bpp::Sequence Class Reference

The sequence interface. More...

#include <Bpp/Seq/Sequence.h>

Inheritance diagram for bpp::Sequence:

Collaboration diagram for bpp::Sequence:

List of all members.

Public Member Functions
virtual	~Sequence ()
Sequence *	clone () const =0
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the list.
virtual size_t	size () const =0
	Get the number of elements in the list.
virtual std::string	toString () const =0
	Convert the list as a string.
Setting/getting the name of the sequence.
virtual const std::string &	getName () const =0
	Get the name of this sequence.
virtual void	setName (const std::string &name)=0
	Set the name of this sequence.
Setting/getting the comments associated to the sequence.
virtual const Comments &	getComments () const =0
	Get the comments associated to this sequence.
virtual void	setComments (const Comments &comments)=0
	Set the comments associated to this sequence.
Adjusting the size of the sequence.
virtual void	setContent (const std::string &sequence)=0 throw (BadCharException)
	Set the whole content of the sequence.
virtual void	setContent (const std::vector< int > &list)=0 throw (BadIntException)
	Set the whole content of the list.
virtual void	setContent (const std::vector< std::string > &list)=0 throw (BadCharException)
	Set the whole content of the list.
virtual void	setToSizeR (size_t newSize)=0
	Set up the size of a sequence from the right side.
virtual void	setToSizeL (size_t newSize)=0
	Set up the size of a sequence from the left side.
virtual void	append (const std::vector< int > &content)=0 throw (BadIntException)
	Append the specified content to the sequence.
virtual void	append (const std::vector< std::string > &content)=0 throw (BadCharException)
	Append the specified content to the sequence.
virtual void	append (const std::string &content)=0 throw (BadCharException)
	Append the specified content to the sequence.
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.
Edition methods.
virtual void	addElement (const std::string &c)=0 throw (BadCharException)
	Add a character to the end of the list.
virtual void	addElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException)
	Add a character at a certain position in the list.
virtual void	addElement (int v)=0 throw (BadIntException)
	Add a character to the end of the list.
virtual void	addElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Add a character at a certain position in the list.
virtual void	setElement (size_t pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'.
virtual void	setElement (size_t pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'.
virtual void	deleteElement (size_t pos)=0 throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'.
virtual void	deleteElements (size_t pos, size_t len)=0 throw (IndexOutOfBoundsException)
	Delete the elements at position 'pos'.
virtual std::string	getChar (size_t pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character.
virtual int	getValue (size_t pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as an int.
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.
virtual int &	operator[] (size_t i)=0
	Operator [] overloaded for quick access to a character in list.
virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity.

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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.

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Constructor & Destructor Documentation

virtual bpp::Sequence::~Sequence

(

)

[inline, virtual]

Definition at line 78 of file Sequence.h.

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Member Function Documentation

virtual void bpp::SymbolList::addElement

(

const std::string &

c

)

throw (BadCharException) [pure virtual, inherited]

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().

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

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.

virtual void bpp::SymbolList::addElement

(

int

v

)

throw (BadIntException) [pure virtual, inherited]

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.

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

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.

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().

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.

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.

Sequence* bpp::Sequence::clone

(

)

const [pure virtual]

Implements bpp::SymbolList.

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

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

virtual void bpp::SymbolList::deleteElement

(

size_t

pos

)

throw (IndexOutOfBoundsException) [pure virtual, inherited]

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().

virtual void bpp::SymbolList::deleteElements	(	size_t	pos,
		size_t	len
	)		throw (IndexOutOfBoundsException) [pure virtual, inherited]

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.

virtual const Alphabet* bpp::SymbolList::getAlphabet

(

)

const [pure virtual, inherited]

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::getSequenceWithoutGaps(), bpp::SequenceTools::invertComplement(), bpp::BasicSymbolList::operator=(), bpp::EdSymbolList::operator=(), and bpp::SequenceTools::removeGaps().

virtual std::string bpp::SymbolList::getChar

(

size_t

pos

)

const throw (IndexOutOfBoundsException) [pure virtual, inherited]

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().

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=().

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

(

)

const [pure virtual, inherited]

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().

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().

virtual int bpp::SymbolList::getValue

(

size_t

pos

)

const throw (IndexOutOfBoundsException) [pure virtual, inherited]

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().

virtual const int& bpp::SymbolList::operator[]

(

size_t

i

)

const [pure virtual, inherited]

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.

virtual int& bpp::SymbolList::operator[]

(

size_t

i

)

[pure virtual, inherited]

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.

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.

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::getSequenceWithoutGaps(), and bpp::SequenceTools::getSequenceWithoutStops().

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.

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.

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

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().

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

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.

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().

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.

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.

virtual void bpp::SymbolList::shuffle

(

)

[pure virtual, inherited]

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

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

virtual size_t bpp::SymbolList::size

(

)

const [pure virtual, inherited]

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::getCounts(), bpp::SymbolListTools::getFrequencies(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SiteContainerTools::getSequencePositions(), 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().

virtual std::string bpp::SymbolList::toString

(

)

const [pure virtual, inherited]

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