Quality type for traditional Sanger and modern Illumina Phred scores (typical range). More...
#include <seqan3/alphabet/quality/phred42.hpp>
Public Types | |
using | char_type = char_t |
The type of the alphabet when converted to char (e.g. via to_char()). | |
using | rank_type = detail::min_viable_uint_t< size - 1 > |
The type of the alphabet when represented as a number (e.g. via to_rank()). | |
Member types | |
using | phred_type = int8_t |
The integer representation of a quality score assignable with =operator. | |
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | phred42 () |
constexpr | phred42 (phred42 const &)=default |
constexpr | phred42 (phred42 &&)=default |
constexpr phred42 & | operator= (phred42 const &)=default |
constexpr phred42 & | operator= (phred42 &&)=default |
~phred42 ()=default | |
constexpr | phred42 (phred_type const p) |
Construct from phred value. | |
Read functions | |
constexpr char_type | to_char () const noexcept |
Return the letter as a character of char_type. More... | |
constexpr phred_type | to_phred () const noexcept |
Return the alphabet's value in phred representation. | |
Write functions | |
constexpr phred42 & | assign_phred (phred_type const p) noexcept |
Assign from the numeric phred value. More... | |
Read functions | |
constexpr rank_type | to_rank () const noexcept |
Return the letter's numeric value (rank in the alphabet). More... | |
Write functions | |
constexpr phred42 & | assign_char (std::conditional_t< std::Same< char_type, void >, char, char_type > const c) noexcept |
Assign from a character. More... | |
constexpr phred42 & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. More... | |
Static Public Attributes | |
static detail::min_viable_uint_t< size > constexpr | value_size |
The size of the alphabet, i.e. the number of different values it can take. | |
Member variables. | |
static constexpr phred_type | offset_phred {0} |
The projection offset between phred and rank score representation. | |
static constexpr char_type | offset_char {'!'} |
The projection offset between char and rank score representation. | |
Static Protected Attributes | |
static std::array< rank_type, 256 > constexpr | char_to_rank |
Char to rank conversion table. | |
static std::array< rank_type, 256 > constexpr | phred_to_rank |
Phred to rank conversion table. | |
Related Functions | |
(Note that these are not member functions.) | |
Requirements for seqan3::alphabet_concept | |
You can expect these functions on all types that implement seqan3::alphabet_concept. | |
template<typename alphabet_type > | |
using | underlying_char_t = typename underlying_char< alphabet_type >::type |
The char_type of the alphabet. [type metafunction shortcut]. More... | |
char_type | to_char (alphabet_concept const alph) |
Returns the alphabet letter's value in character representation. More... | |
alphabet_concept && | assign_char (alphabet_concept &&alph, char_type const chr) |
Returns the alphabet letter's value in character representation. More... | |
Requirements for seqan3::semi_alphabet_concept | |
You can expect these functions on all types that implement seqan3::semi_alphabet_concept. | |
template<typename semi_alphabet_type > | |
using | underlying_rank_t = typename underlying_rank< semi_alphabet_type >::type |
The rank_type of the semi_alphabet. [type metafunction shortcut]. More... | |
template<typename alphabet_type > | |
constexpr auto | alphabet_size_v = alphabet_size<alphabet_type>::value |
The size of the alphabet. [value metafunction shortcut]. More... | |
rank_type | to_rank (semi_alphabet_concept const alph) |
Returns the alphabet letter's value in rank representation. More... | |
semi_alphabet_concept && | assign_rank (semi_alphabet_concept &&alph, rank_type const rank) |
Returns the alphabet letter's value in rank representation. More... | |
Requirements for std::Swappable | |
You can expect these functions on all types that implement std::Swappable. | |
void | swap (t &lhs, t &rhs) |
Swaps the contents of two objects. More... | |
Requirements for std::EqualityComparable | |
You can expect these functions on all types that implement std::Equality_comparable. | |
bool | operator== (type const &lhs, type const &rhs) |
(In-)Equality comparison. More... | |
bool | operator!= (type const &lhs, type const &rhs) |
(In-)Equality comparison. More... | |
Requirements for std::StrictTotallyOrdered | |
You can expect these functions on all types that implement std::StrictTotallyOrdered. | |
bool | operator< (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
bool | operator<= (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
bool | operator> (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
bool | operator>= (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
Quality type for traditional Sanger and modern Illumina Phred scores (typical range).
The phred42 quality alphabet represents the zero-based phred score range [0..41] mapped to the consecutive ASCII range ['!' .. 'J']. It therefore can represent the Illumina 1.8+ standard and the original Sanger score. If you intend to use phred scores exceeding 41, use the larger score type, namely seqan3::phred63, otherwise on construction exceeding scores are mapped to 41.
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inlinenoexceptinherited |
Assign from a character.
Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Assign from the numeric phred value.
Satisfies the seqan3::quality_concept::assign_phred() requirement via the seqan3::assign_rank() wrapper.
Constant.
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inlinenoexceptinherited |
Assign from a numeric value.
Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Return the letter as a character of char_type.
Satisfies the seqan3::alphabet_concept::to_char() requirement via the seqan3::to_char() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Satisfies the seqan3::semi_alphabet_concept::to_rank() requirement via the to_rank() wrapper.
Constant.
Guaranteed not to throw.