bpp::BasicProbabilisticSequence Class Reference

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

#include <Bpp/Seq/ProbabilisticSequence.h>

Inheritance diagram for bpp::BasicProbabilisticSequence:

Collaboration diagram for bpp::BasicProbabilisticSequence:

Public Types
typedef Table< double >	DataTable

Public Member Functions
	BasicProbabilisticSequence (const Alphabet *alpha)
	Empty constructor : build a void ProbabilisticSequence with just an Alphabet. More...
	BasicProbabilisticSequence (const std::string &name, const Table< double > &sequence, const Alphabet *alpha)
	Direct constructor : build a ProbabilisticSequence object from Table<double>. More...
	BasicProbabilisticSequence (const std::string &name, const Table< double > &sequence, const Comments &comments, const Alphabet *alpha)
	Direct constructor : build a ProbabilisticSequence object from Table<double>. More...
	BasicProbabilisticSequence (const BasicProbabilisticSequence &s)
	The copy constructor. This does not perform a hard copy of the alphabet object. More...
BasicProbabilisticSequence &	operator= (const BasicProbabilisticSequence &s)
	The assignment operator. This does not perform a hard cop of the alphabet object. More...
virtual	~BasicProbabilisticSequence ()
void	setContent (const Table< double > &content)
const std::vector< std::vector< double > > &	getContent () const
const DataTable &	getTable () const
	Get contents with alphabet states as column names. More...
void	setToSizeR (size_t newSize)
	Set up the size of a sequence from the right side. More...
void	setToSizeL (size_t newSize)
	Set up the size of a sequence from the left side. More...
void	clearComments ()
	Clear the comments. More...
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the list. More...
virtual size_t	size () const =0
	Get the number of elements in the list. More...
virtual std::string	toString () const =0
	Convert the list as a string. More...
virtual double	getStateValueAt (size_t siteIndex, int state) const
virtual double	operator() (size_t siteIndex, int state) const
virtual const Comments &	getComments () const =0
	Get the comments. More...
virtual void	setComments (const Comments &comments)=0
	Set the comments. More...
const Alphabet *	getAlphabet () const
	Get the alphabet associated to the list. More...
size_t	size () const
	Get the number of elements in the list. More...
void	setContent (const std::vector< std::vector< double > > &list)
	Set the whole content of the list. More...
std::string	toString () const
	Convert the list as a string. More...
void	addElement (const std::vector< double > &element)
	Add a character to the end of the list. More...
void	addElement (size_t pos, const std::vector< double > &element)
	Add a character at a certain position in the list. More...
void	setElement (size_t pos, const std::vector< double > &element)
	Set the element at position 'pos' to character 'c'. More...
const std::vector< double > &	getElement (size_t pos) const
	Get the element at position 'pos' as a character. More...
virtual void	deleteElement (size_t pos)
	Remove the element at position 'pos'. More...
virtual void	deleteElements (size_t pos, size_t len)
	Remove the elements at position 'pos'. More...
const std::vector< double > &	getValue (size_t pos) const
	checked access to a character in list. More...
const std::vector< double > &	operator[] (size_t pos) const
	Operator [] overloaded for quick access to a character in list. More...
std::vector< double > &	operator[] (size_t pos)
	Operator [] overloaded for quick access to a character in list. More...
double	getStateValueAt (size_t siteIndex, int state) const
double	operator() (size_t siteIndex, int state) const
void	shuffle ()
	Randomly shuffle the content of the list, with linear complexity. More...
The Clonable interface
BasicProbabilisticSequence *	clone () const
Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
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 modifiy 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...
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 modifiy 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...
Setting/getting the name of the sequence.
virtual const std::string &	getName () const =0
	Get the name of this sequence. More...
virtual void	setName (const std::string &name)=0
	Set the name of this sequence. More...
Setting/getting the name of the sequence.
const std::string &	getName () const
	Get the name of this sequence. More...
void	setName (const std::string &name)
	Set the name of this sequence. More...
const Comments &	getComments () const
	Get the comments. More...
void	setComments (const Comments &comments)
	Set the comments. More...

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

Private Attributes
std::string	name_
	The sequence name. More...
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 elmements. The states represented by the elements is defined by an alphabet object, which is passed to the contructor by a pointer.

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

See also

Alphabet

Definition at line 102 of file ProbabilisticSequence.h.

