A sequence class which is used to store data from MAF files. More...

#include <Bpp/Seq/Io/Maf/MafSequence.h>

Inheritance diagram for bpp::MafSequence:

Collaboration diagram for bpp::MafSequence:

Public Member Functions
	MafSequence ()
	MafSequence (const std::string &name, const std::string &sequence)
	MafSequence (const std::string &name, const std::string &sequence, unsigned int begin, char strand, unsigned int srcSize)
MafSequence *	clone () const
	~MafSequence ()
bool	hasCoordinates () const
void	removeCoordinates ()
unsigned int	start () const throw (Exception)
unsigned int	stop () const
Range< unsigned int >	getRange () const
void	setName (const std::string &name)
	Set the name of this sequence.
const std::string &	getSpecies () const
const std::string &	getChromosome () const
char	getStrand () const
unsigned int	getGenomicSize () const
unsigned int	getSrcSize () const
void	setStart (unsigned int begin)
void	setChromosome (const std::string &chr)
void	setSpecies (const std::string &species)
void	setStrand (char s)
void	setSrcSize (unsigned int srcSize)
std::string	getDescription () const
MafSequence *	subSequence (unsigned int startAt, unsigned int length) const
	Extract a sub-sequence.
virtual void	addAnnotation (SequenceAnnotation *anno) throw (Exception)
	Add a new annotation to the sequence.
virtual bool	hasAnnotation (const std::string &type) const
virtual const SequenceAnnotation &	getAnnotation (const std::string &type) const
virtual SequenceAnnotation &	getAnnotation (const std::string &type)
virtual std::vector< std::string >	getAnnotationTypes () const
virtual void	merge (const SequenceWithAnnotation &swa) throw (AlphabetMismatchException, Exception)
	Merge a sequence with the current one.
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the list.
virtual const Alphabet *	getAlphabet () const
	Get the alphabet associated to the list.
virtual unsigned int	size () const =0
	Get the number of elements in the list.
virtual unsigned int	size () const
	Get the number of elements in the list.
virtual const std::vector< int > &	getContent () const
	Get the whole content of the list as a vector of int.
virtual std::string	toString () const =0
	Convert the list as a string.
virtual std::string	toString () const
	Convert the list as a string.
virtual void	addElement (const std::string &c) throw (BadCharException)
	Add a character to the end of the list.
virtual void	addElement (unsigned int pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Add a character at a certain position in the list.
virtual void	addElement (int v) throw (BadIntException)
	Add a character to the end of the list.
virtual void	addElement (unsigned int pos, int v) throw (BadIntException, IndexOutOfBoundsException)
	Add a character at a certain position in the list.
virtual void	setElement (unsigned int pos, const std::string &c) throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'.
virtual void	setElement (unsigned int pos, int v) throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'.
virtual void	deleteElement (unsigned int pos) throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'.
virtual void	deleteElements (unsigned int pos, unsigned int len) throw (IndexOutOfBoundsException)
	Delete the elements at position 'pos'.
virtual std::string	getChar (unsigned int pos) const throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character.
virtual int	getValue (unsigned int pos) const throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as an int.
virtual const int &	operator[] (unsigned int i) const
	Operator [] overloaded for quick access to a character in list.
virtual int &	operator[] (unsigned int i)
	Operator [] overloaded for quick access to a character in list.
virtual void	shuffle ()
	Randomly shuffle the content of the list, with linear complexity.
Setting/getting the name of the sequence.
const std::string &	getName () const
	Get the name of this sequence.
Setting/getting the comments associated to the sequence.
const Comments &	getComments () const
	Get the comments associated to this sequence.
void	setComments (const Comments &comments)
	Set the comments associated to this sequence.
Adjusting the size of the sequence.
virtual void	setContent (const std::string &sequence) throw (BadCharException)
	Set the whole content of the sequence.
void	setContent (const std::vector< int > &list) throw (BadIntException)
	Set the whole content of the list.
void	setContent (const std::vector< std::string > &list) throw (BadCharException)
	Set the whole content of the list.
virtual void	setToSizeR (unsigned int newSize)
	Set up the size of a sequence from the right side.
virtual void	setToSizeL (unsigned int newSize)
	Set up the size of a sequence from the left side.
void	append (const std::vector< int > &content) throw (BadIntException)
	Append the specified content to the sequence.
void	append (const std::vector< std::string > &content) throw (BadCharException)
	Append the specified content to the sequence.
void	append (const std::string &content) 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 (unsigned int 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 (unsigned int pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Add a character at a certain position in the list.
virtual void	setElement (unsigned int pos, const std::string &c)=0 throw (BadCharException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'c'.
virtual void	setElement (unsigned int pos, int v)=0 throw (BadIntException, IndexOutOfBoundsException)
	Set the element at position 'pos' to character 'v'.
virtual void	deleteElement (unsigned int pos)=0 throw (IndexOutOfBoundsException)
	Delete the element at position 'pos'.
virtual void	deleteElements (unsigned int pos, unsigned int len)=0 throw (IndexOutOfBoundsException)
	Delete the elements at position 'pos'.
virtual std::string	getChar (unsigned int pos) const =0 throw (IndexOutOfBoundsException)
	Get the element at position 'pos' as a character.
virtual int	getValue (unsigned int 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[] (unsigned int i) const =0
	Operator [] overloaded for quick access to a character in list.
virtual int &	operator[] (unsigned int 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.
Protected Member Functions
void	propagateEvents (bool yn)
bool	propagateEvents () const
Protected Attributes
std::vector< int >	content_
	The list content.
std::vector< SymbolListListener * >	listeners_
	Contains the listeners.
Private Member Functions
void	beforeSequenceChanged (const SymbolListEditionEvent &event)
void	afterSequenceChanged (const SymbolListEditionEvent &event)
void	beforeSequenceInserted (const SymbolListInsertionEvent &event)
void	afterSequenceInserted (const SymbolListInsertionEvent &event)
void	beforeSequenceDeleted (const SymbolListDeletionEvent &event)
void	afterSequenceDeleted (const SymbolListDeletionEvent &event)
void	beforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)
void	afterSequenceSubstituted (const SymbolListSubstitutionEvent &event)
Private Attributes
bool	hasCoordinates_
unsigned int	begin_
std::string	species_
std::string	chromosome_
char	strand_
unsigned int	size_
unsigned int	srcSize_
Events handling
virtual unsigned int	getNumberOfListeners () const
virtual const SymbolListListener &	getListener (unsigned int i) const
virtual SymbolListListener &	getListener (unsigned int i)
virtual void	addSymbolListListener (SymbolListListener *listener)
virtual void	removeSymbolListListener (SymbolListListener *listener)
void	fireBeforeSequenceChanged (const SymbolListEditionEvent &event)
void	fireAfterSequenceChanged (const SymbolListEditionEvent &event)
void	fireBeforeSequenceInserted (const SymbolListInsertionEvent &event)
void	fireAfterSequenceInserted (const SymbolListInsertionEvent &event)
void	fireBeforeSequenceDeleted (const SymbolListDeletionEvent &event)
void	fireAfterSequenceDeleted (const SymbolListDeletionEvent &event)
void	fireBeforeSequenceSubstituted (const SymbolListSubstitutionEvent &event)
void	fireAfterSequenceSubstituted (const SymbolListSubstitutionEvent &event)

