bpp::RNY Class Reference

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

Inheritance diagram for bpp::RNY:

Collaboration diagram for bpp::RNY:

Public Member Functions
	RNY (const NucleicAlphabet &)
	~RNY ()
int	charToInt (const std::string &state) const throw (BadCharException)
	Give the int description of a state given its string description. More...
std::string	intToChar (int state) const throw (BadIntException)
	Give the string description of a state given its int description. More...
bool	containsGap (const std::string &state) const throw (BadCharException)
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	isGap (int state) const
std::vector< int >	getAlias (int state) const throw (BadIntException)
	Get all resolved states that match a generic state. More...
std::vector< std::string >	getAlias (const std::string &state) const throw (BadCharException)
	Get all resolved states that match a generic state. More...
bool	isUnresolved (int state) const
bool	isUnresolved (const std::string &state) const
std::string	getAlphabetType () const
	Identification method. More...
const NucleicAlphabet &	getLetterAlphabet () const
std::string	getRNY (const std::string &, const std::string &, const std::string &) const throw (BadCharException)
	Get the char code for a triplet given the char code of the three underlying positions. More...
int	getRNY (int, int, int, const Alphabet &) const throw (BadCharException)
Implement these methods from the Alphabet interface.
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 throw (BadCharException)
	Get the complete name of a state given its string description. More...
std::string	getName (int state) const throw (BadIntException)
	Get the complete name 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...
bool	isCharInAlphabet (const std::string &state) const
	Tell if a state (specified by its string description) is allowed by the the alphabet. More...
int	getGeneric (const std::vector< int > &states) const throw (BadIntException)
	Get the generic state that match a set of states. More...
std::string	getGeneric (const std::vector< std::string > &states) const throw (AlphabetException)
	Get the generic state that match a set of states. More...
const std::vector< int > &	getSupportedInts () const
const std::vector< std::string > &	getSupportedChars () const
int	getGapCharacterCode () const
bool	isGap (const std::string &state) const
Specific methods to access AlphabetState
const AlphabetState &	getState (const std::string &letter) const throw (BadCharException)
	Get a state by its letter. More...
const AlphabetState &	getState (int num) const throw (BadIntException)
	Get a state by its num. More...

Protected Member Functions
virtual void	registerState (const AlphabetState &st)
	Add a state to the Alphabet. More...
virtual void	setState (size_t pos, const AlphabetState &st) throw (IndexOutOfBoundsException)
	Set a state in the Alphabet. More...
void	resize (unsigned int size)
	Resize the private alphabet_ vector. More...
virtual AlphabetState &	getStateAt (size_t pos) throw (IndexOutOfBoundsException)
	Get a state at a position in the alphabet_ vector. More...
virtual const AlphabetState &	getStateAt (size_t pos) const throw (IndexOutOfBoundsException)
	Get a state at a position in the 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...

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 Attributes
const NucleicAlphabet &	nuclalph_

Detailed Description

Definition at line 65 of file RNY.h.

Constructor & Destructor Documentation

RNY::RNY

(

const NucleicAlphabet &

na

)

Definition at line 51 of file RNY.cpp.

References bpp::AbstractAlphabet::resize(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), bpp::AbstractAlphabet::setState(), and bpp::AbstractAlphabet::setState().

bpp::RNY::~RNY ( )

inline

Definition at line 72 of file RNY.h.

Member Function Documentation

int RNY::charToInt ( const std::string &  state ) const throw (BadCharException)

virtual

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 416 of file RNY.cpp.

References bpp::AbstractAlphabet::charToInt().

bool RNY::containsGap

(

const std::string &

state

)

const throw (BadCharException)

Definition at line 399 of file RNY.cpp.

Referenced by isUnresolved().

vector< int > RNY::getAlias ( int  state ) const throw (BadIntException)

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 177 of file RNY.cpp.

vector< string > RNY::getAlias ( const std::string &  state ) const throw (BadCharException)

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 267 of file RNY.cpp.

References bpp::AbstractAlphabet::intToChar().

std::string bpp::RNY::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 89 of file RNY.h.