Member Typedef Documentation

DataTable

typedef Table<double> bpp::BasicProbabilisticSymbolList::DataTable

inherited

Definition at line 110 of file ProbabilisticSymbolList.h.

Constructor & Destructor Documentation

BasicProbabilisticSequence() [1/4]

BasicProbabilisticSequence::BasicProbabilisticSequence

(

const Alphabet *

alpha

)

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

alpha

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

Definition at line 48 of file ProbabilisticSequence.cpp.

Referenced by clone().

BasicProbabilisticSequence() [2/4]

BasicProbabilisticSequence::BasicProbabilisticSequence	(	const std::string &	name,
		const Table< double > &	sequence,
		const Alphabet *	alpha
	)

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>.
alpha	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 51 of file ProbabilisticSequence.cpp.

References setContent().

BasicProbabilisticSequence() [3/4]

BasicProbabilisticSequence::BasicProbabilisticSequence	(	const std::string &	name,
		const Table< double > &	sequence,
		const Comments &	comments,
		const Alphabet *	alpha
	)

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>.
comments	Comments to add to the sequence.
alpha	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 57 of file ProbabilisticSequence.cpp.

BasicProbabilisticSequence() [4/4]

BasicProbabilisticSequence::BasicProbabilisticSequence

(

const BasicProbabilisticSequence &

s

)

The copy constructor. This does not perform a hard copy of the alphabet object.

Definition at line 62 of file ProbabilisticSequence.cpp.

~BasicProbabilisticSequence()

virtual bpp::BasicProbabilisticSequence::~BasicProbabilisticSequence ( )

inlinevirtual

Definition at line 169 of file ProbabilisticSequence.h.

Member Function Documentation

addElement() [1/4]

void BasicProbabilisticSymbolList::addElement ( const std::vector< double > &  c )

virtualinherited

Add a character to the end of the list.

Parameters

c	The character to add.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 175 of file ProbabilisticSymbolList.cpp.

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

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet().

addElement() [2/4]

template<class T >

virtual void bpp::CoreSymbolList< 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::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

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

addElement() [3/4]

void BasicProbabilisticSymbolList::addElement ( size_t  pos, const std::vector< double > &  c  )

virtualinherited

Add a character at a certain position in the list.

Parameters

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

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 199 of file ProbabilisticSymbolList.cpp.

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

addElement() [4/4]

template<class T >

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

pure virtualinherited

Add a character at a certain position in the list.

Parameters

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

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

clearComments()

void bpp::BasicProbabilisticSequence::clearComments ( )

inlinevirtual

Clear the comments.

Implements bpp::CoreSequence.

Definition at line 189 of file ProbabilisticSequence.h.

References bpp::Commentable::clearComments().

clone()

BasicProbabilisticSequence* bpp::BasicProbabilisticSequence::clone ( ) const

inlinevirtual

Implements bpp::AbstractCoreSequence.

Definition at line 162 of file ProbabilisticSequence.h.

References BasicProbabilisticSequence().

deleteElement() [1/2]

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

inlinevirtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implements bpp::CruxSymbolList.

Definition at line 213 of file ProbabilisticSymbolList.h.

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

deleteElement() [2/2]

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

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implemented in bpp::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::deleteSite(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), bpp::VectorSiteContainer::removeSequence(), bpp::AlignedSequenceContainer::removeSite(), and bpp::SequenceTools::removeStops().

deleteElements() [1/2]

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

inlinevirtualinherited

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::CruxSymbolList.

Definition at line 215 of file ProbabilisticSymbolList.h.

References bpp::BasicProbabilisticSymbolList::content_, and bpp::Table< class >::deleteRows().

deleteElements() [2/2]

virtual void bpp::CruxSymbolList::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::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::deleteSites().

getAlphabet() [1/2]

const Alphabet* bpp::BasicProbabilisticSymbolList::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the list.

Returns

A const pointer to the alphabet.

See also

Alphabet class.

Implements bpp::CruxSymbolList.

Definition at line 183 of file ProbabilisticSymbolList.h.

References bpp::BasicProbabilisticSymbolList::alphabet_.