Detailed Description

A sequence class which is used to store data from MAF files.

It extends the SequenceWithAnnotation class to store MAF-specific features, like the chromosome position. The sequence is its own listener, and recomputes its "genomic" site by using the SequenceTools::getNumberOfSites function when a content modification is performed. Tags like begin and stop, hovever, have to be set by hand.

A MAF sequence is necessarily a DNA sequence.

Definition at line 61 of file MafSequence.h.

Constructor & Destructor Documentation

bpp::MafSequence::MafSequence ( ) [inline]

Definition at line 74 of file MafSequence.h.

References size_.

Referenced by clone().

bpp::MafSequence::MafSequence	(	const std::string &	name,
		const std::string &	sequence
	)		`[inline]`

Definition at line 80 of file MafSequence.h.

References chromosome_, bpp::SequenceTools::getNumberOfSites(), size_, and species_.

bpp::MafSequence::MafSequence	(	const std::string &	name,
		const std::string &	sequence,
		unsigned int	begin,
		char	strand,
		unsigned int	srcSize
	)		`[inline]`

Definition at line 91 of file MafSequence.h.

References bpp::SequenceTools::getNumberOfSites(), setName(), and size_.

bpp::MafSequence::~MafSequence ( ) [inline]

Definition at line 100 of file MafSequence.h.

