A basic implementation of the Sequence interface. More...

#include <Bpp/Seq/Sequence.h>

Inheritance diagram for bpp::BasicSequence:

Collaboration diagram for bpp::BasicSequence:

Public Member Functions
	BasicSequence (const Alphabet *alpha)
	Empty constructor: build a void Sequence with just an Alphabet. More...

	BasicSequence (const std::string &name, const std::string &sequence, const Alphabet *alpha) throw (BadCharException)
	Direct constructor: build a Sequence object from a std::string You can use it safely for RNA, DNA and protein sequences. More...

	BasicSequence (const std::string &name, const std::string &sequence, const Comments &comments, const Alphabet *alpha) throw (BadCharException)
	Direct constructor: build a Sequence object from a std::string. More...

	BasicSequence (const std::string &name, const std::vector< std::string > &sequence, const Alphabet *alpha) throw (BadCharException)
	General purpose constructor, can be used with any alphabet. More...

	BasicSequence (const std::string &name, const std::vector< std::string > &sequence, const Comments &comments, const Alphabet *alpha) throw (BadCharException)
	General purpose constructor, can be used with any alphabet. More...

	BasicSequence (const std::string &name, const std::vector< int > &sequence, const Alphabet *alpha) throw (BadIntException)
	General purpose constructor, can be used with any alphabet. More...

	BasicSequence (const std::string &name, const std::vector< int > &sequence, const Comments &comments, const Alphabet *alpha) throw (BadIntException)
	General purpose constructor, can be used with any alphabet. More...

	BasicSequence (const Sequence &s)
	The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object. More...

	BasicSequence (const BasicSequence &s)
	The Sequence copy constructor. This does not perform a hard copy of the alphabet object. More...

BasicSequence &	operator= (const Sequence &s)
	The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object. More...

BasicSequence &	operator= (const BasicSequence &s)
	The Sequence assignment operator. This does not perform a hard copy of the alphabet object. More...

virtual	~BasicSequence ()

virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the list. More...

virtual size_t	size () const =0
	Get the number of elements in the list. More...

virtual std::string	toString () const =0
	Convert the list as a string. More...

virtual const Alphabet *	getAlphabet () const
	Get the alphabet associated to the list. More...

virtual size_t	size () const
	Get the number of elements in the list. More...

virtual const std::vector< int > &	getContent () const
	Get the whole content of the list as a vector of int. More...

virtual std::string	toString () const
	Convert the list as a string. More...

virtual void	addElement (const std::string &c) throw (BadCharException)
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Add a character at a certain position in the list. More...

virtual void	addElement (int v) throw (BadIntException)
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
	Add a character at a certain position in the list. More...

virtual void	setElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'. More...

virtual void	setElement (size_t pos, int v) throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'. More...

virtual void	deleteElement (size_t pos) throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'. More...

virtual void	deleteElements (size_t pos, size_t len) throw (IndexOutOfBoundsException)
	Delete the elements at position 'pos'. More...

virtual std::string	getChar (size_t pos) const throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character. More...

virtual int	getValue (size_t pos) const throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as an int. More...

virtual const int &	operator[] (size_t i) const
	Operator [] overloaded for quick access to a character in list. More...

virtual int &	operator[] (size_t i)
	Operator [] overloaded for quick access to a character in list. More...

virtual void	shuffle ()
	Randomly shuffle the content of the list, with linear complexity. More...

The Clonable interface
BasicSequence *	clone () const

Setting/getting the name of the sequence.
const std::string &	getName () const
	Get the name of this sequence. More...

void	setName (const std::string &name)
	Set the name of this sequence. More...

Setting/getting the comments associated to the sequence.
const Comments &	getComments () const
	Get the comments associated to this sequence. More...

void	setComments (const Comments &comments)
	Set the comments associated to this sequence. More...