Referenced by bpp::BasicProbabilisticSymbolList::BasicProbabilisticSymbolList(), bpp::BasicProbabilisticSymbolList::getStateValueAt(), and bpp::BasicProbabilisticSymbolList::operator()().

getAlphabet() [2/2]

virtual const Alphabet* bpp::CruxSymbolList::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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::SiteContainerTools::alignNW(), bpp::BasicSequence::append(), 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::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceTools::findFirstOf(), bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceTools::getComplement(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getNumberOfCompleteSites(), 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::CodonSiteTools::hasGapOrStop(), bpp::CodonSiteTools::hasStop(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::SymbolListTools::jointEntropy(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::SymbolListTools::mutualInformation(), bpp::Pasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::SymbolListTools::numberOfGaps(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::SymbolListTools::numberOfUnresolved(), bpp::SymbolList< T >::operator=(), bpp::BasicProbabilisticSymbolList::operator=(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::reverseTranscript(), bpp::SequenceTools::RNYslice(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::AlignedSequenceContainer::setSite(), bpp::CompressedVectorSiteContainer::setSite(), bpp::VectorSiteContainer::setSite(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SequenceTools::transcript(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::WordAlphabet::translate(), bpp::SiteContainerTools::translateAlignment(), bpp::SymbolListTools::variabilityShannon(), and bpp::Pasta::writeSequence().

getComments() [1/2]

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

inlinevirtualinherited

Get the comments.

Returns

The comments.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithQuality, and bpp::SequenceWithAnnotation.

Definition at line 235 of file CoreSequence.h.

References bpp::Commentable::getComments().

getComments() [2/2]

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

pure virtualinherited

Get the comments.

Returns

The comments.

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

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::getComments(), bpp::AbstractSequenceContainer::getComments(), bpp::VectorProbabilisticSequenceContainer::getComments(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

getContent()

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

inlinevirtual

Implements bpp::ProbabilisticSequence.

Definition at line 175 of file ProbabilisticSequence.h.

References bpp::BasicProbabilisticSymbolList::getContent().

getElement() [1/2]

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

inlinevirtualinherited

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

Parameters

pos	The position of the character to retrieve.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 208 of file ProbabilisticSymbolList.h.

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

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

getElement() [2/2]

template<class T >

virtual const T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

getName() [1/2]

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

inlinevirtualinherited

Get the name of this sequence.

Returns

This sequence name.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 231 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

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

getName() [2/2]

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

pure virtualinherited

Get the name of this sequence.

Returns

This sequence name.

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

Referenced by bpp::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::VectorSequenceContainer::deleteSequenceByName(), bpp::AbstractProbabilisticSequenceContainer::getName(), bpp::AbstractSequenceContainer::getName(), bpp::VectorProbabilisticSequenceContainer::getName(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::VectorSequenceContainer::getSequenceByName(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::VectorSequenceContainer::removeSequenceByName(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

getStateValueAt() [1/2]

virtual double bpp::CruxSymbolList::getStateValueAt ( size_t  siteIndex, int  state  ) const

inlinevirtualinherited

Reimplemented in bpp::BasicProbabilisticSymbolList, bpp::BasicIntSymbolList, and bpp::EdCoreSymbolList< T >.

Definition at line 147 of file CoreSymbolList.h.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::BasicProbabilisticSymbolList::BasicProbabilisticSymbolList(), bpp::VectorProbabilisticSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::EdCoreSymbolList< T >::getStateValueAt(), and bpp::Pasta::writeSequence().

getStateValueAt() [2/2]

double bpp::BasicProbabilisticSymbolList::getStateValueAt ( size_t  siteIndex, int  state  ) const

inlinevirtualinherited

Reimplemented from bpp::CruxSymbolList.

Definition at line 239 of file ProbabilisticSymbolList.h.

References bpp::BasicProbabilisticSymbolList::content_, bpp::BasicProbabilisticSymbolList::getAlphabet(), bpp::Table< class >::getColumn(), bpp::Table< class >::getNumberOfColumns(), and bpp::Alphabet::getStateIndex().

getTable()

const DataTable& bpp::BasicProbabilisticSequence::getTable ( ) const

inlinevirtual

Get contents with alphabet states as column names.

Implements bpp::ProbabilisticSequence.

Definition at line 180 of file ProbabilisticSequence.h.

References bpp::BasicProbabilisticSymbolList::getTable().

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet().

getValue() [1/2]

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

inlinevirtualinherited

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 224 of file ProbabilisticSymbolList.h.