Member Function Documentation

virtual void bpp::SequenceWithAnnotation::addAnnotation ( SequenceAnnotation * anno ) throw (Exception) [inline, virtual, inherited]

Add a new annotation to the sequence.

Parameters:

anno	The annotation object to be added. Unless the annotation is shared, the annotation object will be owned by the sequence object, and will be copied and deleted when needed.

Exceptions:

Exception If the annotation is not valid for this sequence.

See also:: SequenceWithAnnotation::isValidWith

Definition at line 380 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::addSymbolListListener().

Referenced by bpp::MafAlignmentParser::analyseCurrentBlock_(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithQuality::SequenceWithQuality(), and subSequence().

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::BasicSymbolList, and bpp::EdSymbolList.

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

virtual void bpp::SymbolList::addElement	(	unsigned int	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::BasicSymbolList, and bpp::EdSymbolList.

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::BasicSymbolList, and bpp::EdSymbolList.

virtual void bpp::SymbolList::addElement	(	unsigned int	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::BasicSymbolList, and bpp::EdSymbolList.

void EdSymbolList::addElement ( const std::string & c ) throw (BadCharException) [virtual, inherited]

Add a character to the end of the list.

Parameters:

c	The character to add, given as a string.

Implements bpp::SymbolList.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 321 of file SymbolList.cpp.

void EdSymbolList::addElement	(	unsigned int	pos,
		const std::string &	c
	)		throw (BadCharException, IndexOutOfBoundsException) `[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.

Implements bpp::SymbolList.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 331 of file SymbolList.cpp.

void EdSymbolList::addElement ( int v ) throw (BadIntException) [virtual, inherited]

Add a character to the end of the list.

Parameters:

v	The character to add, given as an int.

Implements bpp::SymbolList.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 394 of file SymbolList.cpp.

void EdSymbolList::addElement	(	unsigned int	pos,
		int	v
	)		throw (BadIntException, IndexOutOfBoundsException) `[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.

Implements bpp::SymbolList.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 406 of file SymbolList.cpp.

virtual void bpp::EdSymbolList::addSymbolListListener ( SymbolListListener * listener ) [inline, virtual, inherited]

Definition at line 689 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

Referenced by bpp::SequenceWithAnnotation::addAnnotation().

void bpp::MafSequence::afterSequenceChanged ( const SymbolListEditionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 170 of file MafSequence.h.

References bpp::SequenceTools::getNumberOfSites(), and size_.

void bpp::MafSequence::afterSequenceDeleted ( const SymbolListDeletionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 174 of file MafSequence.h.

References bpp::SequenceTools::getNumberOfSites(), and size_.

void bpp::MafSequence::afterSequenceInserted ( const SymbolListInsertionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 172 of file MafSequence.h.

References bpp::SequenceTools::getNumberOfSites(), and size_.

void bpp::MafSequence::afterSequenceSubstituted ( const SymbolListSubstitutionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 176 of file MafSequence.h.

void SequenceWithAnnotation::append ( const std::vector< int > & content ) throw (BadIntException) [virtual, inherited]

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.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 206 of file SequenceWithAnnotation.cpp.

void SequenceWithAnnotation::append ( const std::vector< std::string > & content ) throw (BadCharException) [virtual, inherited]

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.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 221 of file SequenceWithAnnotation.cpp.

void SequenceWithAnnotation::append ( const std::string & content ) throw (BadCharException) [virtual, inherited]

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.

Reimplemented in bpp::SequenceWithQuality.

Definition at line 237 of file SequenceWithAnnotation.cpp.

References bpp::StringSequenceTools::codeSequence().

void bpp::MafSequence::beforeSequenceChanged ( const SymbolListEditionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 169 of file MafSequence.h.

void bpp::MafSequence::beforeSequenceDeleted ( const SymbolListDeletionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 173 of file MafSequence.h.

void bpp::MafSequence::beforeSequenceInserted ( const SymbolListInsertionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 171 of file MafSequence.h.

void bpp::MafSequence::beforeSequenceSubstituted ( const SymbolListSubstitutionEvent & event ) [inline, private, virtual]

Reimplemented from bpp::EdSymbolList.

Definition at line 175 of file MafSequence.h.

MafSequence* bpp::MafSequence::clone ( ) const [inline, virtual]

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 98 of file MafSequence.h.

References MafSequence().

virtual void bpp::SymbolList::deleteElement ( unsigned int pos ) throw (IndexOutOfBoundsException) [pure virtual, inherited]

Delete the element at position 'pos'.