Adjusting the size of the sequence.
virtual void	setContent (const std::string &sequence) throw (BadCharException)
	Set the whole content of the sequence. More...

void	setContent (const std::vector< int > &list) throw (BadIntException)
	Set the whole content of the list. More...

void	setContent (const std::vector< std::string > &list) throw (BadCharException)
	Set the whole content of the list. More...

virtual void	setToSizeR (size_t newSize)
	Set up the size of a sequence from the right side. More...

virtual void	setToSizeL (size_t newSize)
	Set up the size of a sequence from the left side. More...

virtual void	append (const std::vector< int > &content) throw (BadIntException)
	Append the specified content to the sequence. More...

virtual void	append (const std::vector< std::string > &content) throw (BadCharException)
	Append the specified content to the sequence. More...

virtual void	append (const std::string &content) throw (BadCharException)
	Append the specified content to the sequence. More...

Acting on the content of the list.
virtual const std::vector< int > &	getContent () const =0
	Get the whole content of the list as a vector of int. More...

Edition methods.
virtual void	addElement (const std::string &c)=0 throw (BadCharException)
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException)
	Add a character at a certain position in the list. More...

virtual void	addElement (int v)=0 throw (BadIntException)
	Add a character to the end of the list. More...

virtual void	addElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Add a character at a certain position in the list. More...

virtual void	setElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'. More...

virtual void	setElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'. More...

virtual void	deleteElement (size_t pos)=0 throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'. More...

virtual void	deleteElements (size_t pos, size_t len)=0 throw (IndexOutOfBoundsException)
	Delete the elements at position 'pos'. More...

virtual std::string	getChar (size_t pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character. More...

virtual int	getValue (size_t pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as an int. More...

Provide direct access to the list content.
Warning These operators allow you to modifiy the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual const int &	operator[] (size_t i) const =0
	Operator [] overloaded for quick access to a character in list. More...

virtual int &	operator[] (size_t i)=0
	Operator [] overloaded for quick access to a character in list. More...

virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

Protected Attributes
std::vector< int >	content_
	The list content. More...

Private Attributes
std::string	name_
	The sequence name. More...

Comments	comments_
	The sequence comments. More...

Detailed Description

A basic implementation of the Sequence interface.

This is a general purpose container, containing an ordered list of states. The states that allowed to be present in the sequence are defined by an alphabet object, which is passed to the sequence constructor by a pointer.

For programming convenience, the states are stored as integers, but the translation toward and from a char description is easily performed with the Alphabet classes.

Sequence objets also contain a name attribute and potentially several comment lines.

See also: Alphabet

Definition at line 207 of file Sequence.h.

Constructor & Destructor Documentation

◆ BasicSequence() [1/9]

BasicSequence::BasicSequence ( const Alphabet * alpha )

Empty constructor: build a void Sequence with just an Alphabet.

You can use it safely for all type of Alphabet in order to build an empty Sequence i.e. without name nor sequence data.

Parameters

alpha A pointer toward the Alphabet to be used with this Sequence.

Definition at line 56 of file Sequence.cpp.

Referenced by clone().

◆ BasicSequence() [2/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::string &	sequence,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

Direct constructor: build a Sequence object from a std::string You can use it safely for RNA, DNA and protein sequences.

It can be used with codon sequences too, the std::string will be cut into parts of size 3. But for more complicated alphabets, you should use one complete constructors.

Parameters

name	The sequence name.
sequence	The whole sequence to be parsed as a std::string.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 62 of file Sequence.cpp.

◆ BasicSequence() [3/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::string &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

Direct constructor: build a Sequence object from a std::string.

You can use it safely for RNA, DNA and protein sequences.

It can be used with codon sequences too, the std::string will be cut into tokens of size 3. But for more complicated alphabets, you should use one complete constructors.

Parameters

name	The sequence name.
sequence	The whole sequence to be parsed as a std::string.
comments	Comments to add to the sequence.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 72 of file Sequence.cpp.

◆ BasicSequence() [4/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< std::string > &	sequence,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

General purpose constructor, can be used with any alphabet.

You should note that the sequence is stored as a std::vector of int. Hence each std::string in the std::vector will be translated using the alphabet object.

