Copyright	(c) Dominik Schrempf 2021
License	GPL-3.0-or-later
Maintainer	dominik.schrempf@gmail.com
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

ELynx.Data.Character.Codon

Description

Creation date: Thu May 16 07:58:50 2019.

The different universal codes. - https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c - http://www.bioinformatics.org/sms2/genetic_code.html - https://en.wikipedia.org/wiki/Genetic_code

Synopsis

newtype Codon a = Codon (a, a, a)
fromVecUnsafe :: Vector v a => v a -> Codon a
data UniversalCode
- = Standard
- | VertebrateMitochondrial
translate :: UniversalCode -> Codon Nucleotide -> AminoAcidS
translateX :: UniversalCode -> Codon NucleotideX -> AminoAcidS
translateI :: UniversalCode -> Codon NucleotideI -> AminoAcidI

Documentation

newtype Codon a Source #

Codons are triplets of characters.

Constructors

Codon (a, a, a)

Instances

Instances details

Eq a => Eq (Codon a) Source #
Instance details Defined in ELynx.Data.Character.Codon Methods (==) :: Codon a -> Codon a -> Bool # (/=) :: Codon a -> Codon a -> Bool #
Ord a => Ord (Codon a) Source #
Instance details Defined in ELynx.Data.Character.Codon Methods compare :: Codon a -> Codon a -> Ordering # (<) :: Codon a -> Codon a -> Bool # (<=) :: Codon a -> Codon a -> Bool # (>) :: Codon a -> Codon a -> Bool # (>=) :: Codon a -> Codon a -> Bool # max :: Codon a -> Codon a -> Codon a # min :: Codon a -> Codon a -> Codon a #
Read a => Read (Codon a) Source #
Instance details Defined in ELynx.Data.Character.Codon Methods readsPrec :: Int -> ReadS (Codon a) # readList :: ReadS [Codon a] # readPrec :: ReadPrec (Codon a) # readListPrec :: ReadPrec [Codon a] #
Show a => Show (Codon a) Source #
Instance details Defined in ELynx.Data.Character.Codon Methods showsPrec :: Int -> Codon a -> ShowS # show :: Codon a -> String # showList :: [Codon a] -> ShowS #

fromVecUnsafe :: Vector v a => v a -> Codon a Source #

Unsafe conversion from vector with at least three elements; only the first three elements are used, the rest is discarded.

data UniversalCode Source #

Universal codes.

Constructors

Standard
VertebrateMitochondrial

Instances

Instances details

Bounded UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods minBound :: UniversalCode # maxBound :: UniversalCode #
Enum UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods succ :: UniversalCode -> UniversalCode # pred :: UniversalCode -> UniversalCode # toEnum :: Int -> UniversalCode # fromEnum :: UniversalCode -> Int # enumFrom :: UniversalCode -> [UniversalCode] # enumFromThen :: UniversalCode -> UniversalCode -> [UniversalCode] # enumFromTo :: UniversalCode -> UniversalCode -> [UniversalCode] # enumFromThenTo :: UniversalCode -> UniversalCode -> UniversalCode -> [UniversalCode] #
Eq UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods (==) :: UniversalCode -> UniversalCode -> Bool # (/=) :: UniversalCode -> UniversalCode -> Bool #
Ord UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods compare :: UniversalCode -> UniversalCode -> Ordering # (<) :: UniversalCode -> UniversalCode -> Bool # (<=) :: UniversalCode -> UniversalCode -> Bool # (>) :: UniversalCode -> UniversalCode -> Bool # (>=) :: UniversalCode -> UniversalCode -> Bool # max :: UniversalCode -> UniversalCode -> UniversalCode # min :: UniversalCode -> UniversalCode -> UniversalCode #
Read UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods readsPrec :: Int -> ReadS UniversalCode # readList :: ReadS [UniversalCode] # readPrec :: ReadPrec UniversalCode # readListPrec :: ReadPrec [UniversalCode] #
Show UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods showsPrec :: Int -> UniversalCode -> ShowS # show :: UniversalCode -> String # showList :: [UniversalCode] -> ShowS #
Generic UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Associated Types type Rep UniversalCode :: Type -> Type # Methods from :: UniversalCode -> Rep UniversalCode x # to :: Rep UniversalCode x -> UniversalCode #
ToJSON UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods toJSON :: UniversalCode -> Value # toEncoding :: UniversalCode -> Encoding # toJSONList :: [UniversalCode] -> Value # toEncodingList :: [UniversalCode] -> Encoding #
FromJSON UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon Methods parseJSON :: Value -> Parser UniversalCode # parseJSONList :: Value -> Parser [UniversalCode] #
type Rep UniversalCode Source #
Instance details Defined in ELynx.Data.Character.Codon type Rep UniversalCode = D1 ('MetaData "UniversalCode" "ELynx.Data.Character.Codon" "elynx-seq-0.6.0.0-LtTbvishThEEtvOIpTEQaG" 'False) (C1 ('MetaCons "Standard" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "VertebrateMitochondrial" 'PrefixI 'False) (U1 :: Type -> Type))

translate :: UniversalCode -> Codon Nucleotide -> AminoAcidS Source #

Translate a codon to amino acids including translation stops.

translateX :: UniversalCode -> Codon NucleotideX -> AminoAcidS Source #

Translate a codon to amino acids including translation stops. Translate codons including gaps to amino acid gaps. Be careful, single or two character gaps can lead to a reading frame shift and hence, the translated sequence may be bogus.

translateI :: UniversalCode -> Codon NucleotideI -> AminoAcidI Source #

Translate a codon to amino acids including translation stops. Translate gap triplets to amino acid gaps, and triplets including unknowns to amino acid unknowns. Be careful, also translates other IUPAC characters to amino acid Xs!