Utilitary functions dealing with alphabets. More...

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

Collaboration diagram for bpp::AlphabetTools:

Public Member Functions
	AlphabetTools ()

virtual	~AlphabetTools ()

Static Public Member Functions
static int	getType (char state)
	Character identification method for sequence's alphabet identification. More...

static bool	checkAlphabetCodingSize (const Alphabet &alphabet)
	This checks that all characters in the alphabet are coded by a string of same length. More...

static bool	checkAlphabetCodingSize (const Alphabet *alphabet)
	This checks that all characters in the alphabet are coded by a string of same length. More...

static unsigned int	getAlphabetCodingSize (const Alphabet &alphabet)
	In case that all states in the given alphabet have a string description of same length, send this length; e.g. 3 for codon alphabets. More...

static unsigned int	getAlphabetCodingSize (const Alphabet *alphabet)
	In case that all states in the given alphabet have a string description of same length, send this length; e.g. 3 for codon alphabets. More...

static bool	isNucleicAlphabet (const Alphabet &alphabet)

static bool	isDNAAlphabet (const Alphabet &alphabet)

static bool	isRNAAlphabet (const Alphabet &alphabet)

static bool	isProteicAlphabet (const Alphabet &alphabet)

static bool	isCodonAlphabet (const Alphabet &alphabet)

static bool	isWordAlphabet (const Alphabet &alphabet)

static bool	isRNYAlphabet (const Alphabet &alphabet)

static bool	isBinaryAlphabet (const Alphabet &alphabet)

static bool	isIntegerAlphabet (const Alphabet &alphabet)

static bool	isDefaultAlphabet (const Alphabet &alphabet)

static bool	isAllelicAlphabet (const Alphabet &alphabet)

static bool	match (std::shared_ptr< const Alphabet > alphabet, int i, int j)
	Tell if two characters match according to a given alphabet. More...

Static Public Attributes
static std::shared_ptr< const DNA >	DNA_ALPHABET = make_shared<const DNA>()

static std::shared_ptr< const RNA >	RNA_ALPHABET = make_shared<const RNA>()

static std::shared_ptr< const CodonAlphabet >	DNA_CODON_ALPHABET = make_shared<const CodonAlphabet>(dynamic_pointer_cast<const NucleicAlphabet>(DNA_ALPHABET))

static std::shared_ptr< const CodonAlphabet >	RNA_CODON_ALPHABET = make_shared<const CodonAlphabet>(dynamic_pointer_cast<const NucleicAlphabet>(RNA_ALPHABET))

static std::shared_ptr< const ProteicAlphabet >	PROTEIN_ALPHABET = make_shared<const ProteicAlphabet>()

static std::shared_ptr< const DefaultAlphabet >	DEFAULT_ALPHABET = make_shared<const DefaultAlphabet>()

Static Private Member Functions
template<class Y >
static bool	alphabetInheritsFrom (const Alphabet &alphabet)

Detailed Description

Utilitary functions dealing with alphabets.

Definition at line 31 of file AlphabetTools.h.

Constructor & Destructor Documentation

◆ AlphabetTools()

bpp::AlphabetTools::AlphabetTools ( )

inline

Definition at line 42 of file AlphabetTools.h.

◆ ~AlphabetTools()

virtual bpp::AlphabetTools::~AlphabetTools ( )

inlinevirtual

Definition at line 43 of file AlphabetTools.h.

Member Function Documentation

◆ alphabetInheritsFrom()

template<class Y >

static bool bpp::AlphabetTools::alphabetInheritsFrom ( const Alphabet & alphabet )

inlinestaticprivate

Definition at line 201 of file AlphabetTools.h.

◆ checkAlphabetCodingSize() [1/2]

bool AlphabetTools::checkAlphabetCodingSize ( const Alphabet & alphabet )

static

This checks that all characters in the alphabet are coded by a string of same length.

This method is used when states are coded by more than one character, typically: codon alphabets.

Parameters

alphabet The alphabet to check.

Returns: True if all text description have the same length (e.g. 3 for codon alphabet).

Definition at line 57 of file AlphabetTools.cpp.

References bpp::AlphabetState::getNum(), bpp::Alphabet::getNumberOfChars(), bpp::Alphabet::getNumberOfTypes(), bpp::Alphabet::getStateAt(), and bpp::Alphabet::intToChar().

◆ checkAlphabetCodingSize() [2/2]

bool AlphabetTools::checkAlphabetCodingSize ( const Alphabet * alphabet )

static

This checks that all characters in the alphabet are coded by a string of same length.

This function performs the same work as the previous one, but deals with pointers instead of reference. This may be more convenient since we often use pointers on alphabets.

Parameters

alphabet a pointer toward the alphabet to check.

