainer::~PolymorphismSequenceContainer ( )

virtual

Destroy a PolymorphismSequenceContainer.

Definition at line 118 of file PolymorphismSequenceContainer.cpp.

References clear().

Member Function Documentation

◆ addSequence() [1/2]

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

inline

Definition at line 194 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`
	)
throw	(	Exception
	)

inline

Definition at line 197 of file PolymorphismSequenceContainer.h.

References addSequenceWithFrequency().

◆ addSequenceWithFrequency() [1/2]

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

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 181 of file PolymorphismSequenceContainer.cpp.

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

◆ addSequenceWithFrequency() [2/2]

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

Definition at line 198 of file PolymorphismSequenceContainer.cpp.

◆ clear()

void PolymorphismSequenceContainer::clear ( )

Clear the container of all its sequences.

Definition at line 215 of file PolymorphismSequenceContainer.cpp.

References count_, group_, and ingroup_.

Referenced by ~PolymorphismSequenceContainer().

◆ clone()

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

inline

Clone a PolymorphismSequenceContainer.

Definition at line 150 of file PolymorphismSequenceContainer.h.

References PolymorphismSequenceContainer().

Referenced by bpp::PolymorphismSequenceContainerTools::excludeFlankingGap().

◆ decrementSequenceCount() [1/2]

void PolymorphismSequenceContainer::decrementSequenceCount	(	size_t	index	)
throw	(	IndexOutOfBoundsException,
		BadIntegerException
	)

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 413 of file PolymorphismSequenceContainer.cpp.

◆ decrementSequenceCount() [2/2]

void PolymorphismSequenceContainer::decrementSequenceCount	(	const std::string &	name	)
throw	(	SequenceNotFoundException,
		BadIntegerException
	)

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 424 of file PolymorphismSequenceContainer.cpp.

◆ deleteSequence() [1/2]

void PolymorphismSequenceContainer::deleteSequence	(	size_t	index	)
throw	(	IndexOutOfBoundsException
	)

Delete a sequence by index.

Exceptions

IndexOutOfBoundsException if index excedes the number of sequences.

Definition at line 153 of file PolymorphismSequenceContainer.cpp.

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

◆ deleteSequence() [2/2]

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

Delete a sequence by name.

Exceptions

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

Definition at line 167 of file PolymorphismSequenceContainer.cpp.

◆ getAllGroupsIds()

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

Get all the groups identifiers.

Definition at line 248 of file PolymorphismSequenceContainer.cpp.

References group_.

Referenced by getNumberOfGroups().

◆ getGroupId() [1/2]

size_t PolymorphismSequenceContainer::getGroupId	(	size_t	index	)	const
throw	(	IndexOutOfBoundsException
	)

Get the group identifier of the sequence.

Exceptions

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

Definition at line 225 of file PolymorphismSequenceContainer.cpp.

◆ getGroupId() [2/2]

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

Get the group identifier of a sequence.

Exceptions

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

Definition at line 234 of file PolymorphismSequenceContainer.cpp.

◆ getNumberOfGroups()

size_t PolymorphismSequenceContainer::getNumberOfGroups ( ) const

Get the number of groups.

Definition at line 283 of file PolymorphismSequenceContainer.cpp.

References getAllGroupsIds().

◆ getSequenceCount() [1/2]

unsigned int PolymorphismSequenceContainer::getSequenceCount	(	size_t	index	)	const
throw	(	IndexOutOfBoundsException
	)

Get the count of a sequence by index.

Exceptions

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

Definition at line 442 of file PolymorphismSequenceContainer.cpp.

Referenced by bpp::SequenceStatistics::dvh(), bpp::PolymorphismSequenceContainerTools::getCompleteSites(), bpp::PolymorphismSequenceContainerTools::getSelectedSequences(), bpp::PolymorphismSequenceContainerTools::getSitesWithoutGaps(), operator=(), and PolymorphismSequenceContainer().

◆ getSequenceCount() [2/2]

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

Get the count of a sequence by name.

Exceptions

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

Definition at line 451 of file PolymorphismSequenceContainer.cpp.

◆ incrementSequenceCount() [1/2]

void PolymorphismSequenceContainer::incrementSequenceCount	(	size_t	index	)
throw	(	IndexOutOfBoundsException
	)

Add 1 to the sequence count.

Exceptions

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

Definition at line 390 of file PolymorphismSequenceContainer.cpp.

◆ incrementSequenceCount() [2/2]

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

Add 1 to the sequence count.

Exceptions

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

Definition at line 399 of file PolymorphismSequenceContainer.cpp.

◆ isIngroupMember() [1/2]

bool PolymorphismSequenceContainer::isIngroupMember	(	size_t	index	)	const
throw	(	IndexOutOfBoundsException
	)

Tell if the sequence is ingroup by index.

Exceptions

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

Definition at line 290 of file PolymorphismSequenceContainer.cpp.

◆ isIngroupMember() [2/2]

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

Tell if a sequence is ingroup by name.