Parameters

name	The sequence name.
sequence	The sequence content.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 82 of file Sequence.cpp.

◆ BasicSequence() [5/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< std::string > &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

General purpose constructor, can be used with any alphabet.

You should note that the sequence is stored as a std::vector of int. Hence each std::string in the std::vector will be translated using the alphabet object.

Parameters

name	The sequence name.
sequence	The sequence content.
comments	Comments to add to the sequence.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 89 of file Sequence.cpp.

◆ BasicSequence() [6/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< int > &	sequence,
		const Alphabet *	alpha
	)
throw	(	BadIntException
	)

General purpose constructor, can be used with any alphabet.

Parameters

name	The sequence name.
sequence	The sequence content.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 96 of file Sequence.cpp.

◆ BasicSequence() [7/9]

BasicSequence::BasicSequence	(	const std::string &	name,
		const std::vector< int > &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)
throw	(	BadIntException
	)

General purpose constructor, can be used with any alphabet.

Parameters

name	The sequence name.
sequence	The sequence content.
comments	Comments to add to the sequence.
alpha	A pointer toward the alphabet to be used with this sequence.

Definition at line 103 of file Sequence.cpp.

◆ BasicSequence() [8/9]

BasicSequence::BasicSequence ( const Sequence & s )

The Sequence generic copy constructor. This does not perform a hard copy of the alphabet object.

Definition at line 112 of file Sequence.cpp.

◆ BasicSequence() [9/9]

BasicSequence::BasicSequence ( const BasicSequence & s )

The Sequence copy constructor. This does not perform a hard copy of the alphabet object.

Definition at line 118 of file Sequence.cpp.

◆ ~BasicSequence()

virtual bpp::BasicSequence::~BasicSequence ( )

inlinevirtual

Definition at line 333 of file Sequence.h.

Member Function Documentation

◆ addElement() [1/8]

virtual void bpp::SymbolList::addElement	(	const std::string &	c	)
throw	(	BadCharException
	)

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractReverseTransliterator::reverse(), and bpp::AbstractTransliterator::translate().

◆ addElement() [2/8]

virtual void bpp::SymbolList::addElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

pure virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The postion where to insert the element.
c	The character to add, given as a string.

Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ addElement() [3/8]

virtual void bpp::SymbolList::addElement	(	int	v	)
throw	(	BadIntException
	)

pure virtualinherited

Add a character to the end of the list.

Parameters

v	The character to add, given as an int.

Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ addElement() [4/8]

virtual void bpp::SymbolList::addElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

pure virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The postion where to insert the element.
v	The character to add, given as an int.

Implemented in bpp::SequenceWithQuality, bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ addElement() [5/8]

void BasicSymbolList::addElement	(	const std::string &	c	)
throw	(	BadCharException
	)

virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add, given as a string.

Implements bpp::SymbolList.

Definition at line 121 of file SymbolList.cpp.

Referenced by bpp::NucleicAcidsReplication::reverse(), and bpp::NucleicAcidsReplication::translate().

◆ addElement() [6/8]

void BasicSymbolList::addElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The postion where to insert the element.
c	The character to add, given as a string.

Implements bpp::SymbolList.

Definition at line 128 of file SymbolList.cpp.

◆ addElement() [7/8]

void BasicSymbolList::addElement	(	int	v	)
throw	(	BadIntException
	)

virtualinherited

Add a character to the end of the list.

Parameters

v	The character to add, given as an int.

Implements bpp::SymbolList.

Definition at line 181 of file SymbolList.cpp.

◆ addElement() [8/8]

void BasicSymbolList::addElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The postion where to insert the element.
v	The character to add, given as an int.

Implements bpp::SymbolList.

Definition at line 190 of file SymbolList.cpp.

◆ append() [1/3]

void BasicSequence::append	(	const std::vector< int > &	content	)
throw	(	BadIntException
	)

virtual

Append the specified content to the sequence.

Parameters

content The content to append to the sequence.

Exceptions

BadIntException If the content does not match the current alphabet.

Implements bpp::Sequence.

Definition at line 193 of file Sequence.cpp.