Parameters:

pos	The position of the element to delete.

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

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

void EdSymbolList::deleteElement ( unsigned int pos ) throw (IndexOutOfBoundsException) [virtual, inherited]

Delete the element at position 'pos'.

Parameters:

pos	The position of the element to delete.

Implements bpp::SymbolList.

Definition at line 369 of file SymbolList.cpp.

virtual void bpp::SymbolList::deleteElements	(	unsigned int	pos,
		unsigned int	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::BasicSymbolList, and bpp::EdSymbolList.

void EdSymbolList::deleteElements	(	unsigned int	pos,
		unsigned int	len
	)		throw (IndexOutOfBoundsException) `[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.

Implements bpp::SymbolList.

Definition at line 381 of file SymbolList.cpp.

void bpp::EdSymbolList::fireAfterSequenceChanged ( const SymbolListEditionEvent & event ) [inline, protected, inherited]

Definition at line 717 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceChanged(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

void bpp::EdSymbolList::fireAfterSequenceDeleted ( const SymbolListDeletionEvent & event ) [inline, protected, inherited]

Definition at line 745 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceDeleted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

void bpp::EdSymbolList::fireAfterSequenceInserted ( const SymbolListInsertionEvent & event ) [inline, protected, inherited]

Definition at line 731 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceInserted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

void bpp::EdSymbolList::fireAfterSequenceSubstituted ( const SymbolListSubstitutionEvent & event ) [inline, protected, inherited]

Definition at line 759 of file SymbolList.h.

References bpp::EdSymbolList::afterSequenceSubstituted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

void bpp::EdSymbolList::fireBeforeSequenceChanged ( const SymbolListEditionEvent & event ) [inline, protected, inherited]

Definition at line 710 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceChanged(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

void bpp::EdSymbolList::fireBeforeSequenceDeleted ( const SymbolListDeletionEvent & event ) [inline, protected, inherited]

Definition at line 738 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceDeleted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

void bpp::EdSymbolList::fireBeforeSequenceInserted ( const SymbolListInsertionEvent & event ) [inline, protected, inherited]

Definition at line 724 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceInserted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

Referenced by bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

void bpp::EdSymbolList::fireBeforeSequenceSubstituted ( const SymbolListSubstitutionEvent & event ) [inline, protected, inherited]

Definition at line 752 of file SymbolList.h.

References bpp::EdSymbolList::beforeSequenceSubstituted(), bpp::EdSymbolList::listeners_, and bpp::EdSymbolList::propagateEvents_.

virtual const Alphabet* bpp::EdSymbolList::getAlphabet ( ) const [inline, virtual, inherited]

Get the alphabet associated to the list.

Returns:: A const pointer to the alphabet.

See also:: Alphabet class.

Implements bpp::SymbolList.

Definition at line 631 of file SymbolList.h.

References bpp::EdSymbolList::alphabet_.

Referenced by bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::SequenceWithQuality::append(), bpp::EdSymbolList::operator=(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceWithAnnotation::setToSizeL(), and bpp::SequenceWithAnnotation::setToSizeR().

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::BasicSymbolList, and bpp::EdSymbolList.

virtual const SequenceAnnotation& bpp::SequenceWithAnnotation::getAnnotation ( const std::string & type ) const [inline, virtual, inherited]

Definition at line 397 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

Referenced by bpp::QualityFilterMafIterator::analyseCurrentBlock_(), bpp::MaskFilterMafIterator::analyseCurrentBlock_(), bpp::SequenceWithQuality::operator=(), bpp::SequenceWithQuality::SequenceWithQuality(), and bpp::OutputMafIterator::writeBlock().

virtual SequenceAnnotation& bpp::SequenceWithAnnotation::getAnnotation ( const std::string & type ) [inline, virtual, inherited]

Definition at line 407 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

vector< string > SequenceWithAnnotation::getAnnotationTypes ( ) const [virtual, inherited]

Returns:: The list of annotation types contained in this sequence.

Definition at line 244 of file SequenceWithAnnotation.cpp.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

virtual std::string bpp::SymbolList::getChar ( unsigned int 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::BasicSymbolList, and bpp::EdSymbolList.

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

string EdSymbolList::getChar ( unsigned int pos ) const throw (IndexOutOfBoundsException) [virtual, inherited]

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

Parameters:

pos	The position of the character to retrieve.