Returns: True if all text description have the same length (e.g. 3 for codon alphabet).

Definition at line 73 of file AlphabetTools.cpp.

◆ getAlphabetCodingSize() [1/2]

unsigned int AlphabetTools::getAlphabetCodingSize ( const Alphabet & alphabet )

static

In case that all states in the given alphabet have a string description of same length, send this length; e.g. 3 for codon alphabets.

Parameters

alphabet The alphabet to analyse.

Returns: The common size of all text descriptionif there is one. Else throws an AlphabetException.

Definition at line 80 of file AlphabetTools.cpp.

References bpp::Alphabet::intToChar().

Referenced by bpp::StringSequenceTools::codeSequence().

◆ getAlphabetCodingSize() [2/2]

unsigned int AlphabetTools::getAlphabetCodingSize ( const Alphabet * alphabet )

static

In case that all states in the given alphabet have a string description of same length, send this length; e.g. 3 for codon alphabets.

This function performs the same work as the previous one, but deals with pointers instead of reference. This may be more convenient since we often use pointers on alphabets.

Parameters

alphabet a pointer toward the alphabet to analyse.

Returns: The common size of all text descriptionif there is one. Else throws an AlphabetException.

Definition at line 89 of file AlphabetTools.cpp.

◆ getType()

int AlphabetTools::getType ( char state )

static

Character identification method for sequence's alphabet identification.

Return :

-1 gap
1 DNA specific (no character!)
2 RNA specific (U)
3 Protein specific (characters E, F, I, L, P, Q)
4 Nucleotide specific (no character)
5 DNA or Protein specific (T)
6 RNA or Protein specific (no character)
7 Any alphabet (A, B, C, D, G, H, J, K, M, N, O, R, S, V, W, X, Y, Z, 0)
0 Unknown character

Parameters

state The character to test.

Returns: The type code.

Definition at line 28 of file AlphabetTools.cpp.

References bpp::TextTools::toString().

Referenced by bpp::StringSequenceTools::getAlphabetFromSequence().

◆ isAllelicAlphabet()

static bool bpp::AlphabetTools::isAllelicAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the Allelic class.

Parameters

alphabet The alphabet to check.

Definition at line 171 of file AlphabetTools.h.

Referenced by bpp::SequenceApplicationTools::getProbabilisticSiteContainer().

◆ isBinaryAlphabet()

static bool bpp::AlphabetTools::isBinaryAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the BinaryAlphabet class.

Parameters

alphabet The alphabet to check.

Definition at line 153 of file AlphabetTools.h.

◆ isCodonAlphabet()

static bool bpp::AlphabetTools::isCodonAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the Codon class.

Parameters

alphabet The alphabet to check.

Definition at line 135 of file AlphabetTools.h.

◆ isDefaultAlphabet()

static bool bpp::AlphabetTools::isDefaultAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the DefaultAlphabet class.

Parameters

alphabet The alphabet to check.

Definition at line 165 of file AlphabetTools.h.

Referenced by bpp::SiteContainerTools::resolveDottedAlignment().

◆ isDNAAlphabet()

static bool bpp::AlphabetTools::isDNAAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the DNA class.

Parameters

alphabet The alphabet to check.

Definition at line 117 of file AlphabetTools.h.

Referenced by bpp::SequenceTools::complement(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::invertComplement(), bpp::RNY::RNY(), bpp::SequenceTools::RNYslice(), and bpp::SequenceTools::transcript().

◆ isIntegerAlphabet()

static bool bpp::AlphabetTools::isIntegerAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the ProteicAlphabet class.

Parameters

alphabet The alphabet to check.

Definition at line 159 of file AlphabetTools.h.

◆ isNucleicAlphabet()

static bool bpp::AlphabetTools::isNucleicAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the NucleicAlphabet class.

Parameters

alphabet The alphabet to check.

Definition at line 111 of file AlphabetTools.h.

Referenced by bpp::SequenceApplicationTools::getAlphabet(), bpp::GeneticCode::getCodingSequence(), and bpp::RNY::getRNY().

◆ isProteicAlphabet()

static bool bpp::AlphabetTools::isProteicAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the ProteicAlphabet class.

Parameters

alphabet The alphabet to check.

Definition at line 129 of file AlphabetTools.h.

Referenced by bpp::CodonFromProteicAlphabetIndex1::CodonFromProteicAlphabetIndex1(), bpp::CodonFromProteicAlphabetIndex2::CodonFromProteicAlphabetIndex2(), bpp::BppOAlphabetIndex1Format::read(), and bpp::BppOAlphabetIndex2Format::read().

◆ isRNAAlphabet()

static bool bpp::AlphabetTools::isRNAAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the RNA class.

