bpp::Sequence Class Reference

The sequence interface. More...

#include <Bpp/Seq/Sequence.h>

Inheritance diagram for bpp::Sequence:

Collaboration diagram for bpp::Sequence:

Public Member Functions
virtual	~Sequence ()
Sequence *	clone () const =0
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...
Setting/getting the name of the sequence.
virtual const std::string &	getName () const =0
	Get the name of this sequence. More...
virtual void	setName (const std::string &name)=0
	Set the name of this sequence. More...
Setting/getting the comments associated to the sequence.
virtual const Comments &	getComments () const =0
	Get the comments associated to this sequence. More...
virtual void	setComments (const Comments &comments)=0
	Set the comments associated to this sequence. More...
Adjusting the size of the sequence.
virtual void	setContent (const std::string &sequence)=0 throw (BadCharException)
	Set the whole content of the sequence. More...
virtual void	setContent (const std::vector< int > &list)=0 throw (BadIntException)
	Set the whole content of the list. More...
virtual void	setContent (const std::vector< std::string > &list)=0 throw (BadCharException)
	Set the whole content of the list. More...
virtual void	setToSizeR (size_t newSize)=0
	Set up the size of a sequence from the right side. More...
virtual void	setToSizeL (size_t newSize)=0
	Set up the size of a sequence from the left side. More...
virtual void	append (const std::vector< int > &content)=0 throw (BadIntException)
	Append the specified content to the sequence. More...
virtual void	append (const std::vector< std::string > &content)=0 throw (BadCharException)
	Append the specified content to the sequence. More...
virtual void	append (const std::string &content)=0 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...

Detailed Description

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.

Sequence objets also contain a name attribute and potentially several comment lines. A sequence object is also event-driven, allowing easy extension.

See also

Alphabet

Definition at line 74 of file Sequence.h.

Constructor & Destructor Documentation

~Sequence()

virtual bpp::Sequence::~Sequence ( )

inlinevirtual

Definition at line 78 of file Sequence.h.

Member Function Documentation

addElement() [1/4]

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() [2/4]

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() [3/4]

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() [4/4]

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.

append() [1/3]

virtual void bpp::Sequence::append ( const std::vector< int > &  content ) throw ( BadIntException )

pure 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.

Implemented in bpp::SequenceWithQuality, bpp::BasicSequence, and bpp::SequenceWithAnnotation.

Referenced by bpp::WordAlphabet::reverse().

append() [2/3]

virtual void bpp::Sequence::append ( const std::vector< std::string > &  content ) throw ( BadCharException )

pure 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.

Implemented in bpp::SequenceWithQuality, bpp::BasicSequence, and bpp::SequenceWithAnnotation.

append() [3/3]

virtual void bpp::Sequence::append ( const std::string &  content ) throw ( BadCharException )

pure 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.

Implemented in bpp::SequenceWithQuality, bpp::BasicSequence, and bpp::SequenceWithAnnotation.

clone()

Sequence* bpp::Sequence::clone ( ) const

pure virtual

Implements bpp::SymbolList.

Implemented in bpp::SequenceWithQuality, bpp::BasicSequence, and bpp::SequenceWithAnnotation.

Referenced by bpp::SequenceTools::getInvert(), bpp::SequenceTools::getSequenceWithCompleteSites(), and bpp::SequenceTools::getSequenceWithoutGaps().

deleteElement()

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().

deleteElements()

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.

getAlphabet()

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.

Referenced by bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::SymbolListTools::getCounts(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::invertComplement(), bpp::BasicSymbolList::operator=(), bpp::EdSymbolList::operator=(), and bpp::SequenceTools::removeGaps().

getChar()

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().

getComments()

virtual const Comments& bpp::Sequence::getComments ( ) const

pure virtual

Get the comments associated to this sequence.

Returns

The comments of the sequence.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

Referenced by bpp::AbstractSequenceContainer::getComments(), bpp::SequenceWithAnnotation::operator=(), and bpp::BasicSequence::operator=().

getContent()

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().

getName()

virtual const std::string& bpp::Sequence::getName ( ) const

pure virtual

Get the name of this sequence.

Returns

This sequence name.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

Referenced by bpp::MapSequenceContainer::addSequence(), bpp::AbstractSequenceContainer::getName(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceWithAnnotation::operator=(), bpp::BasicSequence::operator=(), and bpp::Clustal::writeAlignment().

getValue()

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().

operator[]() [1/2]

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[]() [2/2]

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.

setComments()

virtual void bpp::Sequence::setComments ( const Comments &  comments )

pure virtual

Set the comments associated to this sequence.

Parameters

comments

The new comments of the sequence.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

setContent() [1/3]

virtual void bpp::Sequence::setContent ( const std::string &  sequence ) throw ( BadCharException )

pure 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.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

Referenced by bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), and bpp::SequenceTools::getSequenceWithoutStops().

setContent() [2/3]

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

pure 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.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

setContent() [3/3]

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

pure 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.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

setElement() [1/2]

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() [2/2]

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.

setName()

virtual void bpp::Sequence::setName ( const std::string &  name )

pure virtual

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

Referenced by bpp::SequenceTools::getPutativeHaplotypes().

setToSizeL()

virtual void bpp::Sequence::setToSizeL ( size_t  newSize )

pure 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.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

setToSizeR()

virtual void bpp::Sequence::setToSizeR ( size_t  newSize )

pure 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.

Implemented in bpp::BasicSequence, and bpp::SequenceWithAnnotation.

shuffle()

virtual void bpp::SymbolList::shuffle ( )

pure virtualinherited

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

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

size()

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.

Referenced by bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::findFirstOf(), bpp::SiteContainerTools::getAlignmentPositions(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SymbolListTools::getFrequencies(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceMask::init(), bpp::SequenceQuality::init(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SequenceTools::removeGaps(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), and bpp::SequenceWalker::SequenceWalker().

toString()

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().

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

• Bpp/Seq/Sequence.h