ELynx.Data.Alphabet.Alphabet

Creation date: Fri May 10 11:10:32 2019.

Hierarchy:

1. Character type.
2. Sets of Characters form Alphabets; each Alphabet has a specification AlphabetSpec.

New alphabets have to be added manually in this module.

This way of handling characters and alphabets IS NOT TYPE SAFE, but much, much faster. A second layer of modules such as Nucleotide depend on a Character type class. Hence, they provide a type safe way of handling alphabets. Conversion is possible, for instance, with fromCVec, and toCVec.

Documentation

data Alphabet

Available alphabets; for details see alphabetSpec.

Constructors

DNA

DNAX

DNAI

Protein

ProteinX

ProteinS

ProteinI

Instances

Bounded Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

minBound :: Alphabet

maxBound :: Alphabet

Enum Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

succ :: Alphabet -> Alphabet

pred :: Alphabet -> Alphabet

toEnum :: Int -> Alphabet

fromEnum :: Alphabet -> Int

enumFrom :: Alphabet -> [Alphabet]

enumFromThen :: Alphabet -> Alphabet -> [Alphabet]

enumFromTo :: Alphabet -> Alphabet -> [Alphabet]

enumFromThenTo :: Alphabet -> Alphabet -> Alphabet -> [Alphabet]

Eq Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

(==) :: Alphabet -> Alphabet -> Bool

(/=) :: Alphabet -> Alphabet -> Bool

Ord Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

compare :: Alphabet -> Alphabet -> Ordering

(<) :: Alphabet -> Alphabet -> Bool

(<=) :: Alphabet -> Alphabet -> Bool

(>) :: Alphabet -> Alphabet -> Bool

(>=) :: Alphabet -> Alphabet -> Bool

max :: Alphabet -> Alphabet -> Alphabet

min :: Alphabet -> Alphabet -> Alphabet

Read Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

readsPrec :: Int -> ReadS Alphabet

readList :: ReadS [Alphabet]

readPrec :: ReadPrec Alphabet

readListPrec :: ReadPrec [Alphabet]

Show Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

showsPrec :: Int -> Alphabet -> ShowS

show :: Alphabet -> String

showList :: [Alphabet] -> ShowS

Generic Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Associated Types

type Rep Alphabet :: Type -> Type

Methods

from :: Alphabet -> Rep Alphabet x

to :: Rep Alphabet x -> Alphabet

ToJSON Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

toJSON :: Alphabet -> Value

toEncoding :: Alphabet -> Encoding

toJSONList :: [Alphabet] -> Value

toEncodingList :: [Alphabet] -> Encoding

FromJSON Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

Methods

parseJSON :: Value -> Parser Alphabet

parseJSONList :: Value -> Parser [Alphabet]

type Rep Alphabet

Defined in ELynx.Data.Alphabet.Alphabet

type Rep Alphabet = D1 (MetaData "Alphabet" "ELynx.Data.Alphabet.Alphabet" "elynx-seq-0.3.3-2lTkw1Ov6dH4xWhrrtrFfv" False) ((C1 (MetaCons "DNA" PrefixI False) (U1 :: Type -> Type) :+: (C1 (MetaCons "DNAX" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "DNAI" PrefixI False) (U1 :: Type -> Type))) :+: ((C1 (MetaCons "Protein" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "ProteinX" PrefixI False) (U1 :: Type -> Type)) :+: (C1 (MetaCons "ProteinS" PrefixI False) (U1 :: Type -> Type) :+: C1 (MetaCons "ProteinI" PrefixI False) (U1 :: Type -> Type))))

data AlphabetSpec

Alphabet specification. Set is used because it provides fast lookups.

Constructors

AlphabetSpec

Fields

• std :: !(Set Character)

  Standard characters.

• gap :: !(Set Character)

  Gap characters.

• unknown :: !(Set Character)

  Unknown characters.

• iupac :: !(Set Character)

  Other IUPAC codes.

• all :: !(Set Character)

  All characters in the alphabet.

• toStd :: Character -> [Character]

  Convert from IUPAC to the corresponding standard characters.

alphabetSpec :: Alphabet -> AlphabetSpec

Get the alphabet specification for a given alphabet.

alphabetDescription :: Alphabet -> String

Verbose alphabet name.

isStd :: Alphabet -> Character -> Bool

Test if standard character.

isGap :: Alphabet -> Character -> Bool

Test if gap.

isUnknown :: Alphabet -> Character -> Bool

Test if unknown.

isIUPAC :: Alphabet -> Character -> Bool

Test if extended IUPAC character (excluding gaps and unknowns).

isMember :: Alphabet -> Character -> Bool

Test if member of alphabet.