bpp-seq3  3.0.0
Public Types | Public Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::IntSymbolList Class Referenceabstract

A basic IntSymbolList object. More...

#include <Bpp/Seq/IntSymbolList.h>

+ Inheritance diagram for bpp::IntSymbolList:
+ Collaboration diagram for bpp::IntSymbolList:

Public Types

typedef int SymbolType
 

Public Member Functions

 IntSymbolList (std::shared_ptr< const Alphabet > alpha)
 
 IntSymbolList (const std::vector< std::string > &list, std::shared_ptr< const Alphabet > alpha)
 Build a new IntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters. More...
 
 IntSymbolList (const std::vector< int > &list, std::shared_ptr< const Alphabet > alpha)
 Build a new IntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers. More...
 
 IntSymbolList (const IntSymbolList &list)
 The copy constructor. More...
 
IntSymbolList & operator= (const IntSymbolListInterface &list)
 The generic assignment operator. More...
 
IntSymbolList & operator= (const IntSymbolList &list)
 The assignment operator. More...
 
virtual ~IntSymbolList ()
 
void setContent (const std::vector< int > &list) override
 
void setContent (const std::vector< std::string > &list) override
 Set the whole content of the list. More...
 
std::string toString () const override
 Convert the list as a string. More...
 
void addElement (const std::string &c) override
 Add a character to the end of the list. More...
 
void addElement (size_t pos, const std::string &c) override
 Add a character at a certain position in the list. More...
 
void setElement (size_t pos, const std::string &c) override
 Set the element at position 'pos' to character 'c'. More...
 
std::string getChar (size_t pos) const override
 Get the element at position 'pos' as a character. More...
 
double getStateValueAt (size_t siteIndex, int state) const override
 get value of a state at a position More...
 
double operator() (size_t siteIndex, int state) const override
 get value of a state at a position More...
 
void addElement (const T &v) override
 
void addElement (size_t pos, const T &v) override
 
void setElement (size_t pos, const T &v) override
 
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...
 
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...
 
virtual const std::vector< int > & getContent () const override
 
void deleteElement (size_t pos) override
 Remove the element at position 'pos'. More...
 
void deleteElements (size_t pos, size_t len) override
 Remove the elements at position 'pos'. More...
 
void addElement (const int &v) override
 Add a character to the end of the list. More...
 
void addElement (size_t pos, const int &v) override
 Add a character at a certain position in the list. More...
 
void setElement (size_t pos, const int &v) override
 Set the element at position 'pos' to character 'c'. More...
 
const int & getElement (size_t pos) const override
 Get the element at position 'pos' as a character. More...
 
const int & getValue (size_t pos) const override
 checked access to a character in list. More...
 
const int & operator[] (size_t pos) const override
 Operator [] overloaded for quick access to a character in list. More...
 
int & operator[] (size_t pos) override
 Operator [] overloaded for quick access to a character in list. More...
 
void shuffle () override
 Randomly shuffle the content of the list, with linear complexity. More...
 
The Clonable interface
IntSymbolList * clone () const override
 
Acting on the content of the list.
virtual void setContent (const std::vector< T > &list)=0
 Set the whole content of the list. 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...
 
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

std::vector< int > content_
 The list content. More...
 

Private Attributes

std::shared_ptr< const Alphabet > alphabet_
 The Alphabet attribute must be initialized in constructor and then can never be changed. More...
 

Detailed Description

A basic IntSymbolList object.

This is a general purpose container, containing an ordered list of states(= letters). The states that allowed to be present in the list are defined by an alphabet object, which is passed to the list constructor by a pointer.

For programming convenience, the states are stored as integers, but the translation toward and from a char description is easily performed with the Alphabet classes.

See also
Alphabet

Definition at line 109 of file IntSymbolList.h.

Member Typedef Documentation

◆ SymbolType

typedef int bpp::IntSymbolListInterface::SymbolType
inherited

Definition at line 31 of file IntSymbolList.h.

Constructor & Destructor Documentation

◆ IntSymbolList() [1/4]

bpp::IntSymbolList::IntSymbolList ( std::shared_ptr< const Alphabet >  alpha)
inline

Definition at line 114 of file IntSymbolList.h.

Referenced by clone().

◆ IntSymbolList() [2/4]

bpp::IntSymbolList::IntSymbolList ( const std::vector< std::string > &  list,
std::shared_ptr< const Alphabet >  alpha 
)
inline

Build a new IntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of characters.

Parameters
listThe content of the site.
alphaThe alphabet to use.

Definition at line 125 of file IntSymbolList.h.

References bpp::IntSymbolListInterface::setContent().

◆ IntSymbolList() [3/4]

bpp::IntSymbolList::IntSymbolList ( const std::vector< int > &  list,
std::shared_ptr< const Alphabet >  alpha 
)
inline

Build a new IntSymbolList object with the specified alphabet. The content of the site is initialized from a vector of integers.

Parameters
listThe content of the site.
alphaThe alphabet to use.

Definition at line 138 of file IntSymbolList.h.

◆ IntSymbolList() [4/4]

bpp::IntSymbolList::IntSymbolList ( const IntSymbolList &  list)
inline

The copy constructor.

Definition at line 145 of file IntSymbolList.h.

◆ ~IntSymbolList()

virtual bpp::IntSymbolList::~IntSymbolList ( )
inlinevirtual

Definition at line 172 of file IntSymbolList.h.

Member Function Documentation

◆ addElement() [1/8]

void bpp::AbstractTemplateSymbolList< int >::addElement ( const int &  v)
inlineoverrideinherited

Add a character to the end of the list.

Parameters
cThe character to add.

Definition at line 152 of file SymbolList.h.

◆ addElement() [2/8]

void bpp::IntSymbolList::addElement ( const std::string &  c)
inlineoverridevirtual

Add a character to the end of the list.

Parameters
cThe character to add, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 185 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

◆ addElement() [3/8]

template<class T >
virtual void bpp::TemplateCoreSymbolListInterface< T >::addElement ( const T &  c)
pure virtualinherited

Add a character to the end of the list.

Parameters
cThe character to add.

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

◆ addElement() [4/8]

void bpp::AbstractTemplateSymbolList< T >::addElement
inlineoverride

Definition at line 152 of file SymbolList.h.

Referenced by bpp::SequenceWithQuality::addElement().

◆ addElement() [5/8]

void bpp::AbstractTemplateSymbolList< int >::addElement ( size_t  pos,
const int &  v 
)
inlineoverrideinherited

Add a character at a certain position in the list.

Parameters
posThe position where to insert the element.
cThe character to add.

Definition at line 157 of file SymbolList.h.

◆ addElement() [6/8]

void bpp::IntSymbolList::addElement ( size_t  pos,
const std::string &  c 
)
inlineoverridevirtual

Add a character at a certain position in the list.

Parameters
posThe position where to insert the element.
cThe character to add, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 192 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, bpp::AbstractTemplateSymbolList< int >::getAlphabet(), and bpp::AbstractTemplateSymbolList< int >::size().

◆ addElement() [7/8]

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
posThe position where to insert the element.
cThe character to add.

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

◆ addElement() [8/8]

void bpp::AbstractTemplateSymbolList< T >::addElement
inlineoverride

Definition at line 157 of file SymbolList.h.

◆ 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::AbstractTemplateSymbolList< int >::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 122 of file SymbolList.h.

◆ clone()

IntSymbolList* bpp::IntSymbolList::clone ( ) const
inlineoverridevirtual

Implements bpp::TemplateCoreSymbolListInterface< T >.

Reimplemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::Sequence, bpp::EventDrivenIntSymbolList, and bpp::Site.

Definition at line 168 of file IntSymbolList.h.

References IntSymbolList().

◆ deleteElement() [1/2]

void bpp::AbstractTemplateSymbolList< int >::deleteElement ( size_t  pos)
inlineoverridevirtualinherited

Remove the element at position 'pos'.

Parameters
posThe position of the element to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 138 of file SymbolList.h.

◆ deleteElement() [2/2]

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

Remove the element at position 'pos'.

Parameters
posThe 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]

void bpp::AbstractTemplateSymbolList< int >::deleteElements ( size_t  pos,
size_t  len 
)
inlineoverridevirtualinherited

Remove the elements at position 'pos'.

Parameters
posThe position of the first element to remove.
lenThe length of the region to remove.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::AbstractTemplateEventDrivenSymbolList< int >.

Definition at line 145 of file SymbolList.h.

◆ deleteElements() [2/2]

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

Remove the elements at position 'pos'.

Parameters
posThe position of the first element to remove.
lenThe 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::AbstractTemplateSymbolList< int >::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 120 of file SymbolList.h.

◆ getChar()

string IntSymbolList::getChar ( size_t  pos) const
overridevirtual

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

Parameters
posThe position of the character to retrieve.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::Sequence, and bpp::EventDrivenIntSymbolList.

Definition at line 52 of file IntSymbolList.cpp.

Referenced by bpp::Sequence::getChar(), and bpp::SiteContainerTools::resolveDottedAlignment().

◆ 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]

virtual const std::vector<int >& bpp::AbstractTemplateSymbolList< int >::getContent ( ) const
inlineoverridevirtualinherited

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 131 of file SymbolList.h.

◆ 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
posThe position of the character to retrieve.

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

◆ getElement() [2/2]

const int & bpp::AbstractTemplateSymbolList< int >::getElement ( size_t  pos) const
inlineoverridevirtualinherited

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

Parameters
posThe position of the character to retrieve.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 173 of file SymbolList.h.

◆ getStateValueAt()

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

get value of a state at a position

Parameters
positionposition in the list
statestate in the alphabet
Returns
The state value at the given position.

Implements bpp::CruxSymbolListInterface.

Reimplemented in bpp::Sequence, and bpp::Site.

Definition at line 210 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

◆ 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
posThe 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 int & bpp::AbstractTemplateSymbolList< int >::getValue ( size_t  pos) const
inlineoverridevirtualinherited

checked access to a character in list.

Parameters
posThe position to retrieve.
Returns
The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 180 of file SymbolList.h.

◆ operator()()

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

get value of a state at a position

Short-cut for getStateValueAt.

Parameters
positionposition in the list
statestate in the alphabet
Returns
The state value at the given position.

Implements bpp::CruxSymbolListInterface.

Definition at line 218 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

◆ operator=() [1/2]

IntSymbolList& bpp::IntSymbolList::operator= ( const IntSymbolList &  list)
inline

The assignment operator.

Definition at line 157 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< T >::operator=().

◆ operator=() [2/2]

IntSymbolList& bpp::IntSymbolList::operator= ( const IntSymbolListInterface &  list)

The generic assignment operator.

Referenced by bpp::EventDrivenIntSymbolList::operator=(), bpp::Sequence::operator=(), and bpp::Site::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
posThe 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 int & bpp::AbstractTemplateSymbolList< int >::operator[] ( size_t  pos) const
inlineoverridevirtualinherited

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

Parameters
posThe position to retrieve.
Returns
The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 187 of file SymbolList.h.

◆ operator[]() [3/4]

int & bpp::AbstractTemplateSymbolList< int >::operator[] ( size_t  pos)
inlineoverridevirtualinherited

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

Parameters
posThe position to retrieve.
Returns
The T value of character at position pos.

Implements bpp::TemplateCoreSymbolListInterface< T >.

Definition at line 189 of file SymbolList.h.

◆ 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
posThe position to retrieve.
Returns
The T value of character at position pos.

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

◆ setContent() [1/4]

void IntSymbolList::setContent ( const std::vector< int > &  list)
overridevirtual

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

Reimplemented in bpp::SequenceWithAnnotation, bpp::Sequence, and bpp::EventDrivenIntSymbolList.

Definition at line 37 of file IntSymbolList.cpp.

References bpp::AbstractTemplateSymbolList< T >::setContent().

◆ setContent() [2/4]

void IntSymbolList::setContent ( const std::vector< std::string > &  list)
overridevirtual

Set the whole content of the list.

Parameters
listThe new content of the list.
See also
The list constructor for information about the way lists are internally stored.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::SequenceWithAnnotation, bpp::Sequence, and bpp::EventDrivenIntSymbolList.

Definition at line 15 of file IntSymbolList.cpp.

References bpp::AbstractTemplateSymbolList< T >::setContent().

◆ setContent() [3/4]

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

Set the whole content of the list.

Parameters
listThe 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() [4/4]

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

Set the whole content of the list.

Parameters
listThe new content of the list.
See also
The list constructor for information about the way lists are internally stored.

Referenced by bpp::EventDrivenIntSymbolList::EventDrivenIntSymbolList(), IntSymbolList(), bpp::SequenceWithAnnotation::operator=(), bpp::Sequence::operator=(), bpp::Sequence::Sequence(), bpp::SequenceWithAnnotation::SequenceWithAnnotation(), bpp::Sequence::setContent(), and bpp::SequenceWithAnnotation::setContent().

◆ setElement() [1/4]

void bpp::AbstractTemplateSymbolList< int >::setElement ( size_t  pos,
const int &  v 
)
inlineoverrideinherited

Set the element at position 'pos' to character 'c'.

Parameters
posThe position of the character to set.
cThe value of the element.

Definition at line 165 of file SymbolList.h.

◆ setElement() [2/4]

void bpp::IntSymbolList::setElement ( size_t  pos,
const std::string &  c 
)
inlineoverridevirtual

Set the element at position 'pos' to character 'c'.

Parameters
posThe position of the character to set.
cThe value of the element, given as a string.

Implements bpp::IntSymbolListInterface.

Reimplemented in bpp::EventDrivenIntSymbolList.

Definition at line 201 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, bpp::AbstractTemplateSymbolList< int >::getAlphabet(), and bpp::AbstractTemplateSymbolList< int >::size().

◆ setElement() [3/4]

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
posThe position of the character to set.
cThe value of the element.

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

◆ setElement() [4/4]

void bpp::AbstractTemplateSymbolList< T >::setElement
inlineoverride

Definition at line 165 of file SymbolList.h.

◆ shuffle() [1/2]

void bpp::AbstractTemplateSymbolList< int >::shuffle ( )
inlineoverridevirtualinherited

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

Implements bpp::CruxSymbolListInterface.

Definition at line 191 of file SymbolList.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::AbstractTemplateSymbolList< int >::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 124 of file SymbolList.h.

◆ toString()

std::string bpp::IntSymbolList::toString ( ) const
inlineoverridevirtual

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.

Reimplemented from bpp::AbstractTemplateSymbolList< int >.

Reimplemented in bpp::Sequence, and bpp::EventDrivenIntSymbolList.

Definition at line 179 of file IntSymbolList.h.

References bpp::AbstractTemplateSymbolList< int >::content_, bpp::StringSequenceTools::decodeSequence(), and bpp::AbstractTemplateSymbolList< int >::getAlphabet().

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

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTemplateSymbolList< int >::alphabet_
privateinherited

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

To apply another alphabet to a list you'll have to create a new list.

Definition at line 41 of file SymbolList.h.

◆ content_

std::vector<int > bpp::AbstractTemplateSymbolList< int >::content_
protectedinherited

The list content.

Definition at line 47 of file SymbolList.h.

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