bpp::AbstractCoreSequence Class Reference

A partial implementation of the CoreSequence interface. More...

#include <Bpp/Seq/CoreSequence.h>

Inheritance diagram for bpp::AbstractCoreSequence:

Collaboration diagram for bpp::AbstractCoreSequence:

Public Member Functions
	AbstractCoreSequence (const std::string &name)
	Constructor of the AbstractCoreSequence object. More...
	AbstractCoreSequence (const std::string &name, const Comments &comments)
	Constructor of the AbstractCoreSequence object. More...
	AbstractCoreSequence ()
	AbstractCoreSequence (const AbstractCoreSequence &s)
AbstractCoreSequence &	operator= (const AbstractCoreSequence &s)
	AbstractCoreSequence (const CoreSequenceInterface &s)
AbstractCoreSequence &	operator= (const CoreSequenceInterface &s)
virtual	~AbstractCoreSequence ()
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the list. More...
virtual const Alphabet &	alphabet () const =0
	Get the alphabet associated to the list. More...
virtual size_t	size () const =0
	Get the number of elements in the list. More...
virtual std::string	toString () const =0
	Convert the list as a string. More...
virtual double	getStateValueAt (size_t position, int state) const =0
	get value of a state at a position More...
virtual double	operator() (size_t position, int state) const =0
	get value of a state at a position More...
virtual const Comments &	getComments () const =0
	Get the comments. More...
virtual void	setComments (const Comments &comments)=0
	Set the comments. More...
virtual void	clearComments ()=0
const Comments &	getComments () const override
	Get the comments. More...
void	setComments (const Comments &comments) override
	Set the comments. More...
void	clearComments () override
The Clonable interface
virtual AbstractCoreSequence *	clone () const override=0
Setting/getting the name of the sequence.
const std::string &	getName () const override
	Get the name of this sequence. More...
void	setName (const std::string &name) override
	Set the name of this sequence. More...
Adjusting the size of the sequence.
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...
Edition methods.
virtual void	deleteElement (size_t pos)=0
	Remove the element at position 'pos'. More...
virtual void	deleteElements (size_t pos, size_t len)=0
	Remove the elements at position 'pos'. More...
Provide direct access to the list content.
Warning These operators allow you to modify the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

Protected Attributes
Comments	comments_

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

Detailed Description

A partial implementation of the CoreSequence interface.

Definition at line 95 of file CoreSequence.h.

Constructor & Destructor Documentation

AbstractCoreSequence() [1/5]

bpp::AbstractCoreSequence::AbstractCoreSequence ( const std::string &  name )

inline

Constructor of the AbstractCoreSequence object.

Parameters

name	The sequence name.

Definition at line 111 of file CoreSequence.h.

AbstractCoreSequence() [2/5]

bpp::AbstractCoreSequence::AbstractCoreSequence ( const std::string &  name, const Comments &  comments  )

inline

Constructor of the AbstractCoreSequence object.

Parameters

name	The sequence name.
comments	Comments to add to the sequence.

Definition at line 121 of file CoreSequence.h.

AbstractCoreSequence() [3/5]

bpp::AbstractCoreSequence::AbstractCoreSequence ( )

inline

Definition at line 125 of file CoreSequence.h.

AbstractCoreSequence() [4/5]

bpp::AbstractCoreSequence::AbstractCoreSequence ( const AbstractCoreSequence &  s )

inline

Definition at line 129 of file CoreSequence.h.

AbstractCoreSequence() [5/5]

bpp::AbstractCoreSequence::AbstractCoreSequence ( const CoreSequenceInterface &  s )

inline

Definition at line 141 of file CoreSequence.h.

~AbstractCoreSequence()

virtual bpp::AbstractCoreSequence::~AbstractCoreSequence ( )

inlinevirtual

Definition at line 153 of file CoreSequence.h.

Member Function Documentation

alphabet()

virtual const Alphabet& bpp::CruxSymbolListInterface::alphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns

A const reference to the alphabet.

See also

Alphabet class.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::concatenate(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::invertComplement(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), and bpp::AbstractTransliterator::translate().

clearComments() [1/2]

void bpp::SimpleCommentable::clearComments ( )

inlineoverridevirtualinherited

Implements bpp::Commentable.

