Copyright	(c) Dominik Schrempf 2019
License	GPL-3
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)
unsafeFromList :: [a] -> Codon a
unsafeFromVec :: 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

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 #

unsafeFromList :: [a] -> Codon a Source #

Unsafe conversion from list with three elements.

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

Unsafe conversion from vector with three elements.

data UniversalCode Source #

Universal codes.

Constructors

Standard
VertebrateMitochondrial

Instances

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 #

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. XXX: Be careful, single or two character gaps could have led 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. XXX: Be careful, also translates other IUPAC characters at the moment (to amino acid Xs)! translateI :: UniversalCode -> Codon NI.NucleotideI -> AI.AminoAcidI translateI _ (Codon (NI.N, _, _ )) = AI.X translateI _ (Codon (_ , NI.N, _ )) = AI.X translateI _ (Codon (_, _, NI.N)) = AI.X translateI code codon = C.convert . translateX code . convert $ codon