ELynx.Character.Codon

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

Documentation

newtype Codon a

Codons are triplets of characters.

Constructors

Codon (a, a, a)

Instances

Eq a => Eq (Codon a)

Defined in ELynx.Character.Codon

Methods

(==) :: Codon a -> Codon a -> Bool

(/=) :: Codon a -> Codon a -> Bool

Ord a => Ord (Codon a)

Defined in ELynx.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)

Defined in ELynx.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)

Defined in ELynx.Character.Codon

Methods

showsPrec :: Int -> Codon a -> ShowS

show :: Codon a -> String

showList :: [Codon a] -> ShowS

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

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

data UniversalCode

Universal codes.

Constructors

Standard

VertebrateMitochondrial

Instances

Bounded UniversalCode

Defined in ELynx.Character.Codon

Methods

minBound :: UniversalCode

maxBound :: UniversalCode

Enum UniversalCode

Defined in ELynx.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

Defined in ELynx.Character.Codon

Methods

(==) :: UniversalCode -> UniversalCode -> Bool

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

Ord UniversalCode

Defined in ELynx.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

Defined in ELynx.Character.Codon

Methods

readsPrec :: Int -> ReadS UniversalCode

readList :: ReadS [UniversalCode]

readPrec :: ReadPrec UniversalCode

readListPrec :: ReadPrec [UniversalCode]

Show UniversalCode

Defined in ELynx.Character.Codon

Methods

showsPrec :: Int -> UniversalCode -> ShowS

show :: UniversalCode -> String

showList :: [UniversalCode] -> ShowS

Generic UniversalCode

Defined in ELynx.Character.Codon

Associated Types

type Rep UniversalCode :: Type -> Type

Methods

from :: UniversalCode -> Rep UniversalCode x

to :: Rep UniversalCode x -> UniversalCode

ToJSON UniversalCode

Defined in ELynx.Character.Codon

Methods

toJSON :: UniversalCode -> Value

toEncoding :: UniversalCode -> Encoding

toJSONList :: [UniversalCode] -> Value

toEncodingList :: [UniversalCode] -> Encoding

FromJSON UniversalCode

Defined in ELynx.Character.Codon

Methods

parseJSON :: Value -> Parser UniversalCode

parseJSONList :: Value -> Parser [UniversalCode]

type Rep UniversalCode

Defined in ELynx.Character.Codon

type Rep UniversalCode = D1 ('MetaData "UniversalCode" "ELynx.Character.Codon" "elynx-seq-0.7.0.1-KZ4lovqHngFJeEM7MLSEql" 'False) (C1 ('MetaCons "Standard" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "VertebrateMitochondrial" 'PrefixI 'False) (U1 :: Type -> Type))

translate :: UniversalCode -> Codon Nucleotide -> AminoAcidS

Translate a codon to amino acids including translation stops.

translateX :: UniversalCode -> Codon NucleotideX -> AminoAcidS

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

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!