Referenced by bpp::SequenceContainerTools::merge().

◆ append() [2/3]

void BasicSequence::append	(	const std::vector< std::string > &	content	)
throw	(	BadCharException
	)

virtual

Append the specified content to the sequence.

Parameters

content The content to append to the sequence.

Exceptions

BadCharException If the content does not match the current alphabet.

Implements bpp::Sequence.

Definition at line 204 of file Sequence.cpp.

◆ append() [3/3]

void BasicSequence::append	(	const std::string &	content	)
throw	(	BadCharException
	)

virtual

Append the specified content to the sequence.

Parameters

content The content to append to the sequence.

Exceptions

BadCharException If the content does not match the current alphabet.

Implements bpp::Sequence.

Definition at line 216 of file Sequence.cpp.

References bpp::StringSequenceTools::codeSequence().

◆ clone()

BasicSequence* bpp::BasicSequence::clone ( ) const

inlinevirtual

Implements bpp::Sequence.

Definition at line 342 of file Sequence.h.

References BasicSequence().

◆ deleteElement() [1/2]

virtual void bpp::SymbolList::deleteElement	(	size_t	pos	)
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Delete the element at position 'pos'.

Parameters

pos	The position of the element to delete.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), and bpp::VectorSiteContainer::removeSequence().

◆ deleteElement() [2/2]

void BasicSymbolList::deleteElement	(	size_t	pos	)
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Delete the element at position 'pos'.

Parameters

pos	The position of the element to delete.

Implements bpp::SymbolList.

Definition at line 163 of file SymbolList.cpp.

Referenced by bpp::AlignedSequenceContainer::removeSite().

◆ deleteElements() [1/2]

virtual void bpp::SymbolList::deleteElements	(	size_t	pos,
		size_t	len
	)
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Delete the elements at position 'pos'.

Parameters

pos	The position of the first element to delete.
len	The length of the region to delete.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ deleteElements() [2/2]

void BasicSymbolList::deleteElements	(	size_t	pos,
		size_t	len
	)
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Delete the elements at position 'pos'.

Parameters

pos	The position of the first element to delete.
len	The length of the region to delete.

Implements bpp::SymbolList.

Definition at line 172 of file SymbolList.cpp.

◆ getAlphabet() [1/2]

virtual const Alphabet* bpp::SymbolList::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ getAlphabet() [2/2]

virtual const Alphabet* bpp::BasicSymbolList::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the list.

Returns: A const pointer to the alphabet.

See also: Alphabet class.

Implements bpp::SymbolList.

Definition at line 348 of file SymbolList.h.

References bpp::BasicSymbolList::alphabet_.

Referenced by bpp::SiteTools::areSitesIdentical(), bpp::SiteTools::hasGap(), bpp::SiteTools::hasUnknown(), bpp::SiteTools::isComplete(), bpp::SiteTools::isGapOnly(), bpp::SiteTools::isGapOrUnresolvedOnly(), bpp::BasicSymbolList::operator=(), setToSizeL(), setToSizeR(), and bpp::AbstractTransliterator::translate().

◆ getChar() [1/2]

virtual std::string bpp::SymbolList::getChar	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Get the element at position 'pos' as a character.

Parameters

pos	The position of the character to retrieve.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SiteContainerTools::resolveDottedAlignment().

◆ getChar() [2/2]

string BasicSymbolList::getChar	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Get the element at position 'pos' as a character.

Parameters

pos	The position of the character to retrieve.

Implements bpp::SymbolList.

Definition at line 145 of file SymbolList.cpp.

Referenced by bpp::SiteContainerTools::resolveDottedAlignment().

◆ getComments()

const Comments& bpp::BasicSequence::getComments ( ) const

inlinevirtual

Get the comments associated to this sequence.

Returns: The comments of the sequence.

Implements bpp::Sequence.

Definition at line 379 of file Sequence.h.

References comments_.

Referenced by operator=().

◆ getContent() [1/2]

virtual const std::vector<int>& bpp::SymbolList::getContent ( ) const

pure virtualinherited

Get the whole content of the list as a vector of int.