Definition at line 88 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

clearComments() [2/2]

virtual void bpp::Commentable::clearComments ( )

pure virtualinherited

Implemented in bpp::SimpleCommentable.

clone()

virtual AbstractCoreSequence* bpp::AbstractCoreSequence::clone ( ) const

overridepure virtual

Implements bpp::CoreSequenceInterface.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::Sequence, and bpp::ProbabilisticSequence.

deleteElement()

virtual void bpp::CruxSymbolListInterface::deleteElement ( size_t  pos )

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

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

deleteElements()

virtual void bpp::CruxSymbolListInterface::deleteElements ( size_t  pos, size_t  len  )

pure virtualinherited

Remove the elements at position 'pos'.

Parameters

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

Implemented in bpp::AbstractTemplateEventDrivenSymbolList< T >, bpp::AbstractTemplateEventDrivenSymbolList< int >, bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::CruxSymbolListInterface::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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::Sequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceWithQualityTools::complement(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::getComplement(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::jointEntropy(), bpp::SequenceWithAnnotation::merge(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::ProbabilisticSymbolList::operator=(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::SequenceWithQualityTools::reverseTranscript(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SequenceWithQualityTools::transcript(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::WordAlphabet::translate(), and bpp::SymbolListTools::variabilityShannon().

getComments() [1/2]

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

pure virtualinherited

Get the comments.

Returns

The comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Mase::appendSequencesFromStream(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SiteContainerTools::getSelectedPositions(), bpp::MaseTools::getSelectedSites(), bpp::SiteContainerTools::getSelectedSites(), operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Stockholm::writeAlignment(), bpp::Fasta::writeSequences(), and bpp::Mase::writeSequences().

getComments() [2/2]

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

inlineoverridevirtualinherited

Get the comments.

Returns

The comments.

Implements bpp::Commentable.

Definition at line 79 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::createEmptyContainer(), bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::TemplateVectorSiteContainer< SiteType, SequenceType >::createEmptyContainer(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

getName()

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

inlineoverridevirtual

Get the name of this sequence.

Returns

This sequence name.

Implements bpp::CoreSequenceInterface.

Definition at line 170 of file CoreSequence.h.

References name_.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceWithAnnotation::merge(), bpp::SequenceWithAnnotation::operator=(), bpp::SequenceWithQualityTools::subseq(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

getStateValueAt()

virtual double bpp::CruxSymbolListInterface::getStateValueAt ( size_t  position, int  state  ) const

pure virtualinherited

get value of a state at a position

Parameters

position	position in the list
state	state in the alphabet

Returns

The state value at the given position.

Implemented in bpp::Sequence, bpp::ProbabilisticSequence, bpp::ProbabilisticSymbolList, bpp::IntSymbolList, bpp::CoreSiteInterface, bpp::Site, and bpp::ProbabilisticSite.

Referenced by bpp::ProbabilisticSymbolList::ProbabilisticSymbolList().

operator()()

virtual double bpp::CruxSymbolListInterface::operator() ( size_t  position, int  state  ) const

pure virtualinherited

get value of a state at a position

Short-cut for getStateValueAt.

Parameters

position	position in the list
state	state in the alphabet

Returns

The state value at the given position.

Implemented in bpp::ProbabilisticSymbolList, and bpp::IntSymbolList.

operator=() [1/2]

AbstractCoreSequence& bpp::AbstractCoreSequence::operator= ( const AbstractCoreSequence &  s )

inline

Definition at line 134 of file CoreSequence.h.

References name_, and bpp::SimpleCommentable::operator=().

Referenced by bpp::ProbabilisticSequence::operator=(), bpp::Sequence::operator=(), and bpp::SequenceWithAnnotation::operator=().

operator=() [2/2]

AbstractCoreSequence& bpp::AbstractCoreSequence::operator= ( const CoreSequenceInterface &  s )

inline

Definition at line 146 of file CoreSequence.h.

References bpp::Commentable::getComments(), bpp::CoreSequenceInterface::getName(), name_, and bpp::SimpleCommentable::setComments().

setComments() [1/2]

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

inlineoverridevirtualinherited

Set the comments.

