This alphabet is used to deal with DNA sequences. More...

#include <Bpp/Seq/Alphabet/DNA.h>

Inheritance diagram for bpp::DNA:

Collaboration diagram for bpp::DNA:

Public Member Functions
	DNA (bool exclamationMarkCountsAsGap=false)

	DNA (const DNA &bia)

DNA &	operator= (const DNA &bia)

DNA *	clone () const

virtual	~DNA ()

bool	isResolvedIn (int state1, int state2) const
	Tells if a given (potentially unresolved) state can be resolved in another resolved state. More...

std::vector< int >	getAlias (int state) const
	Get all resolved states that match a generic state. More...

std::vector< std::string >	getAlias (const std::string &state) const
	Get all resolved states that match a generic state. More...

int	getGeneric (const std::vector< int > &states) const
	Get the generic state that match a set of states. More...

std::string	getGeneric (const std::vector< std::string > &states) const
	Get the generic state that match a set of states. More...

std::string	getAlphabetType () const
	Identification method. More...

unsigned int	getSize () const
	Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases. More...

unsigned int	getNumberOfTypes () const
	Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number of integers used for state description. More...

int	getUnknownCharacterCode () const

bool	isUnresolved (int state) const

bool	isUnresolved (const std::string &state) const

bool	isCharInAlphabet (char state) const

bool	isCharInAlphabet (const std::string &state) const
	Tell if a state (specified by its string description) is allowed by the the alphabet. More...

int	charToInt (const std::string &state) const
	Give the int description of a state given its string description. More...

Specific methods to access AlphabetState
AlphabetState &	getState (const std::string &letter)

AlphabetState &	getState (int num)

int	getIntCodeAt (size_t stateIndex) const

const std::string &	getCharCodeAt (size_t stateIndex) const

size_t	getStateIndex (int state) const

size_t	getStateIndex (const std::string &state) const

Specific methods
const NucleicAlphabetState &	getStateByBinCode (int code) const
	Get a state by its binary representation. More...

int	subtract (int s1, int s2) const
	Subtract states. More...

std::string	subtract (const std::string &s1, const std::string &s2) const
	Subtract states. More...

int	getOverlap (int s1, int s2) const
	Get the overlap between to states. More...

std::string	getOverlap (const std::string &s1, const std::string &s2) const
	Get the overlap between to states. More...

Implement these methods from the Alphabet interface.
size_t	getNumberOfStates () const
	This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int. More...

unsigned int	getNumberOfChars () const
	Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet). More...

std::string	getName (const std::string &state) const
	Get the complete name of a state given its string description. More...

std::string	getName (int state) const
	Get the complete name of a state given its int description. More...

std::string	intToChar (int state) const
	Give the string description of a state given its int description. More...

bool	isIntInAlphabet (int state) const
	Tell if a state (specified by its int description) is allowed by the the alphabet. More...

const std::vector< int > &	getSupportedInts () const

const std::vector< std::string > &	getSupportedChars () const

const std::vector< std::string > &	getResolvedChars () const

int	getGapCharacterCode () const

bool	isGap (int state) const

bool	isGap (const std::string &state) const

Protected Member Functions
void	resize (size_t size)
	Resize the private alphabet_ vector. More...

void	remap ()
	Re-update the maps using the alphabet_ vector content. More...

unsigned int	getStateCodingSize () const
	Get the size of the string coding a state. More...

bool	equals (const Alphabet &alphabet) const
	Comparison of alphabets. More...

Protected Attributes
Available codes
These vectors will be computed the first time you call the getAvailableInts or getAvailableChars method.
std::vector< std::string >	charList_

std::vector< int >	intList_

Private Member Functions
void	updateBinMaps_ (size_t pos, const NucleicAlphabetState &st)

void	updateMaps_ (size_t pos, const AlphabetState &st)
	Update the private maps letters_ and nums_ when adding a state. More...

Private Attributes
std::map< int, size_t >	binCodes_

std::vector< int >	letters_

bool	caseSensitive_

std::vector< AlphabetState * >	alphabet_
	Alphabet: vector of AlphabetState. More...

maps used to quick search for letter and num.
std::map< int, size_t >	nums_

Static Private Attributes
static const int	LETTER_UNDEF_VALUE = -99

Overloaded methods from AbstractAlphabet
const NucleicAlphabetState &	getStateAt (size_t stateIndex) const
	Get a state at a position in the alphabet_ vector. More...

NucleicAlphabetState &	getStateAt (size_t stateIndex)
	Get a state at a position in the alphabet_ vector. More...

const NucleicAlphabetState &	getState (const std::string &letter) const
	Get a state by its letter. More...

const NucleicAlphabetState &	getState (int num) const
	Get a state by its num. More...

void	registerState (AlphabetState *st)
	Add a state to the Alphabet. More...

void	setState (size_t pos, AlphabetState *st)
	Set a state in the Alphabet. More...

Detailed Description

This alphabet is used to deal with DNA sequences.

It supports all 4 nucleotides (A, T, G and C) with their standard denomination. Gaps are coded by '-', unresolved characters are coded by 'X, N, O, 0 or ?'. Extensive support for generic characters (e.g. 'P', 'Y', etc.) is provided.

Definition at line 24 of file DNA.h.

Constructor & Destructor Documentation

◆ DNA() [1/2]

DNA::DNA ( bool exclamationMarkCountsAsGap = false )

Parameters

exclamationMarkCountsAsGap If yes, '!' characters are replaced by gaps. Otherwise, they are counted as unknown characters.

Definition at line 20 of file DNA.cpp.

Referenced by clone().

◆ DNA() [2/2]

bpp::DNA::DNA ( const DNA & bia )

inline

Definition at line 34 of file DNA.h.

◆ ~DNA()

virtual bpp::DNA::~DNA ( )

inlinevirtual

Definition at line 47 of file DNA.h.

Member Function Documentation

◆ charToInt()

int bpp::LetterAlphabet::charToInt ( const std::string & state ) const

inlinevirtualinherited

Give the int description of a state given its string description.

Parameters

state The string description.

Returns: The int description.

Exceptions

BadCharException When state is not a valid char description.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 60 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet(), and bpp::LetterAlphabet::letters_.

Referenced by bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), bpp::NucleicAlphabet::getOverlap(), bpp::NucleicAlphabet::isUnresolved(), bpp::ProteicAlphabet::isUnresolved(), and bpp::NucleicAlphabet::subtract().

◆ clone()

DNA* bpp::DNA::clone ( ) const

inlinevirtual

Implements bpp::NucleicAlphabet.

Definition at line 42 of file DNA.h.

References DNA().

◆ equals()

bool bpp::AbstractAlphabet::equals ( const Alphabet & alphabet ) const

inlineprotectedvirtualinherited

Comparison of alphabets.

Returns: true If the two instances are of the same class.

Implements bpp::Alphabet.

Definition at line 243 of file AbstractAlphabet.h.

References bpp::Alphabet::getAlphabetType().

◆ getAlias() [1/2]

std::vector< std::string > DNA::getAlias ( const std::string & state ) const

virtual

Get all resolved states that match a generic state.

If the given state is not a generic code then the output vector will contain this unique code.

Parameters

state The alias to resolve.

Returns: A vector of resolved states.

Exceptions

BadCharException When state is not a valid char description.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 107 of file DNA.cpp.

References bpp::TextTools::toUpper().

◆ getAlias() [2/2]

std::vector< int > DNA::getAlias ( int state ) const

virtual

Get all resolved states that match a generic state.

If the given state is not a generic code then the output vector will contain this unique code.

Parameters

state The alias to resolve.

Returns: A vector of resolved states.

Exceptions

BadIntException When state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 85 of file DNA.cpp.

References bpp::NucleicAlphabetState::getBinaryCode().

◆ getAlphabetType()

std::string bpp::DNA::getAlphabetType ( ) const

inlinevirtual

Identification method.

Used to tell if two alphabets describe the same type of sequences. For instance, this method is used by sequence containers to compare two alphabets and allow or deny addition of sequences.

Returns: A text describing the alphabet.

Implements bpp::Alphabet.

Definition at line 56 of file DNA.h.

◆ getCharCodeAt()

const std::string& bpp::AbstractAlphabet::getCharCodeAt ( size_t stateIndex ) const

inlinevirtualinherited

Returns: The char code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 192 of file AbstractAlphabet.h.

References bpp::AlphabetState::getLetter(), and bpp::AbstractAlphabet::getStateAt().

◆ getGapCharacterCode()

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 130 of file AbstractAlphabet.h.

◆ getGeneric() [1/2]

int DNA::getGeneric ( const std::vector< int > & states ) const

virtual

Get the generic state that match a set of states.

If the given states contain generic code, each generic code is first resolved and then the new generic state is returned. If only a single resolved state is given the function return this state.

Parameters

states A vector of states to resolve.

Returns: A int code for the computed state.

Exceptions

BadIntException When a state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 123 of file DNA.cpp.

◆ getGeneric() [2/2]

std::string DNA::getGeneric ( const std::vector< std::string > & states ) const

virtual

Get the generic state that match a set of states.

If the given states contain generic code, each generic code is first resolved and then the new generic state is returned. If only a single resolved state is given the function return this state.

Parameters

states A vector of states to resolve.

Returns: A string code for the computed state.

Exceptions

BadCharException	when a state is not a valid char description.
CharStateNotSupportedException	when the alphabet does not support Char state for unresolved state.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 137 of file DNA.cpp.

◆ getIntCodeAt()

int bpp::AbstractAlphabet::getIntCodeAt ( size_t stateIndex ) const

inlinevirtualinherited

Returns: The int code of a given state.

Parameters

stateIndex The index of the state to fetch.

Implements bpp::Alphabet.

Definition at line 187 of file AbstractAlphabet.h.

References bpp::AlphabetState::getNum(), and bpp::AbstractAlphabet::getStateAt().

◆ getName() [1/2]

std::string AbstractAlphabet::getName ( const std::string & state ) const

virtualinherited

Get the complete name of a state given its string description.

In case of several states with identical number (i.e. N and X for nucleic alphabets), this method will return the name of the first found in the vector.

Parameters

state The string description of the given state.

Returns: The name of the state.

Exceptions

BadCharException When state is not a valid char description.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 139 of file AbstractAlphabet.cpp.

Referenced by bpp::WordAlphabet::getName(), and bpp::LexicalAlphabet::LexicalAlphabet().

◆ getName() [2/2]

std::string AbstractAlphabet::getName ( int state ) const

virtualinherited

Get the complete name of a state given its int description.

In case of several states with identical number (i.e. N and X for nucleic alphabets), this method returns the name of the first found in the vector.

Parameters

state The int description of the given state.

Returns: The name of the state.

Exceptions

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Definition at line 146 of file AbstractAlphabet.cpp.

◆ getNumberOfChars()

unsigned int bpp::AbstractAlphabet::getNumberOfChars ( ) const

inlinevirtualinherited

Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet).

Returns: The total number of supported character descriptions.

Implements bpp::Alphabet.

Definition at line 115 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::LexicalAlphabet::getNumberOfTypes(), bpp::AllelicAlphabet::getNumberOfTypes(), bpp::WordAlphabet::getNumberOfTypes(), bpp::LexicalAlphabet::getSize(), bpp::AllelicAlphabet::getSize(), bpp::WordAlphabet::getSize(), and bpp::NucleicAlphabet::registerState().

◆ getNumberOfStates()

size_t bpp::AbstractAlphabet::getNumberOfStates ( ) const

inlinevirtualinherited

This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int.

This function is typically used il loops over all states of an alphabet.

Implements bpp::Alphabet.

Definition at line 114 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::LexicalAlphabet::getAlphabetType().

◆ getNumberOfTypes()

unsigned int bpp::NucleicAlphabet::getNumberOfTypes ( ) const

inlinevirtualinherited

Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number of integers used for state description.

Returns: The number of distinct states.

Implements bpp::Alphabet.

Definition at line 236 of file NucleicAlphabet.h.

◆ getOverlap() [1/2]

std::string bpp::NucleicAlphabet::getOverlap	(	const std::string &	s1,
		const std::string &	s2
	)		const

inlineinherited

Get the overlap between to states.

Get the overlapping states between two steps.

string m = "M";
string r = R;
 
cout << alpha->getOverlap(m, r) << endl;
 
// should print A because M = A/C and R = A/G

Parameters

s1	the first state as a string
s2	the second state as a string

Exceptions

BadCharException if one of the states is not valid

Returns: The overlapping state

Author: Sylvain Gaillard

Definition at line 224 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::charToInt(), bpp::NucleicAlphabet::getOverlap(), and bpp::AbstractAlphabet::intToChar().

◆ getOverlap() [2/2]

int bpp::NucleicAlphabet::getOverlap	(	int	s1,
		int	s2
	)		const

inlineinherited

Get the overlap between to states.

Get the overlapping states between two steps.

int m = alpha->charToInt("M");
int r = alpha->charToInt("R");
int a = alpha->getOverlap(m, r);
 
cout << alpha->intToChar(a) << endl;
 
// should print A because M = A/C and R = A/G

Parameters

s1	the first state as an int
s2	the second state as an int

Exceptions

BadIntException if one of the states is not valid

Returns: The overlapping state

Author: Sylvain Gaillard

Definition at line 199 of file NucleicAlphabet.h.

References bpp::AlphabetState::getNum(), bpp::NucleicAlphabet::getState(), and bpp::NucleicAlphabet::getStateByBinCode().

Referenced by bpp::NucleicAlphabet::getOverlap().

◆ getResolvedChars()

const std::vector< std::string > & AbstractAlphabet::getResolvedChars ( ) const

virtualinherited

Returns: A list of all resolved character codes.

Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.

Implements bpp::Alphabet.

Definition at line 327 of file AbstractAlphabet.cpp.

◆ getSize()

unsigned int bpp::NucleicAlphabet::getSize ( ) const

inlinevirtualinherited

Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases.

Returns: The number of resolved states.

Implements bpp::Alphabet.

Definition at line 233 of file NucleicAlphabet.h.

◆ getState() [1/4]

AlphabetState & AbstractAlphabet::getState ( const std::string & letter )

inherited

Definition at line 101 of file AbstractAlphabet.cpp.

◆ getState() [2/4]

const NucleicAlphabetState& bpp::NucleicAlphabet::getState ( const std::string & letter ) const

inlinevirtualinherited

Get a state by its letter.

This method must be overloaded in specialized classes to send back a reference of the correct type.

Parameters

letter The letter of the state to find.

Exceptions

BadCharException If the letter is not in the Alphabet.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 92 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getState().

Referenced by bpp::NucleicAlphabet::getOverlap(), and bpp::NucleicAlphabet::subtract().

◆ getState() [3/4]

AlphabetState & AbstractAlphabet::getState ( int num )

inherited

Definition at line 111 of file AbstractAlphabet.cpp.

◆ getState() [4/4]

const NucleicAlphabetState& bpp::NucleicAlphabet::getState ( int num ) const

inlinevirtualinherited

Get a state by its num.

This method must be overloaded in specialized classes to send back a reference of the correct type.

Parameters

num	The num of the state to find.

Exceptions

BadIntException If the num is not in the Alphabet.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 98 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getState().

◆ getStateAt() [1/2]

NucleicAlphabetState& bpp::NucleicAlphabet::getStateAt ( size_t stateIndex )

inlinevirtualinherited

Get a state at a position in the alphabet_ vector.

This method must be overloaded in specialized classes to send back a reference of the correct type.

Parameters

stateIndex The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If the index is invalid.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 86 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getStateAt().

◆ getStateAt() [2/2]

const NucleicAlphabetState& bpp::NucleicAlphabet::getStateAt ( size_t stateIndex ) const

inlinevirtualinherited

Get a state at a position in the alphabet_ vector.

This method must be overloaded in specialized classes to send back a reference of the correct type.

Parameters

stateIndex The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException If the index is invalid.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 80 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getStateAt().

Referenced by bpp::NucleicAlphabet::getStateByBinCode().

◆ getStateByBinCode()

const NucleicAlphabetState& bpp::NucleicAlphabet::getStateByBinCode ( int code ) const

inlineinherited

Get a state by its binary representation.

Parameters

code	The binary representation as an unsigned char.

Returns: The NucleicAlphabetState.

Exceptions

BadIntException If the code is not a valid state.

Author: Sylvain Gaillard

Definition at line 119 of file NucleicAlphabet.h.

References bpp::NucleicAlphabet::binCodes_, and bpp::NucleicAlphabet::getStateAt().

Referenced by bpp::NucleicAlphabet::getOverlap(), and bpp::NucleicAlphabet::subtract().

◆ getStateCodingSize()

unsigned int bpp::AbstractAlphabet::getStateCodingSize ( ) const

inlineprotectedvirtualinherited

Get the size of the string coding a state.

Returns: The size of the string coding each states in the Alphabet.

Author: Sylvain Gaillard

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::CodonAlphabet, and bpp::AllelicAlphabet.

Definition at line 241 of file AbstractAlphabet.h.

◆ getStateIndex() [1/2]

size_t AbstractAlphabet::getStateIndex ( const std::string & state ) const

virtualinherited

Returns: The index of the state with corresponding char code.

Implements bpp::Alphabet.

Definition at line 71 of file AbstractAlphabet.cpp.

◆ getStateIndex() [2/2]

size_t AbstractAlphabet::getStateIndex ( int state ) const

virtualinherited

Returns: The indices of the states with corresponding int code.

Implements bpp::Alphabet.

Definition at line 91 of file AbstractAlphabet.cpp.

◆ getSupportedChars()

const std::vector< std::string > & AbstractAlphabet::getSupportedChars ( ) const

virtualinherited

Returns: A list of all supported character codes.

Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.

Implements bpp::Alphabet.

Definition at line 310 of file AbstractAlphabet.cpp.

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

◆ getSupportedInts()

const std::vector< int > & AbstractAlphabet::getSupportedInts ( ) const

virtualinherited

Returns: A list of all supported int codes.

Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.

Implements bpp::Alphabet.

Definition at line 293 of file AbstractAlphabet.cpp.

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

◆ getUnknownCharacterCode()

int bpp::NucleicAlphabet::getUnknownCharacterCode ( ) const

inlinevirtualinherited

Returns: The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 238 of file NucleicAlphabet.h.

◆ intToChar()

std::string AbstractAlphabet::intToChar ( int state ) const

virtualinherited

Give the string description of a state given its int description.

Parameters

state The int description.

Returns: The string description.

Exceptions

BadIntException When state is not a valid integer.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY.

Definition at line 160 of file AbstractAlphabet.cpp.

Referenced by bpp::RNY::getAlias(), bpp::WordAlphabet::getAlias(), bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), bpp::WordAlphabet::getNPosition(), bpp::NucleicAlphabet::getOverlap(), bpp::WordAlphabet::getPositions(), bpp::WordAlphabet::getWord(), bpp::BinaryAlphabet::isResolvedIn(), and bpp::NucleicAlphabet::subtract().

◆ isCharInAlphabet() [1/2]

bool bpp::LetterAlphabet::isCharInAlphabet ( char state ) const

inlineinherited

Definition at line 52 of file LetterAlphabet.h.

References bpp::LetterAlphabet::LETTER_UNDEF_VALUE, and bpp::LetterAlphabet::letters_.

Referenced by bpp::LetterAlphabet::charToInt(), bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), and bpp::LetterAlphabet::isCharInAlphabet().

◆ isCharInAlphabet() [2/2]

bool bpp::LetterAlphabet::isCharInAlphabet ( const std::string & state ) const

inlinevirtualinherited

Tell if a state (specified by its string description) is allowed by the the alphabet.

Parameters

state The string description.

Returns: 'true' if the state in known.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 56 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet().

◆ isGap() [1/2]

bool bpp::AbstractAlphabet::isGap ( const std::string & state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is a gap.

Implements bpp::Alphabet.

Definition at line 132 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

◆ isGap() [2/2]

bool bpp::AbstractAlphabet::isGap ( int state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is a gap.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY, and bpp::NumericAlphabet.

Definition at line 131 of file AbstractAlphabet.h.

Referenced by bpp::WordAlphabet::containsGap().

◆ isIntInAlphabet()

bool AbstractAlphabet::isIntInAlphabet ( int state ) const

virtualinherited

Tell if a state (specified by its int description) is allowed by the the alphabet.

Parameters

state The int description.

Returns: 'true' if the state in known.

Implements bpp::Alphabet.

Definition at line 167 of file AbstractAlphabet.cpp.

Referenced by bpp::BinaryAlphabet::getAlias(), bpp::RNY::getAlias(), bpp::AllelicAlphabet::getAlias(), bpp::WordAlphabet::getAlias(), bpp::CaseMaskedAlphabet::getMaskedEquivalentState(), bpp::BinaryAlphabet::isResolvedIn(), bpp::RNY::isResolvedIn(), bpp::AllelicAlphabet::isResolvedIn(), and bpp::WordAlphabet::isResolvedIn().

◆ isResolvedIn()

bool DNA::isResolvedIn	(	int	state1,
		int	state2
	)		const

virtual

Tells if a given (potentially unresolved) state can be resolved in another resolved state.

Parameters

state1	The alias to resolve.
state2	The candidate for resolution.

Returns: A boolean

Exceptions

BadIntException When state is not a valid integer.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 52 of file DNA.cpp.

References bpp::NucleicAlphabetState::getBinaryCode().

◆ isUnresolved() [1/2]

bool bpp::NucleicAlphabet::isUnresolved ( const std::string & state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 241 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::charToInt().

◆ isUnresolved() [2/2]

bool bpp::NucleicAlphabet::isUnresolved ( int state ) const

inlinevirtualinherited

Parameters

state The state to test.

Returns: 'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 240 of file NucleicAlphabet.h.

◆ operator=()

DNA& bpp::DNA::operator= ( const DNA & bia )

inline

Definition at line 36 of file DNA.h.

References bpp::NucleicAlphabet::operator=().

◆ registerState()

void bpp::NucleicAlphabet::registerState ( AlphabetState * st )

inlineprotectedvirtualinherited

Add a state to the Alphabet.

Parameters

st	The state to add.

Exceptions

Exception If a wrong alphabet state is provided.

Reimplemented from bpp::LetterAlphabet.

Definition at line 55 of file NucleicAlphabet.h.

References bpp::AbstractAlphabet::getNumberOfChars(), bpp::LetterAlphabet::registerState(), and bpp::NucleicAlphabet::updateBinMaps_().

◆ remap()

void bpp::AbstractAlphabet::remap ( )

inlineprotectedinherited

Re-update the maps using the alphabet_ vector content.

Definition at line 231 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_, bpp::AbstractAlphabet::letters_, bpp::AbstractAlphabet::nums_, and bpp::AbstractAlphabet::updateMaps_().

Referenced by bpp::NumericAlphabet::remap().

◆ resize()

void bpp::AbstractAlphabet::resize ( size_t size )

inlineprotectedinherited

Resize the private alphabet_ vector.

Parameters

size	The new size of the Alphabet.

Definition at line 226 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

◆ setState()

void bpp::NucleicAlphabet::setState	(	size_t	pos,
		AlphabetState *	st
	)

inlineprotectedvirtualinherited

Set a state in the Alphabet.

Parameters

pos	The index of the state in the alphabet_ vector.
st	The new state to put in the Alphabet.

Exceptions

Exception	If a wrong alphabet state is provided.
IndexOutOfBoundsException	If an incorrect index is provided.

Reimplemented from bpp::LetterAlphabet.

Definition at line 64 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::setState(), and bpp::NucleicAlphabet::updateBinMaps_().

◆ subtract() [1/2]

std::string bpp::NucleicAlphabet::subtract	(	const std::string &	s1,
		const std::string &	s2
	)		const

inlineinherited

Subtract states.

Get the remaining state when subtracting one state to another.

string a = "A";
string m = "M";
 
cout << alpha->subtract(m, a) << endl;
 
// should print C because M - A = C

Parameters

s1	the first state as a string
s2	the second state as a string

Exceptions

BadCharException if one of the states is not valid.

Returns: The remaining state as a string

Author: Sylvain Gaillard

Definition at line 173 of file NucleicAlphabet.h.

References bpp::LetterAlphabet::charToInt(), bpp::AbstractAlphabet::intToChar(), and bpp::NucleicAlphabet::subtract().

◆ subtract() [2/2]

int bpp::NucleicAlphabet::subtract	(	int	s1,
		int	s2
	)		const

inlineinherited

Subtract states.

Get the remaining state when subtracting one state to another.

int a = alpha->charToInt("A");
int m = alpha->charToInt("M");
int c = alpha->subtract(m, a);
 
cout << alpha->intToChar(c) << endl;
 
// should print C because M - A = C

Parameters

s1	the first state as an int
s2	the second state as an int

Exceptions

BadIntException if one of the states is not valid.

Returns: The remaining state as an int

Author: Sylvain Gaillard

Definition at line 148 of file NucleicAlphabet.h.

References bpp::AlphabetState::getNum(), bpp::NucleicAlphabet::getState(), and bpp::NucleicAlphabet::getStateByBinCode().

Referenced by bpp::NucleicAlphabet::subtract().

◆ updateBinMaps_()

void bpp::NucleicAlphabet::updateBinMaps_	(	size_t	pos,
		const NucleicAlphabetState &	st
	)

inlineprivateinherited

Definition at line 28 of file NucleicAlphabet.h.

References bpp::NucleicAlphabet::binCodes_, and bpp::NucleicAlphabetState::getBinaryCode().

Referenced by bpp::NucleicAlphabet::registerState(), and bpp::NucleicAlphabet::setState().

◆ updateMaps_()

void AbstractAlphabet::updateMaps_	(	size_t	pos,
		const AlphabetState &	st
	)

privateinherited

Update the private maps letters_ and nums_ when adding a state.

Parameters

pos	The index of the state in the alphabet_ vector.
st	The state that has been added or modified

Definition at line 22 of file AbstractAlphabet.cpp.

References bpp::AlphabetState::getLetter(), and bpp::AlphabetState::getNum().

Referenced by bpp::AbstractAlphabet::remap().

Member Data Documentation

◆ alphabet_

std::vector<AlphabetState*> bpp::AbstractAlphabet::alphabet_

privateinherited

Alphabet: vector of AlphabetState.

Definition at line 37 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::AbstractAlphabet(), bpp::AbstractAlphabet::getNumberOfChars(), bpp::AbstractAlphabet::getNumberOfStates(), bpp::AbstractAlphabet::operator=(), bpp::AbstractAlphabet::remap(), bpp::AbstractAlphabet::resize(), and bpp::AbstractAlphabet::~AbstractAlphabet().

◆ binCodes_

std::map<int, size_t> bpp::NucleicAlphabet::binCodes_

privateinherited

Definition at line 27 of file NucleicAlphabet.h.

Referenced by bpp::NucleicAlphabet::getStateByBinCode(), bpp::NucleicAlphabet::operator=(), and bpp::NucleicAlphabet::updateBinMaps_().

◆ caseSensitive_

bool bpp::LetterAlphabet::caseSensitive_

privateinherited

Definition at line 31 of file LetterAlphabet.h.

Referenced by bpp::LetterAlphabet::operator=(), bpp::LetterAlphabet::registerState(), and bpp::LetterAlphabet::setState().

◆ charList_

std::vector<std::string> bpp::AbstractAlphabet::charList_

mutableprotectedinherited

Definition at line 63 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=().

◆ intList_

std::vector<int> bpp::AbstractAlphabet::intList_

mutableprotectedinherited

Definition at line 64 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=().

◆ LETTER_UNDEF_VALUE

const int LetterAlphabet::LETTER_UNDEF_VALUE = -99

staticprivateinherited

Definition at line 29 of file LetterAlphabet.h.

Referenced by bpp::LetterAlphabet::isCharInAlphabet().

◆ letters_

std::vector<int> bpp::LetterAlphabet::letters_

privateinherited

Definition at line 30 of file LetterAlphabet.h.

Referenced by bpp::LetterAlphabet::charToInt(), bpp::LetterAlphabet::isCharInAlphabet(), bpp::LetterAlphabet::operator=(), bpp::LetterAlphabet::registerState(), and bpp::LetterAlphabet::setState().

◆ nums_

std::map<int, size_t> bpp::AbstractAlphabet::nums_

privateinherited

Definition at line 44 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=(), and bpp::AbstractAlphabet::remap().

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

Bpp/Seq/Alphabet/DNA.h
Bpp/Seq/Alphabet/DNA.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Overloaded methods from AbstractAlphabet

Detailed Description

Constructor & Destructor Documentation

◆ DNA() [1/2]

◆ DNA() [2/2]

◆ ~DNA()

Member Function Documentation

◆ charToInt()

◆ clone()

◆ equals()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAlphabetType()

◆ getCharCodeAt()

◆ getGapCharacterCode()

◆ getGeneric() [1/2]

◆ getGeneric() [2/2]

◆ getIntCodeAt()

◆ getName() [1/2]

◆ getName() [2/2]

◆ getNumberOfChars()

◆ getNumberOfStates()

◆ getNumberOfTypes()

◆ getOverlap() [1/2]

◆ getOverlap() [2/2]

◆ getResolvedChars()

◆ getSize()

◆ getState() [1/4]

◆ getState() [2/4]

◆ getState() [3/4]

◆ getState() [4/4]

◆ getStateAt() [1/2]

◆ getStateAt() [2/2]

◆ getStateByBinCode()

◆ getStateCodingSize()

◆ getStateIndex() [1/2]

◆ getStateIndex() [2/2]

◆ getSupportedChars()

◆ getSupportedInts()

◆ getUnknownCharacterCode()

◆ intToChar()

◆ isCharInAlphabet() [1/2]

◆ isCharInAlphabet() [2/2]

◆ isGap() [1/2]

◆ isGap() [2/2]

◆ isIntInAlphabet()

◆ isResolvedIn()

◆ isUnresolved() [1/2]

◆ isUnresolved() [2/2]

◆ operator=()

◆ registerState()

◆ remap()

◆ resize()

◆ setState()

◆ subtract() [1/2]

◆ subtract() [2/2]

◆ updateBinMaps_()

◆ updateMaps_()

Member Data Documentation

◆ alphabet_

◆ binCodes_

◆ caseSensitive_

◆ charList_

◆ intList_

◆ LETTER_UNDEF_VALUE

◆ letters_

◆ nums_