Returns: A reference to the content of the list.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SequenceWithQualityTools::complement(), bpp::AbstractSequenceContainer::getContent(), bpp::SymbolListTools::getCounts(), bpp::BasicSymbolList::operator=(), bpp::EdSymbolList::operator=(), bpp::SequenceWithQualityTools::reverseTranscript(), and bpp::SequenceWithQualityTools::transcript().

◆ getContent() [2/2]

virtual const std::vector<int>& bpp::BasicSymbolList::getContent ( ) const

inlinevirtualinherited

Get the whole content of the list as a vector of int.

Returns: A reference to the content of the list.

Implements bpp::SymbolList.

Definition at line 352 of file SymbolList.h.

References bpp::BasicSymbolList::content_.

Referenced by bpp::Site::operator=(), and bpp::BasicSymbolList::operator=().

◆ getName()

const std::string& bpp::BasicSequence::getName ( ) const

inlinevirtual

Get the name of this sequence.

Returns: This sequence name.

Implements bpp::Sequence.

Definition at line 357 of file Sequence.h.

References name_.

Referenced by operator=().

◆ getValue() [1/2]

virtual int bpp::SymbolList::getValue	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

pure virtualinherited

Get the element at position 'pos' as an int.

Parameters

pos	The position of the character to retrieve.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::invert(), and bpp::SequenceTools::invertComplement().

◆ getValue() [2/2]

int BasicSymbolList::getValue	(	size_t	pos	)	const
throw	(	IndexOutOfBoundsException
	)

virtualinherited

Get the element at position 'pos' as an int.

Parameters

pos	The position of the character to retrieve.

Implements bpp::SymbolList.

Definition at line 212 of file SymbolList.cpp.

Referenced by bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::CodonSiteTools::isFourFoldDegenerated(), and bpp::CodonSiteTools::numberOfSubsitutions().

◆ operator=() [1/2]

BasicSequence & BasicSequence::operator= ( const Sequence & s )

The Sequence generic assignment operator. This does not perform a hard copy of the alphabet object.

Returns: A ref toward the assigned Sequence.

Definition at line 126 of file Sequence.cpp.

References comments_, bpp::Sequence::getComments(), bpp::Sequence::getName(), name_, and bpp::BasicSymbolList::operator=().

◆ operator=() [2/2]

BasicSequence & BasicSequence::operator= ( const BasicSequence & s )

The Sequence assignment operator. This does not perform a hard copy of the alphabet object.

Returns: A ref toward the assigned Sequence.

Definition at line 134 of file Sequence.cpp.

References comments_, getComments(), getName(), name_, and bpp::BasicSymbolList::operator=().

◆ operator[]() [1/4]

virtual const int& bpp::SymbolList::operator[] ( size_t i ) const

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ operator[]() [2/4]

virtual int& bpp::SymbolList::operator[] ( size_t i )

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ operator[]() [3/4]

virtual const int& bpp::BasicSymbolList::operator[] ( size_t i ) const

inlinevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implements bpp::SymbolList.

Definition at line 380 of file SymbolList.h.

References bpp::BasicSymbolList::content_.

◆ operator[]() [4/4]

virtual int& bpp::BasicSymbolList::operator[] ( size_t i )

inlinevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

i	The position to retrieve.

Returns: The integer value of character at position i.

Implements bpp::SymbolList.

Definition at line 382 of file SymbolList.h.

References bpp::BasicSymbolList::content_.

◆ setComments()

void bpp::BasicSequence::setComments ( const Comments & comments )

inlinevirtual

Set the comments associated to this sequence.

Parameters

comments The new comments of the sequence.

Implements bpp::Sequence.

Definition at line 386 of file Sequence.h.

References comments_.

◆ setContent() [1/3]

void BasicSequence::setContent	(	const std::string &	sequence	)
throw	(	BadCharException
	)

virtual

Set the whole content of the sequence.

Parameters

sequence The new content of the sequence.

See also: The Sequence constructor for information about the way sequences are internaly stored.