Parameters

comments

The new comments.

Implements bpp::Commentable.

Definition at line 86 of file Commentable.h.

References bpp::SimpleCommentable::comments_.

Referenced by bpp::CompressedVectorSiteContainer::createEmptyContainer(), bpp::TemplateVectorSequenceContainer< SequenceType >::createEmptyContainer(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::AbstractTemplateSequenceContainer< SequenceType, HashType >::operator=(), bpp::TemplateVectorSequenceContainer< SequenceType >::operator=(), bpp::TemplateAlignedSequenceContainer< SequenceType, SiteType >::TemplateAlignedSequenceContainer(), and bpp::TemplateVectorSequenceContainer< SequenceType >::TemplateVectorSequenceContainer().

setComments() [2/2]

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

pure virtualinherited

Set the comments.

Parameters

comments

The new comments.

Implemented in bpp::SimpleCommentable.

Referenced by bpp::Pasta::appendAlignmentFromStream(), bpp::Clustal::appendAlignmentFromStream(), bpp::Fasta::appendSequencesFromStream(), and bpp::Mase::appendSequencesFromStream().

setName()

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

inlineoverridevirtual

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::CoreSequenceInterface.

Definition at line 172 of file CoreSequence.h.

References name_.

Referenced by bpp::Pasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPhd::nextSequence(), and bpp::SequenceWithAnnotation::operator=().

setToSizeL()

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

pure virtualinherited

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::SequenceWithAnnotation, bpp::Sequence, and bpp::ProbabilisticSequence.

setToSizeR()

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

pure virtualinherited

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::SequenceWithAnnotation, bpp::Sequence, and bpp::ProbabilisticSequence.

shuffle()

virtual void bpp::CruxSymbolListInterface::shuffle ( )

pure virtualinherited

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

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

size()

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

pure virtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implemented in bpp::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, and bpp::ProbabilisticSymbolList.

Referenced by bpp::AbstractTemplateSymbolList< T >::AbstractTemplateSymbolList(), bpp::SequenceWithQuality::addElement(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceTools::findFirstOf(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getCountsResolveUnknowns(), bpp::SymbolListTools::getFrequencies(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getMajorAllele(), bpp::SymbolListTools::getMajorAlleleFrequency(), bpp::SymbolListTools::getMinorAllele(), bpp::SymbolListTools::getMinorAlleleFrequency(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SymbolListTools::getNumberOfDistinctCharacters(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::SymbolListTools::hasSingleton(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SymbolListTools::heterozygosity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isDoubleton(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::SymbolListTools::isParsimonyInformativeSite(), bpp::SymbolListTools::isTriplet(), bpp::SequenceMask::isValidWith(), bpp::SequenceQuality::isValidWith(), bpp::SymbolListTools::jointEntropy(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::SymbolListTools::numberOfUnresolved(), bpp::AbstractTemplateSymbolList< T >::operator=(), bpp::SiteInterface::operator==(), bpp::SequenceWithQualityTools::removeGaps(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceWalker::SequenceWalker(), bpp::SequenceTools::subseq(), bpp::SequenceWithQualityTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::SymbolListTools::variabilityFactorial(), and bpp::SymbolListTools::variabilityShannon().

toString()

virtual std::string bpp::CruxSymbolListInterface::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::AbstractTemplateSymbolList< T >, bpp::AbstractTemplateSymbolList< int >, bpp::Sequence, bpp::ProbabilisticSymbolList, bpp::EventDrivenIntSymbolList, and bpp::IntSymbolList.

Member Data Documentation

comments_

Comments bpp::SimpleCommentable::comments_

protectedinherited

Definition at line 50 of file Commentable.h.

Referenced by bpp::SimpleCommentable::clearComments(), bpp::SimpleCommentable::getComments(), bpp::SimpleCommentable::operator=(), and bpp::SimpleCommentable::setComments().

name_

std::string bpp::AbstractCoreSequence::name_

private

The sequence name.

Definition at line 103 of file CoreSequence.h.

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

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

• Bpp/Seq/CoreSequence.h