bpp::BasicSymbolList Class Reference

A basic SymbolList object. More...

#include <Bpp/Seq/SymbolList.h>

Inheritance diagram for bpp::BasicSymbolList:

Collaboration diagram for bpp::BasicSymbolList:

Public Member Functions
	BasicSymbolList (const Alphabet *alpha)
	Build a new void BasicSymbolList object with the specified alphabet. More...
	BasicSymbolList (const std::vector< std::string > &list, const Alphabet *alpha) throw (BadCharException)
	Build a new BasicSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters. More...
	BasicSymbolList (const std::vector< int > &list, const Alphabet *alpha) throw (BadIntException)
	Build a new BasicSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers. More...
	BasicSymbolList (const SymbolList &list)
	The generic copy constructor. More...
	BasicSymbolList (const BasicSymbolList &list)
	The copy constructor. More...
BasicSymbolList &	operator= (const SymbolList &list)
	The generic assignment operator. More...
BasicSymbolList &	operator= (const BasicSymbolList &list)
	The assignment operator. More...
virtual	~BasicSymbolList ()
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 void	setContent (const std::vector< int > &list) throw (BadIntException)
	Set the whole content of the list. More...
virtual void	setContent (const std::vector< std::string > &list) throw (BadCharException)
	Set the whole content of the list. 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	setElement (size_t pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'. 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 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, int v) throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'. 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
BasicSymbolList *	clone () const

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

Private Attributes
const Alphabet *	alphabet_
	The Alphabet attribute must be initialized in constructor and then can never be changed. More...

Detailed Description

A basic SymbolList object.

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

See also

Alphabet

Definition at line 264 of file SymbolList.h.

Constructor & Destructor Documentation

BasicSymbolList() [1/5]

bpp::BasicSymbolList::BasicSymbolList ( const Alphabet *  alpha )

inline

Build a new void BasicSymbolList object with the specified alphabet.

Parameters

alpha

The alphabet to use.

Definition at line 288 of file SymbolList.h.

Referenced by clone().

BasicSymbolList() [2/5]

BasicSymbolList::BasicSymbolList	(	const std::vector< std::string > &	list,
		const Alphabet *	alpha
	)
throw	(	BadCharException
	)

Build a new BasicSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters.

Parameters

list	The content of the site.
alpha	The alphabet to use.

Exceptions

BadCharException

If the content does not match the specified alphabet.

Definition at line 49 of file SymbolList.cpp.

BasicSymbolList() [3/5]

BasicSymbolList::BasicSymbolList	(	const std::vector< int > &	list,
		const Alphabet *	alpha
	)
throw	(	BadIntException
	)

Build a new BasicSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers.

Parameters

list	The content of the site.
alpha	The alphabet to use.

Exceptions

BadIntException

If the content does not match the specified alphabet.

Definition at line 55 of file SymbolList.cpp.

BasicSymbolList() [4/5]

BasicSymbolList::BasicSymbolList

(

const SymbolList &

list

)

The generic copy constructor.

Definition at line 63 of file SymbolList.cpp.

BasicSymbolList() [5/5]

BasicSymbolList::BasicSymbolList

(

const BasicSymbolList &

list

)

The copy constructor.

Definition at line 66 of file SymbolList.cpp.

~BasicSymbolList()

virtual bpp::BasicSymbolList::~BasicSymbolList ( )

inlinevirtual

Definition at line 344 of file SymbolList.h.

Member Function Documentation

addElement() [1/4]

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

virtual

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() [2/4]

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

virtual

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() [3/4]

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

virtual

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() [4/4]

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

virtual

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.

clone()

BasicSymbolList* bpp::BasicSymbolList::clone ( ) const

inlinevirtual

Implements bpp::SymbolList.

Definition at line 340 of file SymbolList.h.

References BasicSymbolList().

deleteElement()

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

virtual

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()

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

virtual

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()

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

inlinevirtual

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 alphabet_.

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

getChar()

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

virtual

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().

getContent()

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

inlinevirtual

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 content_.

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

getValue()

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

virtual

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]

BasicSymbolList & BasicSymbolList::operator=

(

const SymbolList &

list

)

The generic assignment operator.

Definition at line 69 of file SymbolList.cpp.

References alphabet_, content_, bpp::SymbolList::getAlphabet(), and bpp::SymbolList::getContent().

Referenced by bpp::BasicSequence::operator=().

operator=() [2/2]

BasicSymbolList & BasicSymbolList::operator=

(

const BasicSymbolList &

list

)

The assignment operator.

Definition at line 76 of file SymbolList.cpp.

References alphabet_, content_, getAlphabet(), and getContent().

operator[]() [1/2]

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

inlinevirtual

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 content_.

operator[]() [2/2]

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

inlinevirtual

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 content_.

setContent() [1/2]

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

virtual

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::SymbolList.

Reimplemented in bpp::BasicSequence.

Definition at line 101 of file SymbolList.cpp.

Referenced by bpp::BasicSequence::setContent().

setContent() [2/2]

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

virtual

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::SymbolList.

Reimplemented in bpp::BasicSequence.

Definition at line 85 of file SymbolList.cpp.

setElement() [1/2]

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

virtual

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() [2/2]

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

virtual

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.

shuffle()

virtual void bpp::BasicSymbolList::shuffle ( )

inlinevirtual

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

Implements bpp::SymbolList.

Definition at line 384 of file SymbolList.h.

References content_.

size()

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

inlinevirtual

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 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()

string BasicSymbolList::toString ( ) const

virtual

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

Member Data Documentation

alphabet_

const Alphabet* bpp::BasicSymbolList::alphabet_

private

The Alphabet attribute must be initialized in constructor and then can never be changed.

To apply another alphabet to a list you'll have to create a new list.

Definition at line 274 of file SymbolList.h.

Referenced by getAlphabet(), operator=(), and toString().

content_

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

protected

The list content.

Definition at line 280 of file SymbolList.h.

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

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

• Bpp/Seq/SymbolList.h
• Bpp/Seq/SymbolList.cpp