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const

inlinevirtualinherited

Returns

The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 132 of file AbstractAlphabet.h.

Referenced by bpp::SequenceTools::replaceStopsWithGaps().

int AbstractAlphabet::getGeneric ( const std::vector< int > &  states ) const throw (BadIntException)

virtualinherited

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 191 of file AbstractAlphabet.cpp.

References bpp::MapTools::getKeys(), and bpp::TextTools::toString().

std::string AbstractAlphabet::getGeneric ( const std::vector< std::string > &  states ) const throw (AlphabetException)

virtualinherited

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.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 217 of file AbstractAlphabet.cpp.

References bpp::MapTools::getKeys(), and bpp::TextTools::toString().

const NucleicAlphabet & RNY::getLetterAlphabet

(

)

const

Definition at line 260 of file RNY.cpp.

References nuclalph_.

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

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 123 of file AbstractAlphabet.cpp.

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

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

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 130 of file AbstractAlphabet.cpp.

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 119 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), bpp::WordAlphabet::getNumberOfTypes(), bpp::WordAlphabet::getSize(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::NucleicAlphabet::registerState(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

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

inlinevirtual

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 81 of file RNY.h.

string RNY::getRNY	(	const std::string &	pos1,
		const std::string &	pos2,
		const std::string &	pos3
	)		const throw (BadCharException)

Get the char code for a triplet given the char code of the three underlying positions.

The char code of each position must match the nucleic alphabet specified for this alphabet. NB: This performs pos1 + pos2 + pos3 after checking for each position validity.

Parameters

pos1	Char description for position 1.
pos2	Char description for position 2.
pos3	Char description for position 3.

Returns

The Char code of the triplet.

Definition at line 285 of file RNY.cpp.

int RNY::getRNY	(	int	i,
		int	j,
		int	k,
		const Alphabet &	alph
	)		const throw (BadCharException)

Definition at line 307 of file RNY.cpp.

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

inlinevirtual

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 80 of file RNY.h.

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

virtualinherited

Get a state by its letter.

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

Parameters

letter

The letter of the state to find.

Exceptions

BadCharException

If the letter is not in the Alphabet.

Implements bpp::Alphabet.

Reimplemented in bpp::NucleicAlphabet, and bpp::ProteicAlphabet.

Definition at line 89 of file AbstractAlphabet.cpp.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::ProteicAlphabet::getState(), bpp::ProteicAlphabet::getState(), bpp::NucleicAlphabet::getState(), and bpp::NucleicAlphabet::getState().

const AlphabetState & AbstractAlphabet::getState ( int  num ) const throw (BadIntException)

virtualinherited

Get a state by its num.

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

Parameters

num	The num of the state to find.

Exceptions

BadIntException

If the num is not in the Alphabet.

Implements bpp::Alphabet.

Reimplemented in bpp::NucleicAlphabet, and bpp::ProteicAlphabet.

Definition at line 98 of file AbstractAlphabet.cpp.

AlphabetState & AbstractAlphabet::getStateAt ( size_t  pos ) throw (IndexOutOfBoundsException)

protectedvirtualinherited

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 corect type.

Parameters

pos	The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException

If pos is out of the vector.

Definition at line 107 of file AbstractAlphabet.cpp.

Referenced by bpp::WordAlphabet::build_(), bpp::WordAlphabet::build_(), bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), bpp::EchinodermMitochondrialCodonAlphabet::EchinodermMitochondrialCodonAlphabet(), bpp::ProteicAlphabet::getStateAt(), bpp::ProteicAlphabet::getStateAt(), bpp::NucleicAlphabet::getStateAt(), bpp::NucleicAlphabet::getStateAt(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::InvertebrateMitochondrialCodonAlphabet::InvertebrateMitochondrialCodonAlphabet(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::StandardCodonAlphabet::StandardCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), bpp::VertebrateMitochondrialCodonAlphabet::VertebrateMitochondrialCodonAlphabet(), bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet(), and bpp::YeastMitochondrialCodonAlphabet::YeastMitochondrialCodonAlphabet().

const AlphabetState & AbstractAlphabet::getStateAt ( size_t  pos ) const throw (IndexOutOfBoundsException)

protectedvirtualinherited

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 corect type.

Parameters

pos	The index of the state in the alphabet_ vector.

Exceptions

IndexOutOfBoundsException

If pos is out of the vector.

Definition at line 115 of file AbstractAlphabet.cpp.

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

inlineprotectedvirtualinherited

Get the size of the string coding a state.

Returns

The size of the tring coding each states in the Alphabet.

Author

Sylvain Gaillard

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 213 of file AbstractAlphabet.h.

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 260 of file AbstractAlphabet.cpp.

Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet().

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 243 of file AbstractAlphabet.cpp.

int bpp::RNY::getUnknownCharacterCode ( ) const

inlinevirtual

Returns

The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 82 of file RNY.h.

string RNY::intToChar ( int  state ) const throw (BadIntException)

virtual

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.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 426 of file RNY.cpp.

bool AbstractAlphabet::isCharInAlphabet ( const std::string &  state ) const

virtualinherited

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.

Implements bpp::Alphabet.

Reimplemented in bpp::LetterAlphabet.

Definition at line 161 of file AbstractAlphabet.cpp.

bool RNY::isGap ( int  state ) const

virtual

Parameters

state

The state to test.

Returns

'True' if the state is a gap.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 394 of file RNY.cpp.

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 134 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

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 151 of file AbstractAlphabet.cpp.

bool RNY::isUnresolved ( int  state ) const

virtual

Parameters

state

The state to test.

Returns

'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 409 of file RNY.cpp.

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

virtual

Parameters

state

The state to test.

Returns

'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 404 of file RNY.cpp.

References containsGap().

void AbstractAlphabet::registerState ( const AlphabetState &  st )

protectedvirtualinherited

Add a state to the Alphabet.

Parameters

st	The state to add.

Reimplemented in bpp::LetterAlphabet, bpp::DefaultAlphabet, and bpp::BinaryAlphabet.

Definition at line 65 of file AbstractAlphabet.cpp.

References bpp::AlphabetState::clone().

Referenced by bpp::BinaryAlphabet::registerState(), bpp::DefaultAlphabet::registerState(), and bpp::LetterAlphabet::registerState().

void bpp::AbstractAlphabet::remap ( )

inlineprotectedinherited

Re-update the maps using the alphabet_ vector content.

Definition at line 207 of file AbstractAlphabet.h.

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

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

void bpp::AbstractAlphabet::resize ( unsigned int  size )

inlineprotectedinherited

Resize the private alphabet_ vector.

Parameters

size	The new size of the Alphabet.

Definition at line 182 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::BinaryAlphabet::BinaryAlphabet(), bpp::WordAlphabet::build_(), bpp::DefaultAlphabet::DefaultAlphabet(), and RNY().

void AbstractAlphabet::setState ( size_t  pos, const AlphabetState &  st  ) throw (IndexOutOfBoundsException)

protectedvirtualinherited

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.

Reimplemented in bpp::LetterAlphabet.

Definition at line 74 of file AbstractAlphabet.cpp.

Referenced by bpp::BinaryAlphabet::BinaryAlphabet(), bpp::BinaryAlphabet::BinaryAlphabet(), bpp::WordAlphabet::build_(), bpp::WordAlphabet::build_(), bpp::WordAlphabet::build_(), RNY(), RNY(), RNY(), RNY(), RNY(), RNY(), RNY(), RNY(), RNY(), and bpp::LetterAlphabet::setState().

Member Data Documentation

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

mutableprotectedinherited

Definition at line 99 of file AbstractAlphabet.h.

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

mutableprotectedinherited

Definition at line 100 of file AbstractAlphabet.h.

const NucleicAlphabet& bpp::RNY::nuclalph_

private

Definition at line 68 of file RNY.h.

Referenced by getLetterAlphabet().

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

• Bpp/Seq/Alphabet/RNY.h
• Bpp/Seq/Alphabet/RNY.cpp