Implements bpp::SymbolList.

Definition at line 354 of file SymbolList.cpp.

const std::string& bpp::MafSequence::getChromosome ( ) const [inline]

Definition at line 133 of file MafSequence.h.

References chromosome_.

Referenced by bpp::FeatureExtractor::analyseCurrentBlock_(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::BlockMergerMafIterator::analyseCurrentBlock_(), bpp::CsvStatisticsOutputIterationListener::iterationMoves(), and bpp::OutputAlignmentMafIterator::writeBlock().

const Comments& bpp::SequenceWithAnnotation::getComments ( ) const [inline, virtual, inherited]

Get the comments associated to this sequence.

Returns:: The comments of the sequence.

Implements bpp::Sequence.

Definition at line 290 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::comments_.

Referenced by bpp::SequenceWithAnnotation::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::BasicSymbolList, and bpp::EdSymbolList.

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

virtual const std::vector<int>& bpp::EdSymbolList::getContent ( ) const [inline, virtual, inherited]

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 635 of file SymbolList.h.

References bpp::EdSymbolList::content_.

Referenced by bpp::AlignmentFilter2MafIterator::analyseCurrentBlock_(), bpp::AlignmentFilterMafIterator::analyseCurrentBlock_(), bpp::SequenceWithQualityTools::invert(), and bpp::EdSymbolList::operator=().

std::string bpp::MafSequence::getDescription ( ) const [inline]

Definition at line 157 of file MafSequence.h.

References bpp::SequenceWithAnnotation::getName(), hasCoordinates_, start(), stop(), strand_, and bpp::EdSymbolList::toString().

unsigned int bpp::MafSequence::getGenomicSize ( ) const [inline]

Definition at line 137 of file MafSequence.h.

References size_.

Referenced by bpp::MafAlignmentParser::analyseCurrentBlock_(), and bpp::OutputMafIterator::writeBlock().

virtual const SymbolListListener& bpp::EdSymbolList::getListener ( unsigned int i ) const [inline, virtual, inherited]

Definition at line 679 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

Referenced by bpp::SequenceWithAnnotation::getAnnotation(), bpp::SequenceWithAnnotation::getAnnotationTypes(), and bpp::SequenceWithAnnotation::hasAnnotation().

virtual SymbolListListener& bpp::EdSymbolList::getListener ( unsigned int i ) [inline, virtual, inherited]

Definition at line 684 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

const std::string& bpp::SequenceWithAnnotation::getName ( ) const [inline, virtual, inherited]

Get the name of this sequence.

Returns:: This sequence name.

Implements bpp::Sequence.

Definition at line 268 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::name_.

Referenced by bpp::MafAlignmentParser::analyseCurrentBlock_(), getDescription(), getRange(), bpp::SequenceWithAnnotation::operator=(), start(), stop(), and bpp::OutputMafIterator::writeBlock().

virtual unsigned int bpp::EdSymbolList::getNumberOfListeners ( ) const [inline, virtual, inherited]

Definition at line 677 of file SymbolList.h.

References bpp::EdSymbolList::listeners_.

Referenced by bpp::SequenceWithAnnotation::getAnnotation(), bpp::SequenceWithAnnotation::getAnnotationTypes(), and bpp::SequenceWithAnnotation::hasAnnotation().

Range<unsigned int> bpp::MafSequence::getRange ( ) const [inline]

Definition at line 117 of file MafSequence.h.

References bpp::SequenceWithAnnotation::getName(), hasCoordinates_, start(), and stop().

const std::string& bpp::MafSequence::getSpecies ( ) const [inline]

Definition at line 131 of file MafSequence.h.

References species_.

Referenced by bpp::FullGapFilterMafIterator::analyseCurrentBlock_(), bpp::DuplicateFilterMafIterator::analyseCurrentBlock_(), bpp::ChromosomeMafIterator::analyseCurrentBlock_(), bpp::SequenceFilterMafIterator::analyseCurrentBlock_(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafBlock::getSequencesForSpecies(), bpp::MafBlock::hasSequenceForSpecies(), and bpp::OutputAlignmentMafIterator::writeBlock().

unsigned int bpp::MafSequence::getSrcSize ( ) const [inline]

Definition at line 139 of file MafSequence.h.

References srcSize_.