Exceptions

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

Definition at line 299 of file PolymorphismSequenceContainer.cpp.

◆ operator=()

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

Operator= : copy operator.

Definition at line 97 of file PolymorphismSequenceContainer.cpp.

References count_, getGroupId(), getSequenceCount(), group_, ingroup_, and isIngroupMember().

◆ removeSequence() [1/2]

Sequence * PolymorphismSequenceContainer::removeSequence	(	size_t	index	)
throw	(	IndexOutOfBoundsException
	)

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

Exceptions

IndexOutOfBoundsException if index excedes the number of sequences.

Definition at line 127 of file PolymorphismSequenceContainer.cpp.

◆ removeSequence() [2/2]

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

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

Exceptions

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

Definition at line 139 of file PolymorphismSequenceContainer.cpp.

◆ setAsIngroupMember() [1/2]

void PolymorphismSequenceContainer::setAsIngroupMember	(	size_t	index	)
throw	(	IndexOutOfBoundsException
	)

Set a sequence as ingroup member by index.

Exceptions

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

Definition at line 313 of file PolymorphismSequenceContainer.cpp.

◆ setAsIngroupMember() [2/2]

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

Set a sequence as ingroup member by name.

Exceptions

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

Definition at line 322 of file PolymorphismSequenceContainer.cpp.

◆ setAsOutgroupMember() [1/2]

void PolymorphismSequenceContainer::setAsOutgroupMember	(	size_t	index	)
throw	(	IndexOutOfBoundsException
	)

Set a sequence as outgroup member by index.

Exceptions

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

Definition at line 337 of file PolymorphismSequenceContainer.cpp.

◆ setAsOutgroupMember() [2/2]

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

Set a sequence as outgroup member by name.

Exceptions

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

Definition at line 346 of file PolymorphismSequenceContainer.cpp.

◆ setGroupId() [1/2]

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

Set the group identifier of a sequence.

Exceptions

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

Definition at line 260 of file PolymorphismSequenceContainer.cpp.

◆ setGroupId() [2/2]

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

Set the group identifier of a sequence.

Exceptions

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

Definition at line 269 of file PolymorphismSequenceContainer.cpp.

◆ setSequenceCount() [1/2]

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

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 361 of file PolymorphismSequenceContainer.cpp.

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

◆ setSequenceCount() [2/2]

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

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 372 of file PolymorphismSequenceContainer.cpp.

Member Data Documentation

◆ count_

std::vector<unsigned int> bpp::PolymorphismSequenceContainer::count_

private

Definition at line 107 of file PolymorphismSequenceContainer.h.

Referenced by clear(), operator=(), and PolymorphismSequenceContainer().

◆ group_

std::vector<size_t> bpp::PolymorphismSequenceContainer::group_

private

Definition at line 108 of file PolymorphismSequenceContainer.h.

Referenced by clear(), getAllGroupsIds(), operator=(), and PolymorphismSequenceContainer().

◆ ingroup_

std::vector<bool> bpp::PolymorphismSequenceContainer::ingroup_

private

Definition at line 106 of file PolymorphismSequenceContainer.h.

Referenced by clear(), operator=(), and PolymorphismSequenceContainer().

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

Bpp/PopGen/PolymorphismSequenceContainer.h
Bpp/PopGen/PolymorphismSequenceContainer.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PolymorphismSequenceContainer() [1/5]

◆ PolymorphismSequenceContainer() [2/5]

◆ PolymorphismSequenceContainer() [3/5]

◆ PolymorphismSequenceContainer() [4/5]

◆ PolymorphismSequenceContainer() [5/5]

◆ ~PolymorphismSequenceContainer()

Member Function Documentation

◆ addSequence() [1/2]

◆ addSequence() [2/2]

◆ addSequenceWithFrequency() [1/2]

◆ addSequenceWithFrequency() [2/2]

◆ clear()

◆ clone()

◆ decrementSequenceCount() [1/2]

◆ decrementSequenceCount() [2/2]

◆ deleteSequence() [1/2]

◆ deleteSequence() [2/2]

◆ getAllGroupsIds()

◆ getGroupId() [1/2]

◆ getGroupId() [2/2]

◆ getNumberOfGroups()

◆ getSequenceCount() [1/2]

◆ getSequenceCount() [2/2]

◆ incrementSequenceCount() [1/2]

◆ incrementSequenceCount() [2/2]

◆ isIngroupMember() [1/2]

◆ isIngroupMember() [2/2]

◆ operator=()

◆ removeSequence() [1/2]

◆ removeSequence() [2/2]

◆ setAsIngroupMember() [1/2]

◆ setAsIngroupMember() [2/2]

◆ setAsOutgroupMember() [1/2]

◆ setAsOutgroupMember() [2/2]

◆ setGroupId() [1/2]

◆ setGroupId() [2/2]

◆ setSequenceCount() [1/2]

◆ setSequenceCount() [2/2]

Member Data Documentation

◆ count_

◆ group_

◆ ingroup_