Parameters

alphabet The alphabet to check.

Definition at line 123 of file AlphabetTools.h.

Referenced by bpp::SequenceTools::complement(), bpp::SequenceTools::getComplement(), bpp::SequenceTools::invertComplement(), bpp::SequenceTools::reverseTranscript(), and bpp::RNY::RNY().

◆ isRNYAlphabet()

static bool bpp::AlphabetTools::isRNYAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the RNY class.

Parameters

alphabet The alphabet to check.

Definition at line 147 of file AlphabetTools.h.

Referenced by bpp::SequenceApplicationTools::getProbabilisticSiteContainer(), and bpp::SequenceApplicationTools::getSiteContainer().

◆ isWordAlphabet()

static bool bpp::AlphabetTools::isWordAlphabet ( const Alphabet & alphabet )

inlinestatic

Returns: True if the alphabet is an instantiation of the WordAlphabet class.

Parameters

alphabet The alphabet to check.

Definition at line 141 of file AlphabetTools.h.

◆ match()

static bool bpp::AlphabetTools::match	(	std::shared_ptr< const Alphabet >	alphabet,
		int	i,
		int	j
	)

inlinestatic

Tell if two characters match according to a given alphabet.

Example (DNA):

* A,T: false
* A,A: true
* A,N: true
* A,Y: false
* N,Y: true
* N,N: true
*

Returns: True if the two characters are identical, or are compatible if at least one of them is a generic character.

Parameters

alphabet	The alphabet to use.
i	First character to check.
j	Secondt character to check.

Definition at line 191 of file AlphabetTools.h.

References bpp::VectorTools::vectorIntersection().

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

Member Data Documentation

◆ DEFAULT_ALPHABET

shared_ptr< const DefaultAlphabet > AlphabetTools::DEFAULT_ALPHABET = make_shared<const DefaultAlphabet>()

static

Definition at line 39 of file AlphabetTools.h.

Referenced by bpp::NexusIOSequence::appendAlignmentFromStream().

◆ DNA_ALPHABET

shared_ptr< const DNA > AlphabetTools::DNA_ALPHABET = make_shared<const DNA>()

static

Definition at line 34 of file AlphabetTools.h.

Referenced by bpp::StringSequenceTools::getAlphabetFromSequence().

◆ DNA_CODON_ALPHABET

shared_ptr< const CodonAlphabet > AlphabetTools::DNA_CODON_ALPHABET = make_shared<const CodonAlphabet>(dynamic_pointer_cast<const NucleicAlphabet>(DNA_ALPHABET))

static

Definition at line 36 of file AlphabetTools.h.

◆ PROTEIN_ALPHABET

shared_ptr< const ProteicAlphabet > AlphabetTools::PROTEIN_ALPHABET = make_shared<const ProteicAlphabet>()

static

Definition at line 38 of file AlphabetTools.h.

Referenced by bpp::StringSequenceTools::getAlphabetFromSequence().

◆ RNA_ALPHABET

shared_ptr< const RNA > AlphabetTools::RNA_ALPHABET = make_shared<const RNA>()

static

Definition at line 35 of file AlphabetTools.h.

Referenced by bpp::StringSequenceTools::getAlphabetFromSequence().

◆ RNA_CODON_ALPHABET

shared_ptr< const CodonAlphabet > AlphabetTools::RNA_CODON_ALPHABET = make_shared<const CodonAlphabet>(dynamic_pointer_cast<const NucleicAlphabet>(RNA_ALPHABET))

static

Definition at line 37 of file AlphabetTools.h.

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

Bpp/Seq/Alphabet/AlphabetTools.h
Bpp/Seq/Alphabet/AlphabetTools.cpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Static Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AlphabetTools()

◆ ~AlphabetTools()

Member Function Documentation

◆ alphabetInheritsFrom()

◆ checkAlphabetCodingSize() [1/2]

◆ checkAlphabetCodingSize() [2/2]

◆ getAlphabetCodingSize() [1/2]

◆ getAlphabetCodingSize() [2/2]

◆ getType()

◆ isAllelicAlphabet()

◆ isBinaryAlphabet()

◆ isCodonAlphabet()

◆ isDefaultAlphabet()

◆ isDNAAlphabet()

◆ isIntegerAlphabet()

◆ isNucleicAlphabet()

◆ isProteicAlphabet()

◆ isRNAAlphabet()

◆ isRNYAlphabet()

◆ isWordAlphabet()

◆ match()

Member Data Documentation

◆ DEFAULT_ALPHABET

◆ DNA_ALPHABET

◆ DNA_CODON_ALPHABET

◆ PROTEIN_ALPHABET

◆ RNA_ALPHABET

◆ RNA_CODON_ALPHABET