Referenced by bpp::BlockMergerMafIterator::analyseCurrentBlock_(), and bpp::OutputMafIterator::writeBlock().

char bpp::MafSequence::getStrand ( ) const [inline]

Definition at line 135 of file MafSequence.h.

References strand_.

Referenced by bpp::BlockMergerMafIterator::analyseCurrentBlock_(), bpp::OutputAlignmentMafIterator::writeBlock(), and bpp::OutputMafIterator::writeBlock().

virtual int bpp::SymbolList::getValue ( unsigned int 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::BasicSymbolList, and bpp::EdSymbolList.

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

int EdSymbolList::getValue ( unsigned int pos ) const throw (IndexOutOfBoundsException) [virtual, inherited]

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

Parameters:

pos	The position of the character to retrieve.

Implements bpp::SymbolList.

Definition at line 434 of file SymbolList.cpp.

virtual bool bpp::SequenceWithAnnotation::hasAnnotation ( const std::string & type ) const [inline, virtual, inherited]

Definition at line 386 of file SequenceWithAnnotation.h.

References bpp::EdSymbolList::getListener(), bpp::EdSymbolList::getNumberOfListeners(), and bpp::SequenceAnnotation::getType().

Referenced by bpp::QualityFilterMafIterator::analyseCurrentBlock_(), bpp::MaskFilterMafIterator::analyseCurrentBlock_(), and bpp::OutputMafIterator::writeBlock().

bool bpp::MafSequence::hasCoordinates ( ) const [inline]

Definition at line 103 of file MafSequence.h.

References hasCoordinates_.

Referenced by bpp::BlockMergerMafIterator::analyseCurrentBlock_(), and bpp::OutputMafIterator::writeBlock().

void SequenceWithAnnotation::merge ( const SequenceWithAnnotation & swa ) throw (AlphabetMismatchException, Exception) [virtual, inherited]

Merge a sequence with the current one.

Sequences must have the same name and alphabets. Only first sequence's commentaries are kept. Annotations that could not be merged will not be added in the concatenated sequence. See the documentation of each annotation class for more details.

Parameters:

swa	The sequence to merge with.

Exceptions:

AlphabetMismatchException	If the two alphabets do not match.
Exception	If the sequence names do not match.

Definition at line 257 of file SequenceWithAnnotation.cpp.

References bpp::SequenceAnnotation::clone(), bpp::SequenceAnnotation::init(), and bpp::SequenceAnnotation::merge().

virtual const int& bpp::SymbolList::operator[] ( unsigned int 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::BasicSymbolList, and bpp::EdSymbolList.

virtual int& bpp::SymbolList::operator[] ( unsigned int 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::BasicSymbolList, and bpp::EdSymbolList.

virtual int& bpp::EdSymbolList::operator[] ( unsigned int i ) [inline, 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.

Implements bpp::SymbolList.

Definition at line 665 of file SymbolList.h.

References bpp::EdSymbolList::content_.

virtual const int& bpp::EdSymbolList::operator[] ( unsigned int i ) const [inline, 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.

Implements bpp::SymbolList.

Definition at line 663 of file SymbolList.h.

References bpp::EdSymbolList::content_.

bool bpp::EdSymbolList::propagateEvents ( ) const [inline, protected, inherited]

Definition at line 769 of file SymbolList.h.

References bpp::EdSymbolList::propagateEvents_.

void bpp::EdSymbolList::propagateEvents ( bool yn ) [inline, protected, inherited]

Definition at line 768 of file SymbolList.h.

References bpp::EdSymbolList::propagateEvents_.

void bpp::MafSequence::removeCoordinates ( ) [inline]

Definition at line 105 of file MafSequence.h.

References begin_, and hasCoordinates_.

Referenced by subSequence().

virtual void bpp::EdSymbolList::removeSymbolListListener ( SymbolListListener * listener ) [inline, virtual, inherited]

Definition at line 693 of file SymbolList.h.

References bpp::SymbolListListener::isRemovable(), and bpp::EdSymbolList::listeners_.

void bpp::MafSequence::setChromosome ( const std::string & chr ) [inline]

Definition at line 143 of file MafSequence.h.

References chromosome_, setName(), and species_.

void bpp::SequenceWithAnnotation::setComments ( const Comments & comments ) [inline, virtual, inherited]

Set the comments associated to this sequence.

Parameters:

comments The new comments of the sequence.

Implements bpp::Sequence.