References bpp::BasicProbabilisticSymbolList::getElement().

getValue() [2/2]

template<class T >

virtual const T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorSiteContainer::addSequence(), 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::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

operator()() [1/2]

virtual double bpp::CruxSymbolList::operator() ( size_t  siteIndex, int  state  ) const

inlinevirtualinherited

Reimplemented in bpp::BasicProbabilisticSymbolList, bpp::BasicIntSymbolList, and bpp::EdCoreSymbolList< T >.

Definition at line 154 of file CoreSymbolList.h.

Referenced by bpp::EdCoreSymbolList< T >::operator()().

operator()() [2/2]

double bpp::BasicProbabilisticSymbolList::operator() ( size_t  siteIndex, int  state  ) const

inlinevirtualinherited

Reimplemented from bpp::CruxSymbolList.

Definition at line 246 of file ProbabilisticSymbolList.h.

References bpp::BasicProbabilisticSymbolList::content_, bpp::BasicProbabilisticSymbolList::getAlphabet(), bpp::Table< class >::getColumn(), and bpp::Alphabet::getStateIndex().

operator=()

BasicProbabilisticSequence & BasicProbabilisticSequence::operator=

(

const BasicProbabilisticSequence &

s

)

The assignment operator. This does not perform a hard cop of the alphabet object.

Returns

A reference to the assigned BasicProbabilisticSequence.

Definition at line 65 of file ProbabilisticSequence.cpp.

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

operator[]() [1/4]

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

inlinevirtualinherited

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::CoreSymbolList< std::vector< double > >.

Definition at line 234 of file ProbabilisticSymbolList.h.

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

operator[]() [2/4]

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

inlinevirtualinherited

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::CoreSymbolList< std::vector< double > >.

Definition at line 229 of file ProbabilisticSymbolList.h.

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

operator[]() [3/4]

template<class T >

virtual const T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

operator[]() [4/4]

template<class T >

virtual T& bpp::CoreSymbolList< 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::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

setComments() [1/2]

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

inlinevirtualinherited

Set the comments.

Parameters

comments

The new comments.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithQuality, and bpp::SequenceWithAnnotation.

Definition at line 240 of file CoreSequence.h.

References bpp::Commentable::setComments().

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet().

setComments() [2/2]

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

pure virtualinherited

Set the comments.

Parameters

comments

The new comments.

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

Referenced by bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setComments(), bpp::VectorSequenceContainer::setComments(), and bpp::SequenceTools::subseq().

setContent() [1/3]

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

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 internaly stored.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 161 of file ProbabilisticSymbolList.cpp.

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

Referenced by bpp::BasicProbabilisticSymbolList::BasicProbabilisticSymbolList(), bpp::BasicProbabilisticSymbolList::operator=(), and setContent().

setContent() [2/3]

template<class T >

virtual void bpp::CoreSymbolList< 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 internaly stored.

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

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

setContent() [3/3]

void bpp::BasicProbabilisticSequence::setContent ( const Table< double > &  content )

inline

Definition at line 173 of file ProbabilisticSequence.h.

References bpp::BasicProbabilisticSymbolList::setContent().

Referenced by BasicProbabilisticSequence().

setElement() [1/2]

void BasicProbabilisticSymbolList::setElement ( size_t  pos, const std::vector< double > &  c  )

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.

Implements bpp::CoreSymbolList< std::vector< double > >.

Definition at line 216 of file ProbabilisticSymbolList.cpp.

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

setElement() [2/2]

template<class T >

virtual void bpp::CoreSymbolList< 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::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::SequenceTools::complement(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SequenceTools::replaceStopsWithGaps(), and bpp::AlignedSequenceContainer::setSite().

setName() [1/2]

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

inlinevirtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implements bpp::CoreSequence.

Reimplemented in bpp::SequenceWithAnnotation.

Definition at line 233 of file CoreSequence.h.

References bpp::AbstractCoreSequence::name_.

Referenced by bpp::AllelicAlphabet::convertFromStateAlphabet(), and bpp::SequenceWithAnnotation::setName().

setName() [2/2]

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

pure virtualinherited

Set the name of this sequence.

Parameters

name	The new name of the sequence.