Implements bpp::Sequence.

Definition at line 144 of file Sequence.cpp.

References bpp::StringSequenceTools::codeSequence().

◆ setContent() [2/3]

void bpp::BasicSequence::setContent	(	const std::vector< int > &	list	)
throw	(	BadIntException
	)

inlinevirtual

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internaly stored.

Implements bpp::Sequence.

Definition at line 404 of file Sequence.h.

References bpp::BasicSymbolList::setContent().

◆ setContent() [3/3]

void bpp::BasicSequence::setContent	(	const std::vector< std::string > &	list	)
throw	(	BadCharException
	)

inlinevirtual

Set the whole content of the list.

Parameters

list	The new content of the list.

See also: The list constructor for information about the way lists are internaly stored.

Implements bpp::Sequence.

Definition at line 408 of file Sequence.h.

References bpp::BasicSymbolList::setContent().

◆ setElement() [1/4]

virtual void bpp::SymbolList::setElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

pure virtualinherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element, given as a string.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::SequenceTools::invert(), and bpp::SequenceTools::invertComplement().

◆ setElement() [2/4]

virtual void bpp::SymbolList::setElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

pure virtualinherited

Set the element at position 'pos' to character 'v'.

Parameters

pos	The position of the character to set.
v	The value of the element, given as an int.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ setElement() [3/4]

void BasicSymbolList::setElement	(	size_t	pos,
		const std::string &	c
	)
throw	(	BadCharException,
		IndexOutOfBoundsException
	)

virtualinherited

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element, given as a string.

Implements bpp::SymbolList.

Definition at line 136 of file SymbolList.cpp.

◆ setElement() [4/4]

void BasicSymbolList::setElement	(	size_t	pos,
		int	v
	)
throw	(	BadIntException,
		IndexOutOfBoundsException
	)

virtualinherited

Set the element at position 'pos' to character 'v'.

Parameters

pos	The position of the character to set.
v	The value of the element, given as an int.

Implements bpp::SymbolList.

Definition at line 201 of file SymbolList.cpp.

◆ setName()

void bpp::BasicSequence::setName ( const std::string & name )

inlinevirtual

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::Sequence.

Definition at line 364 of file Sequence.h.

References name_.

◆ setToSizeL()

void BasicSequence::setToSizeL ( size_t newSize )

virtual

Set up the size of a sequence from the left side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize The new size of the sequence.

Implements bpp::Sequence.

Definition at line 172 of file Sequence.cpp.

References bpp::BasicSymbolList::content_, bpp::BasicSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

◆ setToSizeR()

void BasicSequence::setToSizeR ( size_t newSize )

virtual

Set up the size of a sequence from the right side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize The new size of the sequence.

Implements bpp::Sequence.

Definition at line 153 of file Sequence.cpp.

References bpp::BasicSymbolList::content_, bpp::BasicSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

◆ shuffle() [1/2]

virtual void bpp::SymbolList::shuffle ( )

pure virtualinherited

Randomly shuffle the content of the list, with linear complexity.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ shuffle() [2/2]

virtual void bpp::BasicSymbolList::shuffle ( )

inlinevirtualinherited

Randomly shuffle the content of the list, with linear complexity.

Implements bpp::SymbolList.

Definition at line 384 of file SymbolList.h.

References bpp::BasicSymbolList::content_.

◆ size() [1/2]

virtual size_t bpp::SymbolList::size ( ) const

pure virtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

◆ size() [2/2]

virtual size_t bpp::BasicSymbolList::size ( ) const

inlinevirtualinherited

Get the number of elements in the list.

Returns: The number of sites in the list.

Implements bpp::SymbolList.

Definition at line 350 of file SymbolList.h.

References bpp::BasicSymbolList::content_.