Definition at line 297 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::comments_.

void bpp::SequenceWithAnnotation::setContent ( const std::vector< std::string > & list ) throw (BadCharException) [inline, virtual, inherited]

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 319 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::setContent().

void bpp::SequenceWithAnnotation::setContent ( const std::vector< int > & list ) throw (BadIntException) [inline, virtual, inherited]

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 315 of file SequenceWithAnnotation.h.

References bpp::SequenceWithAnnotation::setContent().

void SequenceWithAnnotation::setContent ( const std::string & sequence ) throw (BadCharException) [virtual, inherited]

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 143 of file SequenceWithAnnotation.cpp.

References bpp::StringSequenceTools::codeSequence(), and bpp::TextTools::removeWhiteSpaces().

Referenced by bpp::SequenceWithQualityTools::invert(), bpp::SequenceWithQualityTools::removeGaps(), and bpp::SequenceWithAnnotation::setContent().

virtual void bpp::SymbolList::setElement	(	unsigned int	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::BasicSymbolList, and bpp::EdSymbolList.

void EdSymbolList::setElement	(	unsigned int	pos,
		const std::string &	c
	)		throw (BadCharException, IndexOutOfBoundsException) `[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.

Implements bpp::SymbolList.

Definition at line 342 of file SymbolList.cpp.

void EdSymbolList::setElement	(	unsigned int	pos,
		int	v
	)		throw (BadIntException, IndexOutOfBoundsException) `[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.

Implements bpp::SymbolList.

Definition at line 420 of file SymbolList.cpp.

virtual void bpp::SymbolList::setElement	(	unsigned int	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::BasicSymbolList, and bpp::EdSymbolList.

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

void bpp::MafSequence::setName ( const std::string & name ) [inline, virtual]

Set the name of this sequence.

Parameters:

name	The new name of the sequence.

Reimplemented from bpp::SequenceWithAnnotation.

Definition at line 122 of file MafSequence.h.

References chromosome_, and species_.

Referenced by MafSequence(), setChromosome(), and setSpecies().

void bpp::MafSequence::setSpecies ( const std::string & species ) [inline]

Definition at line 148 of file MafSequence.h.

References chromosome_, setName(), and species_.

void bpp::MafSequence::setSrcSize ( unsigned int srcSize ) [inline]

Definition at line 155 of file MafSequence.h.

References srcSize_.

void bpp::MafSequence::setStart ( unsigned int begin ) [inline]

Definition at line 141 of file MafSequence.h.

References begin_, and hasCoordinates_.

void bpp::MafSequence::setStrand ( char s ) [inline]

Definition at line 153 of file MafSequence.h.

References strand_.

void SequenceWithAnnotation::setToSizeL ( unsigned int newSize ) [virtual, inherited]

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 180 of file SequenceWithAnnotation.cpp.

References bpp::EdSymbolList::content_, bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

void SequenceWithAnnotation::setToSizeR ( unsigned int newSize ) [virtual, inherited]

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 155 of file SequenceWithAnnotation.cpp.

References bpp::EdSymbolList::content_, bpp::EdSymbolList::fireAfterSequenceDeleted(), bpp::EdSymbolList::fireAfterSequenceInserted(), bpp::EdSymbolList::fireBeforeSequenceDeleted(), bpp::EdSymbolList::fireBeforeSequenceInserted(), bpp::EdSymbolList::getAlphabet(), and bpp::Alphabet::getGapCharacterCode().

virtual void bpp::EdSymbolList::shuffle ( ) [inline, virtual, inherited]

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

Implements bpp::SymbolList.

Definition at line 667 of file SymbolList.h.

References bpp::EdSymbolList::content_.

virtual void bpp::SymbolList::shuffle ( ) [pure virtual, inherited]

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

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

virtual unsigned int 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::BasicSymbolList, and bpp::EdSymbolList.

virtual unsigned int bpp::EdSymbolList::size ( ) const [inline, virtual, inherited]

Get the number of elements in the list.

Returns:: The number of sites in the list.

Implements bpp::SymbolList.

Definition at line 633 of file SymbolList.h.

References bpp::EdSymbolList::content_.

Referenced by bpp::SequenceWithQuality::addElement(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::QualityFilterMafIterator::analyseCurrentBlock_(), bpp::MaskFilterMafIterator::analyseCurrentBlock_(), bpp::MafAlignmentParser::analyseCurrentBlock_(), bpp::SequenceQuality::isValidWith(), bpp::SequenceMask::isValidWith(), bpp::SequenceWithQualityTools::removeGaps(), bpp::OutputMafIterator::writeBlock(), and bpp::Fastq::writeSequence().

unsigned int bpp::MafSequence::start ( ) const throw (Exception) [inline]

Definition at line 107 of file MafSequence.h.