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

Referenced by bpp::SequenceTools::getPutativeHaplotypes(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::PhredPhd::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setSequenceNames(), bpp::VectorSequenceContainer::setSequenceNames(), and bpp::SequenceTools::subseq().

setToSizeL()

void bpp::BasicProbabilisticSequence::setToSizeL ( size_t  newSize )

inlinevirtual

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::CoreSequence.

Definition at line 187 of file ProbabilisticSequence.h.

setToSizeR()

void bpp::BasicProbabilisticSequence::setToSizeR ( size_t  newSize )

inlinevirtual

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::CoreSequence.

Definition at line 185 of file ProbabilisticSequence.h.

shuffle() [1/2]

void bpp::BasicProbabilisticSymbolList::shuffle ( )

inlinevirtualinherited

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

Implements bpp::CruxSymbolList.

Definition at line 251 of file ProbabilisticSymbolList.h.

shuffle() [2/2]

virtual void bpp::CruxSymbolList::shuffle ( )

pure virtualinherited

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

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

size() [1/2]

size_t bpp::BasicProbabilisticSymbolList::size ( ) const

inlinevirtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implements bpp::CruxSymbolList.

Definition at line 185 of file ProbabilisticSymbolList.h.

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

Referenced by bpp::BasicProbabilisticSymbolList::BasicProbabilisticSymbolList(), and bpp::BasicProbabilisticSymbolList::setContent().

size() [2/2]

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

pure virtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::AlignedSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::BasicSequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::AlignedSequenceContainer::checkSize_(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceTools::findFirstOf(), bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SiteContainerTools::getAlignmentPositions(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SymbolListTools::getCounts(), bpp::SequenceContainerTools::getCounts(), bpp::SymbolListTools::getFrequencies(), bpp::SequenceContainerTools::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::SiteContainerTools::getSequencePositions(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::CompressedVectorSiteContainer::getSiteIndex_(), bpp::VectorProbabilisticSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::CodonAlphabet::getWord(), bpp::WordAlphabet::getWord(), bpp::SymbolListTools::hasGap(), bpp::CodonSiteTools::hasGapOrStop(), bpp::SimpleSequencePositionIterator::hasMorePositions(), bpp::SymbolListTools::hasSingleton(), bpp::CodonSiteTools::hasStop(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SymbolListTools::heterozygosity(), bpp::SequenceMask::init(), bpp::SequenceQuality::init(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isDoubleton(), bpp::CodonSiteTools::isFourFoldDegenerated(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::SymbolListTools::isParsimonyInformativeSite(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::SymbolListTools::isTriplet(), bpp::SymbolListTools::jointEntropy(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::SymbolListTools::numberOfUnresolved(), bpp::SymbolList< T >::operator=(), operator==(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::SequenceWalker::SequenceWalker(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::AlignedSequenceContainer::setSequence(), bpp::AlignedSequenceContainer::setSite(), bpp::CompressedVectorSiteContainer::setSite(), bpp::VectorSiteContainer::setSite(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SymbolList< T >::SymbolList(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::SiteContainerTools::translateAlignment(), bpp::SymbolListTools::variabilityFactorial(), bpp::SymbolListTools::variabilityShannon(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequence(), bpp::Pasta::writeSequence(), and bpp::Phylip::writeSequential().

toString() [1/2]

string BasicProbabilisticSymbolList::toString ( ) const

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.

Implements bpp::CruxSymbolList.

Definition at line 136 of file ProbabilisticSymbolList.cpp.

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

toString() [2/2]

virtual std::string bpp::CruxSymbolList::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::SymbolList< T >, bpp::SymbolList< int >, bpp::BasicSequence, bpp::BasicProbabilisticSymbolList, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::toString(), bpp::AbstractSequenceContainer::toString(), bpp::VectorProbabilisticSequenceContainer::toString(), bpp::Clustal::writeAlignment(), and bpp::Stockholm::writeAlignment().

Member Data Documentation

alphabet_

const Alphabet* bpp::BasicProbabilisticSymbolList::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 119 of file ProbabilisticSymbolList.h.

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

comments_

Comments bpp::Commentable::comments_

protectedinherited

Definition at line 63 of file Commentable.h.

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

content_

DataTable bpp::BasicProbabilisticSymbolList::content_

protectedinherited

The list content.

Definition at line 125 of file ProbabilisticSymbolList.h.

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

name_

std::string bpp::AbstractCoreSequence::name_

privateinherited

The sequence name.

Definition at line 163 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