Referenced by bpp::SiteTools::areSitesIdentical(), bpp::CompressedVectorSiteContainer::getSiteIndex_(), bpp::SiteTools::hasGap(), bpp::SiteTools::hasUnknown(), bpp::SiteTools::isComplete(), bpp::CodonSiteTools::isFourFoldDegenerated(), bpp::SiteTools::isGapOnly(), bpp::SiteTools::isGapOrUnresolvedOnly(), bpp::CodonSiteTools::numberOfSubsitutions(), bpp::operator==(), and bpp::WordAlphabet::reverse().

◆ toString() [1/2]

virtual std::string bpp::SymbolList::toString ( ) const

pure virtualinherited

Convert the list as a string.

This method is useful for dumping a list to a file or to the screen for display.

Returns: The whole list as a string.

Implemented in bpp::EdSymbolList, and bpp::BasicSymbolList.

Referenced by bpp::AbstractSequenceContainer::toString().

◆ toString() [2/2]

string BasicSymbolList::toString ( ) const

virtualinherited

Convert the list as a string.

This method is useful for dumping a list to a file or to the screen for display.

Returns: The whole list as a string.

Implements bpp::SymbolList.

Definition at line 114 of file SymbolList.cpp.

References bpp::BasicSymbolList::alphabet_, bpp::BasicSymbolList::content_, and bpp::StringSequenceTools::decodeSequence().

Member Data Documentation

◆ comments_

Comments bpp::BasicSequence::comments_

private

The sequence comments.

Definition at line 221 of file Sequence.h.

Referenced by getComments(), operator=(), and setComments().

◆ content_

std::vector<int> bpp::BasicSymbolList::content_

protectedinherited

The list content.

Definition at line 280 of file SymbolList.h.

Referenced by bpp::BasicSymbolList::getContent(), bpp::Site::operator=(), bpp::BasicSymbolList::operator=(), bpp::BasicSymbolList::operator[](), setToSizeL(), setToSizeR(), bpp::BasicSymbolList::shuffle(), bpp::BasicSymbolList::size(), and bpp::BasicSymbolList::toString().

◆ name_

std::string bpp::BasicSequence::name_

private

The sequence name.

Definition at line 216 of file Sequence.h.

Referenced by getName(), operator=(), and setName().

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

Bpp/Seq/Sequence.h
Bpp/Seq/Sequence.cpp

Public Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BasicSequence() [1/9]

◆ BasicSequence() [2/9]

◆ BasicSequence() [3/9]

◆ BasicSequence() [4/9]

◆ BasicSequence() [5/9]

◆ BasicSequence() [6/9]

◆ BasicSequence() [7/9]

◆ BasicSequence() [8/9]

◆ BasicSequence() [9/9]

◆ ~BasicSequence()

Member Function Documentation

◆ addElement() [1/8]

◆ addElement() [2/8]

◆ addElement() [3/8]

◆ addElement() [4/8]

◆ addElement() [5/8]

◆ addElement() [6/8]

◆ addElement() [7/8]

◆ addElement() [8/8]

◆ append() [1/3]

◆ append() [2/3]

◆ append() [3/3]

◆ clone()

◆ deleteElement() [1/2]

◆ deleteElement() [2/2]

◆ deleteElements() [1/2]

◆ deleteElements() [2/2]

◆ getAlphabet() [1/2]

◆ getAlphabet() [2/2]

◆ getChar() [1/2]

◆ getChar() [2/2]

◆ getComments()

◆ getContent() [1/2]

◆ getContent() [2/2]

◆ getName()

◆ getValue() [1/2]

◆ getValue() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator[]() [1/4]

◆ operator[]() [2/4]

◆ operator[]() [3/4]

◆ operator[]() [4/4]

◆ setComments()

◆ setContent() [1/3]

◆ setContent() [2/3]

◆ setContent() [3/3]

◆ setElement() [1/4]

◆ setElement() [2/4]

◆ setElement() [3/4]

◆ setElement() [4/4]

◆ setName()

◆ setToSizeL()

◆ setToSizeR()

◆ shuffle() [1/2]

◆ shuffle() [2/2]

◆ size() [1/2]

◆ size() [2/2]

◆ toString() [1/2]

◆ toString() [2/2]

Member Data Documentation

◆ comments_

◆ content_

◆ name_