References begin_, bpp::SequenceWithAnnotation::getName(), and hasCoordinates_.

Referenced by bpp::FeatureExtractor::analyseCurrentBlock_(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::BlockMergerMafIterator::analyseCurrentBlock_(), getDescription(), getRange(), bpp::CsvStatisticsOutputIterationListener::iterationMoves(), bpp::OutputAlignmentMafIterator::writeBlock(), and bpp::OutputMafIterator::writeBlock().

unsigned int bpp::MafSequence::stop ( ) const [inline]

Definition at line 112 of file MafSequence.h.

References begin_, bpp::SequenceWithAnnotation::getName(), hasCoordinates_, and size_.

Referenced by bpp::FeatureExtractor::analyseCurrentBlock_(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::BlockMergerMafIterator::analyseCurrentBlock_(), getDescription(), getRange(), bpp::CsvStatisticsOutputIterationListener::iterationMoves(), and bpp::OutputAlignmentMafIterator::writeBlock().

MafSequence * MafSequence::subSequence	(	unsigned int	startAt,
		unsigned int	length
	)		const

Extract a sub-sequence.

Returns:: A subsequence.

Parameters:

startAt	Begining of sub-sequence.
length	the length of the sub-sequence.

Definition at line 48 of file MafSequence.cpp.

References bpp::SequenceWithAnnotation::addAnnotation(), and removeCoordinates().

Referenced by bpp::WindowSplitMafIterator::analyseCurrentBlock_(), bpp::FeatureExtractor::analyseCurrentBlock_(), bpp::FeatureFilterMafIterator::analyseCurrentBlock_(), bpp::QualityFilterMafIterator::analyseCurrentBlock_(), bpp::MaskFilterMafIterator::analyseCurrentBlock_(), bpp::AlignmentFilter2MafIterator::analyseCurrentBlock_(), and bpp::AlignmentFilterMafIterator::analyseCurrentBlock_().

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::BasicSymbolList, and bpp::EdSymbolList.

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

string EdSymbolList::toString ( ) const [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.

Implements bpp::SymbolList.

Definition at line 314 of file SymbolList.cpp.

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

Referenced by getDescription(), and bpp::OutputMafIterator::writeBlock().

Member Data Documentation

unsigned int bpp::MafSequence::begin_ [private]

Definition at line 66 of file MafSequence.h.

Referenced by removeCoordinates(), setStart(), start(), and stop().

std::string bpp::MafSequence::chromosome_ [private]

Definition at line 68 of file MafSequence.h.

Referenced by getChromosome(), MafSequence(), setChromosome(), setName(), and setSpecies().

std::vector<int> bpp::EdSymbolList::content_ [protected, inherited]

The list content.

Definition at line 550 of file SymbolList.h.

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

bool bpp::MafSequence::hasCoordinates_ [private]

Definition at line 65 of file MafSequence.h.

Referenced by getDescription(), getRange(), hasCoordinates(), removeCoordinates(), setStart(), start(), and stop().

std::vector<SymbolListListener*> bpp::EdSymbolList::listeners_ [protected, inherited]

Contains the listeners.

Definition at line 555 of file SymbolList.h.

unsigned int bpp::MafSequence::size_ [private]

Definition at line 70 of file MafSequence.h.

Referenced by afterSequenceChanged(), afterSequenceDeleted(), afterSequenceInserted(), getGenomicSize(), MafSequence(), and stop().

std::string bpp::MafSequence::species_ [private]

Definition at line 67 of file MafSequence.h.

Referenced by getSpecies(), MafSequence(), setChromosome(), setName(), and setSpecies().

unsigned int bpp::MafSequence::srcSize_ [private]

Definition at line 71 of file MafSequence.h.

Referenced by getSrcSize(), and setSrcSize().

char bpp::MafSequence::strand_ [private]

Definition at line 69 of file MafSequence.h.

Referenced by getDescription(), getStrand(), and setStrand().

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

Bpp/Seq/Io/Maf/MafSequence.h
Bpp/Seq/Io/Maf/MafSequence.cpp

bpp::MafSequence Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Events handling

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation