The interface class for word alphabets. More...

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

Inheritance diagram for bpp::CoreWordAlphabet:

Public Member Functions
	CoreWordAlphabet ()

virtual	~CoreWordAlphabet ()

virtual unsigned int	getLength () const =0

virtual unsigned int	getSize () const =0

virtual bool	hasUniqueAlphabet () const =0

virtual std::shared_ptr< const Alphabet >	getNAlphabet (size_t n) const =0

virtual int	getWord (const Sequence &seq, size_t pos=0) const =0

virtual int	getWord (const std::vector< int > &vint, size_t pos=0) const =0
	Get the int code for a word given the int code of the underlying positions. More...

virtual std::string	getWord (const std::vector< std::string > &vpos, size_t pos=0) const =0
	Get the char code for a word given the char code of the underlying positions. More...

virtual int	getNPosition (int word, size_t n) const =0
	Get the int code of the n-position of a word given its int description. More...

virtual std::vector< int >	getPositions (int word) const =0
	Get the int codes of each position of a word given its int description. More...

virtual std::string	getNPosition (const std::string &word, size_t n) const =0
	Get the char code of the n-position of a word given its char description. More...

virtual std::vector< std::string >	getPositions (const std::string &word) const =0
	Get the char codes of each position of a word given its char description. More...

virtual std::unique_ptr< SequenceInterface >	translate (const SequenceInterface &sequence, size_t pos=0) const =0
	Translate a whole sequence from letters alphabet to words alphabet. More...

virtual std::unique_ptr< SequenceInterface >	reverse (const SequenceInterface &sequence) const =0
	Translate a whole sequence from words alphabet to letters alphabet. More...

Private Member Functions
Inner utilitary functions
virtual bool	containsUnresolved (const std::string &state) const =0

virtual bool	containsGap (const std::string &state) const =0

Detailed Description

The interface class for word alphabets.

Definition at line 24 of file WordAlphabet.h.

Constructor & Destructor Documentation

◆ CoreWordAlphabet()

bpp::CoreWordAlphabet::CoreWordAlphabet ( )

inline

Definition at line 27 of file WordAlphabet.h.

◆ ~CoreWordAlphabet()

virtual bpp::CoreWordAlphabet::~CoreWordAlphabet ( )

inlinevirtual

Definition at line 29 of file WordAlphabet.h.

Member Function Documentation

◆ containsGap()

virtual bool bpp::CoreWordAlphabet::containsGap ( const std::string & state ) const

privatepure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ containsUnresolved()

virtual bool bpp::CoreWordAlphabet::containsUnresolved ( const std::string & state ) const

privatepure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getLength()

virtual unsigned int bpp::CoreWordAlphabet::getLength ( ) const

pure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getNAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::CoreWordAlphabet::getNAlphabet ( size_t n ) const

pure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getNPosition() [1/2]

virtual std::string bpp::CoreWordAlphabet::getNPosition	(	const std::string &	word,
		size_t	n
	)		const

pure virtual

Get the char code of the n-position of a word given its char description.

Parameters

word	The char description of the word.
n	The position in the word (starting at 0).

Returns: The char description of the n-position of the word.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getNPosition() [2/2]

virtual int bpp::CoreWordAlphabet::getNPosition	(	int	word,
		size_t	n
	)		const

pure virtual

Get the int code of the n-position of a word given its int description.

Parameters

word	The int description of the word.
n	The position in the word (starting at 0).

Returns: The int description of the n-position of the word.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getPositions() [1/2]

virtual std::vector<std::string> bpp::CoreWordAlphabet::getPositions ( const std::string & word ) const

pure virtual

Get the char codes of each position of a word given its char description.

Parameters

word	The char description of the word.

Returns: The char description of the three positions of the word.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getPositions() [2/2]

virtual std::vector<int> bpp::CoreWordAlphabet::getPositions ( int word ) const

pure virtual

Get the int codes of each position of a word given its int description.

Parameters

word	The int description of the word.

Returns: The int description of the positions of the codon.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getSize()

virtual unsigned int bpp::CoreWordAlphabet::getSize ( ) const

pure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getWord() [1/3]

virtual int bpp::CoreWordAlphabet::getWord	(	const Sequence &	seq,
		size_t	pos = `0`
	)		const

pure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ getWord() [2/3]

virtual int bpp::CoreWordAlphabet::getWord	(	const std::vector< int > &	vint,
		size_t	pos = `0`
	)		const

pure virtual

Get the int code for a word given the int code of the underlying positions.

The int code of each position must match the corresponding alphabet specified at this position.

Parameters

vint	description for all the positions.
pos	the start position to match in the vector.

Returns: The int code of the word.

Exceptions

IndexOutOfBoundsException In case of wrong position.

Implemented in bpp::CodonAlphabet, and bpp::WordAlphabet.

◆ getWord() [3/3]

virtual std::string bpp::CoreWordAlphabet::getWord	(	const std::vector< std::string > &	vpos,
		size_t	pos = `0`
	)		const

pure virtual

Get the char code for a word given the char code of the underlying positions.

The char code of each position must match the corresponding alphabet specified at this position.

Parameters

vpos	vector description for all the positions.
pos	the start position to match in the vector.

Returns: The string of the word.

Exceptions

IndexOutOfBoundsException In case of wrong position.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ hasUniqueAlphabet()

virtual bool bpp::CoreWordAlphabet::hasUniqueAlphabet ( ) const

pure virtual

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ reverse()

virtual std::unique_ptr<SequenceInterface> bpp::CoreWordAlphabet::reverse ( const SequenceInterface & sequence ) const

pure virtual

Translate a whole sequence from words alphabet to letters alphabet.

Parameters

sequence A sequence in words alphabet.

Returns: The corresponding sequence in letters alphabet.

Exceptions

AlphabetMismatchException	If the sequence alphabet do not match the target alphabet.
Exception	Other kind of error, depending on the implementation.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

◆ translate()

virtual std::unique_ptr<SequenceInterface> bpp::CoreWordAlphabet::translate	(	const SequenceInterface &	sequence,
		size_t	pos = `0`
	)		const

pure virtual

Translate a whole sequence from letters alphabet to words alphabet.

Parameters

sequence	A sequence in letters alphabet.
pos	the start position (default 0)

Returns: The corresponding sequence in words alphabet.

Exceptions

AlphabetMismatchException	If the sequence alphabet do not match the source alphabet.
Exception	Other kind of error, depending on the implementation.

Implemented in bpp::WordAlphabet, and bpp::CodonAlphabet.

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

Bpp/Seq/Alphabet/WordAlphabet.h

Public Member Functions

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ CoreWordAlphabet()

◆ ~CoreWordAlphabet()

Member Function Documentation

◆ containsGap()

◆ containsUnresolved()

◆ getLength()

◆ getNAlphabet()

◆ getNPosition() [1/2]

◆ getNPosition() [2/2]

◆ getPositions() [1/2]

◆ getPositions() [2/2]

◆ getSize()

◆ getWord() [1/3]

◆ getWord() [2/3]

◆ getWord() [3/3]

◆ hasUniqueAlphabet()

◆ reverse()

◆ translate()