bpp::ProbabilisticSequence Class Reference

A basic implementation of the ProbabilisticSequence interface. More...

#include <Bpp/Seq/ProbabilisticSequence.h>

Inheritance diagram for bpp::ProbabilisticSequence:

Collaboration diagram for bpp::ProbabilisticSequence:

Public Types
typedef std::vector< double >	ElementType
typedef std::vector< double >	SymbolType
typedef Table< double >	DTable

Public Member Functions
	ProbabilisticSequence (std::shared_ptr< const Alphabet > &alphabet)
	Empty constructor : build a void ProbabilisticSequence with just an Alphabet. More...
	ProbabilisticSequence (const std::string &name, const std::vector< ProbabilisticSequence::SymbolType > &sequence, std::shared_ptr< const Alphabet > &alphabet)
	Direct constructor : build a ProbabilisticSequence object from a vector. More...
	ProbabilisticSequence (const std::string &name, const DTable &sequence, std::shared_ptr< const Alphabet > &alphabet)
	Direct constructor : build a ProbabilisticSequence object from Table<double>. More...
	ProbabilisticSequence (const std::string &name, const std::vector< ProbabilisticSequence::SymbolType > &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alphabet)
	Direct constructor : build a ProbabilisticSequence object from a vector. More...
	ProbabilisticSequence (const std::string &name, const DTable &sequence, const Comments &comments, std::shared_ptr< const Alphabet > &alphabet)
	Direct constructor : build a ProbabilisticSequence object from a DTable. More...
	ProbabilisticSequence (const ProbabilisticSequence &sequence)
	The copy constructor. More...
ProbabilisticSequence &	operator= (const ProbabilisticSequence &sequence)
	The assignment operator. More...
virtual	~ProbabilisticSequence ()
void	setToSizeR (size_t newSize) override
	Set up the size of a sequence from the right side. More...
void	setToSizeL (size_t newSize) override
	Set up the size of a sequence from the left side. More...
double	getStateValueAt (size_t sitePosition, int state) const override
	get value of a state at a position More...
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	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
virtual const DTable &	getTable () const =0
virtual void	setContent (const DTable &list)=0
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
const Comments &	getComments () const override
	Get the comments. More...
void	setComments (const Comments &comments) override
	Set the comments. More...
void	clearComments () override
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the list. More...
const Alphabet &	alphabet () const override
	Get the alphabet associated to the list. More...
size_t	size () const override
	Get the number of elements in the list. More...
void	setContent (const std::vector< std::vector< double >> &list) override
void	setContent (const DTable &list) override
std::string	toString () const override
	Convert the list as a string. More...
void	addElement (const std::vector< double > &element) override
void	addElement (size_t pos, const std::vector< double > &element) override
void	setElement (size_t pos, const std::vector< double > &element) override
const std::vector< double > &	getElement (size_t pos) const override
	Get the element at position 'pos' as a character. More...
virtual void	deleteElement (size_t pos) override
	Remove the element at position 'pos'. More...
virtual void	deleteElements (size_t pos, size_t len) override
	Remove the elements at position 'pos'. More...
const std::vector< std::vector< double > > &	getContent () const override
const DTable &	getTable () const override
const std::vector< double > &	getValue (size_t pos) const override
	checked access to a character in list. More...
const std::vector< double > &	operator[] (size_t pos) const override
	Operator [] overloaded for quick access to a character in list. More...
std::vector< double > &	operator[] (size_t pos) override
	Operator [] overloaded for quick access to a character in list. More...
double	operator() (size_t siteIndex, int state) const override
	get value of a state at a position More...
void	shuffle () override
	Randomly shuffle the content of the list, with linear complexity. More...
The Clonable interface
ProbabilisticSequence *	clone () const override
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...
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...
Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
virtual const std::vector< T > &	getContent () const =0
Edition methods.
virtual void	addElement (const T &c)=0
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const T &c)=0
	Add a character at a certain position in the list. More...
virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...
virtual const T &	getElement (size_t pos) const =0
	Get the element at position 'pos' as a character. 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 const T &	getValue (size_t pos) const =0
	checked access to a character in list. More...
virtual const T &	operator[] (size_t pos) const =0
	Operator [] overloaded for quick access to a character in list. More...
virtual T &	operator[] (size_t pos)=0
	Operator [] overloaded for quick access to a character in list. More...
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...

Protected Attributes
Comments	comments_
DTable	content_
	The list content. More...

Private Attributes
std::string	name_
	The sequence name. More...
std::shared_ptr< const Alphabet >	alphabet_
	The Alphabet attribute must be initialized in the constructor and then can never be changed. More...

Detailed Description

A basic implementation of the ProbabilisticSequence interface.

This is a general purpose container, containing an ordered list of elements. The states represented by the elements is defined by an alphabet object, which is passed to the constructor by a pointer.

ProbabilisticSequence objects also contain a name attribute and potentially several comment lines.

See also

Alphabet

Definition at line 56 of file ProbabilisticSequence.h.

Member Typedef Documentation

DTable

typedef Table<double> bpp::ProbabilisticSymbolListInterface::DTable

inherited

Definition at line 35 of file ProbabilisticSymbolList.h.

ElementType

typedef std::vector<double> bpp::ProbabilisticSequenceInterface::ElementType

inherited

Definition at line 35 of file ProbabilisticSequence.h.

SymbolType

typedef std::vector<double> bpp::ProbabilisticSymbolListInterface::SymbolType

inherited

Definition at line 34 of file ProbabilisticSymbolList.h.

Constructor & Destructor Documentation

ProbabilisticSequence() [1/6]

bpp::ProbabilisticSequence::ProbabilisticSequence ( std::shared_ptr< const Alphabet > &  alphabet )

inline

Empty constructor : build a void ProbabilisticSequence with just an Alphabet.

One can use it safely for all types of Alphabet in order to build an empty ProbabilisticSequence, i.e., without name nor sequence data.

Parameters

alphabet

A pointer to the Alphabet to be used with this ProbabilisticSequence.

Definition at line 71 of file ProbabilisticSequence.h.

Referenced by clone().

ProbabilisticSequence() [2/6]

bpp::ProbabilisticSequence::ProbabilisticSequence ( const std::string &  name, const std::vector< ProbabilisticSequence::SymbolType > &  sequence, std::shared_ptr< const Alphabet > &  alphabet  )

inline

Direct constructor : build a ProbabilisticSequence object from a vector.

Parameters

name	The sequence name.
sequence	The entire sequence to parsed as a vector.
alphabet	A pointer to the alphabet associated with this sequence.

Exceptions

Exception

if the content is internally inconsistent, or is inconsistent with the specified alphabet.

Definition at line 83 of file ProbabilisticSequence.h.

ProbabilisticSequence() [3/6]

bpp::ProbabilisticSequence::ProbabilisticSequence ( const std::string &  name, const DTable &  sequence, std::shared_ptr< const Alphabet > &  alphabet  )

inline

Direct constructor : build a ProbabilisticSequence object from Table<double>.

One can use it safely for RNA, DNA and protein sequences.

Parameters

name	The sequence name.
sequence	The entire sequence to parsed as a Table<double>.
alphabet	A pointer to the alphabet associated with this sequence.

Exceptions

Exception

if the content is internally inconsistent, or is inconsistent with the specified alphabet.

Definition at line 100 of file ProbabilisticSequence.h.

ProbabilisticSequence() [4/6]

bpp::ProbabilisticSequence::ProbabilisticSequence ( const std::string &  name, const std::vector< ProbabilisticSequence::SymbolType > &  sequence, const Comments &  comments, std::shared_ptr< const Alphabet > &  alphabet  )

inline

Direct constructor : build a ProbabilisticSequence object from a vector.

Parameters

name	The sequence name.
sequence	The entire sequence to parsed as a vector.
comments	Comments to add to the sequence.
alphabet	A pointer to the alphabet associated with this sequence.

Exceptions

Exception

if the content is internally inconsistent, or is inconsistent with the specified alphabet.

Definition at line 117 of file ProbabilisticSequence.h.

ProbabilisticSequence() [5/6]

bpp::ProbabilisticSequence::ProbabilisticSequence ( const std::string &  name, const DTable &  sequence, const Comments &  comments, std::shared_ptr< const Alphabet > &  alphabet  )

inline

Direct constructor : build a ProbabilisticSequence object from a DTable.

One can use it safely for RNA, DNA and protein sequences.

Parameters

name	The sequence name.
sequence	The entire sequence to parsed as a DTable.
comments	Comments to add to the sequence.
alphabet	A pointer to the alphabet associated with this sequence.

Exceptions

Exception

if the content is internally inconsistent, or is inconsistent with the specified alphabet.

Definition at line 137 of file ProbabilisticSequence.h.

ProbabilisticSequence() [6/6]

bpp::ProbabilisticSequence::ProbabilisticSequence ( const ProbabilisticSequence &  sequence )

inline

The copy constructor.

Definition at line 149 of file ProbabilisticSequence.h.

~ProbabilisticSequence()

virtual bpp::ProbabilisticSequence::~ProbabilisticSequence ( )

inlinevirtual

Definition at line 183 of file ProbabilisticSequence.h.

Member Function Documentation

addElement() [1/4]

void ProbabilisticSymbolList::addElement ( const std::vector< double > &  element )

overrideinherited

Definition at line 146 of file ProbabilisticSymbolList.cpp.

References bpp::Table< class >::addColumn(), bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getNumberOfRows().

addElement() [2/4]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement ( const T &  c )

pure virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

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

addElement() [3/4]

void ProbabilisticSymbolList::addElement ( size_t  pos, const std::vector< double > &  element  )

overrideinherited

Definition at line 171 of file ProbabilisticSymbolList.cpp.

References bpp::Table< class >::addColumn(), bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getNumberOfRows().

addElement() [4/4]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement ( size_t  pos, const T &  c  )

pure virtualinherited

Add a character at a certain position in the list.

Parameters

pos	The position where to insert the element.
c	The character to add.

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

alphabet() [1/2]

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().

alphabet() [2/2]

const Alphabet& bpp::ProbabilisticSymbolList::alphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to the list.

Returns

A const reference to the alphabet.

See also

Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 144 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::alphabet_.

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()

ProbabilisticSequence* bpp::ProbabilisticSequence::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractCoreSequence.

Definition at line 173 of file ProbabilisticSequence.h.

References ProbabilisticSequence().

deleteElement() [1/2]

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

inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Definition at line 172 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::deleteColumn().

deleteElement() [2/2]

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() [1/2]

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

inlineoverridevirtualinherited

Remove the elements at position 'pos'.

Parameters

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

Implements bpp::CruxSymbolListInterface.

Definition at line 177 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::deleteColumns().

deleteElements() [2/2]

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() [1/2]

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().

getAlphabet() [2/2]

std::shared_ptr<const Alphabet> bpp::ProbabilisticSymbolList::getAlphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to the list.

Returns

A const pointer to the alphabet.

See also

Alphabet class.

Implements bpp::CruxSymbolListInterface.

Definition at line 142 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::alphabet_.

Referenced by bpp::ProbabilisticSymbolList::getStateValueAt(), bpp::Pasta::nextSequence(), bpp::ProbabilisticSymbolList::operator()(), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), and bpp::Pasta::writeSequence().

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(), bpp::AbstractCoreSequence::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().

getContent() [1/2]

template<class T >

virtual const std::vector<T>& bpp::TemplateCoreSymbolListInterface< T >::getContent ( ) const

pure virtualinherited

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

Referenced by bpp::Sequence::append(), bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::SequenceWithAnnotation::merge(), bpp::ProbabilisticSymbolList::operator=(), and bpp::Sequence::operator=().

getContent() [2/2]

const std::vector<std::vector<double> >& bpp::ProbabilisticSymbolList::getContent ( ) const

inlineoverridevirtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 182 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getData().

Referenced by bpp::Pasta::writeSequence().

getElement() [1/2]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< T >::getElement ( size_t  pos ) const

pure virtualinherited

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

Parameters

pos	The position of the character to retrieve.

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

getElement() [2/2]

const std::vector<double>& bpp::ProbabilisticSymbolList::getElement ( size_t  pos ) const

inlineoverridevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 167 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getColumn().

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

getName() [1/2]

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

pure virtualinherited

Get the name of this sequence.

Returns

This sequence name.

Implemented in bpp::AbstractCoreSequence.

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractCoreSequence::operator=(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), and bpp::WordAlphabet::translate().

getName() [2/2]

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

inlineoverridevirtualinherited

Get the name of this sequence.

Returns

This sequence name.

Implements bpp::CoreSequenceInterface.

Definition at line 170 of file CoreSequence.h.

References bpp::AbstractCoreSequence::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()

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

inlineoverridevirtual

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.

Implements bpp::CruxSymbolListInterface.

Definition at line 204 of file ProbabilisticSequence.h.

References bpp::ProbabilisticSymbolList::size().

getTable() [1/2]

virtual const DTable& bpp::ProbabilisticSymbolListInterface::getTable ( ) const

pure virtualinherited

Implemented in bpp::ProbabilisticSymbolList.

getTable() [2/2]

const DTable& bpp::ProbabilisticSymbolList::getTable ( ) const

inlineoverridevirtualinherited

Implements bpp::ProbabilisticSymbolListInterface.

Definition at line 187 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_.

getValue() [1/2]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< T >::getValue ( size_t  pos ) const

pure virtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

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

Referenced by bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::findFirstOf(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

getValue() [2/2]

const std::vector<double>& bpp::ProbabilisticSymbolList::getValue ( size_t  pos ) const

inlineoverridevirtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 192 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::getElement().

operator()() [1/2]

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()() [2/2]

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

inlineoverridevirtualinherited

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.

Implements bpp::CruxSymbolListInterface.

Definition at line 214 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, bpp::ProbabilisticSymbolList::getAlphabet(), and bpp::Table< class >::getColumn().

operator=()

ProbabilisticSequence& bpp::ProbabilisticSequence::operator= ( const ProbabilisticSequence &  sequence )

inline

The assignment operator.

Returns

A reference to the assigned ProbabilisticSequence.

Definition at line 160 of file ProbabilisticSequence.h.

References bpp::AbstractCoreSequence::operator=(), and bpp::ProbabilisticSymbolList::operator=().

operator[]() [1/4]

template<class T >

virtual const T& bpp::TemplateCoreSymbolListInterface< T >::operator[] ( size_t  pos ) const

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

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

operator[]() [2/4]

const std::vector<double>& bpp::ProbabilisticSymbolList::operator[] ( size_t  pos ) const

inlineoverridevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 197 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getColumn().

operator[]() [3/4]

std::vector<double>& bpp::ProbabilisticSymbolList::operator[] ( size_t  pos )

inlineoverridevirtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 202 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getColumn().

operator[]() [4/4]

template<class T >

virtual T& bpp::TemplateCoreSymbolListInterface< T >::operator[] ( size_t  pos )

pure virtualinherited

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

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

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(), bpp::AbstractCoreSequence::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().

setContent() [1/5]

void ProbabilisticSymbolList::setContent ( const DTable &  list )

overridevirtualinherited

Implements bpp::ProbabilisticSymbolListInterface.

Definition at line 76 of file ProbabilisticSymbolList.cpp.

References bpp::ProbabilisticSymbolList::alphabet_, bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::getNumberOfRows(), bpp::Table< class >::getRowNames(), bpp::Table< class >::hasRowNames(), bpp::Table< class >::setRowNames(), bpp::ProbabilisticSymbolList::size(), and bpp::TextTools::toString().

setContent() [2/5]

virtual void bpp::ProbabilisticSymbolListInterface::setContent ( const DTable &  list )

pure virtualinherited

Implemented in bpp::ProbabilisticSymbolList.

setContent() [3/5]

void ProbabilisticSymbolList::setContent ( const std::vector< std::vector< double >> &  list )

overrideinherited

Definition at line 132 of file ProbabilisticSymbolList.cpp.

References bpp::ProbabilisticSymbolList::alphabet_, bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::setRowNames(), and bpp::ProbabilisticSymbolList::size().

Referenced by bpp::Pasta::nextSequence().

setContent() [4/5]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::setContent ( const std::vector< T > &  list )

pure virtualinherited

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 internally stored.

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

setContent() [5/5]

virtual void bpp::TemplateCoreSymbolListInterface< T >::setContent

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 internally stored.

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

setElement() [1/2]

void ProbabilisticSymbolList::setElement ( size_t  pos, const std::vector< double > &  element  )

overrideinherited

Definition at line 188 of file ProbabilisticSymbolList.cpp.

References bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::getNumberOfRows(), and bpp::Table< class >::setColumn().

setElement() [2/2]

template<class T >

virtual void bpp::TemplateCoreSymbolListInterface< T >::setElement ( size_t  pos, const T &  c  )

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.

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

setName() [1/2]

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

inlineoverridevirtualinherited

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 bpp::AbstractCoreSequence::name_.

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

setName() [2/2]

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

pure virtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::AbstractCoreSequence.

setToSizeL()

void ProbabilisticSequence::setToSizeL ( size_t  newSize )

overridevirtual

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::CoreSequenceInterface.

Definition at line 40 of file ProbabilisticSequence.cpp.

setToSizeR()

void ProbabilisticSequence::setToSizeR ( size_t  newSize )

overridevirtual

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::CoreSequenceInterface.

Definition at line 16 of file ProbabilisticSequence.cpp.

shuffle() [1/2]

void bpp::ProbabilisticSymbolList::shuffle ( )

inlineoverridevirtualinherited

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

Implements bpp::CruxSymbolListInterface.

Definition at line 219 of file ProbabilisticSymbolList.h.

shuffle() [2/2]

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() [1/2]

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().

size() [2/2]

size_t bpp::ProbabilisticSymbolList::size ( ) const

inlineoverridevirtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implements bpp::CruxSymbolListInterface.

Definition at line 146 of file ProbabilisticSymbolList.h.

References bpp::ProbabilisticSymbolList::content_, and bpp::Table< class >::getNumberOfColumns().

Referenced by bpp::SequenceContainerTools::getFrequencies(), bpp::ProbabilisticSite::getStateValueAt(), getStateValueAt(), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), and bpp::ProbabilisticSymbolList::setContent().

toString() [1/2]

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.

toString() [2/2]

string ProbabilisticSymbolList::toString ( ) const

overridevirtualinherited

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::CruxSymbolListInterface.

Definition at line 108 of file ProbabilisticSymbolList.cpp.

References bpp::ProbabilisticSymbolList::content_, bpp::Table< class >::getNumberOfColumns(), bpp::Table< class >::getNumberOfRows(), and bpp::Table< class >::getRowName().

Member Data Documentation

alphabet_

std::shared_ptr<const Alphabet> bpp::ProbabilisticSymbolList::alphabet_

privateinherited

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

To apply another alphabet to the list requires creating another list.

Definition at line 71 of file ProbabilisticSymbolList.h.

Referenced by bpp::ProbabilisticSymbolList::alphabet(), bpp::ProbabilisticSymbolList::getAlphabet(), bpp::ProbabilisticSymbolList::operator=(), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), and bpp::ProbabilisticSymbolList::setContent().

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().

content_

DTable bpp::ProbabilisticSymbolList::content_

protectedinherited

The list content.

Definition at line 77 of file ProbabilisticSymbolList.h.

Referenced by bpp::ProbabilisticSymbolList::addElement(), bpp::ProbabilisticSymbolList::deleteElement(), bpp::ProbabilisticSymbolList::deleteElements(), bpp::ProbabilisticSymbolList::getContent(), bpp::ProbabilisticSymbolList::getElement(), bpp::ProbabilisticSymbolList::getStateValueAt(), bpp::ProbabilisticSymbolList::getTable(), bpp::ProbabilisticSymbolList::operator()(), bpp::ProbabilisticSymbolList::operator=(), bpp::ProbabilisticSymbolList::operator[](), bpp::ProbabilisticSymbolList::ProbabilisticSymbolList(), bpp::ProbabilisticSymbolList::setContent(), bpp::ProbabilisticSymbolList::setElement(), bpp::ProbabilisticSymbolList::size(), and bpp::ProbabilisticSymbolList::toString().

name_

std::string bpp::AbstractCoreSequence::name_

privateinherited

The sequence name.

Definition at line 103 of file CoreSequence.h.

Referenced by bpp::AbstractCoreSequence::getName(), bpp::AbstractCoreSequence::operator=(), and bpp::AbstractCoreSequence::setName().

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

• Bpp/Seq/ProbabilisticSequence.h
• Bpp/Seq/ProbabilisticSequence.cpp