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module Bio.Alphabet where
import Foreign.String -- For CPPString
import Data.Text (Text)
import qualified Data.Text as T
data Alphabet
data GeneticCode
-- This should only take a Triplets or Codons!
foreign import bpcall "Alphabet:" getNucleotides :: Alphabet -> Alphabet
-- This should only take a Triplets or Codons!
foreign import bpcall "Alphabet:" getAminoAcids :: Alphabet -> Alphabet
foreign import bpcall "Alphabet:" alphabetSize :: Alphabet -> Int
foreign import bpcall "Alphabet:alphabet_letters" builtin_letters :: Alphabet -> EVector CPPString
getLetters a = map listFromString (vectorToList (builtin_letters a) )
foreign import bpcall "Alphabet:find_letter" builtin_find_letter :: Alphabet -> CPPString -> Int
findLetter a letter = builtin_find_letter a (list_to_string letter)
foreign import bpcall "Alphabet:" translate :: Alphabet -> Int -> Int
foreign import bpcall "Alphabet:" mkDoublets :: Alphabet -> Alphabet
foreign import bpcall "Alphabet:" mkRNAEdits :: Alphabet -> Alphabet
foreign import bpcall "Alphabet:" mkTriplets :: Alphabet -> Alphabet
foreign import bpcall "Alphabet:" mkCodons :: Alphabet -> GeneticCode -> Alphabet
foreign import bpcall "Alphabet:dna" builtin_dna :: () -> Alphabet
dna = builtin_dna ()
foreign import bpcall "Alphabet:rna" builtin_rna :: () -> Alphabet
rna = builtin_rna ()
foreign import bpcall "Alphabet:aa" builtin_aa :: () -> Alphabet
aa = builtin_aa ()
amino_acids = builtin_aa
foreign import bpcall "Alphabet:aaWithStop" builtin_aaWithStop :: () -> Alphabet
aaWithStop = builtin_aaWithStop ()
amino_acids_with_stop = builtin_aaWithStop ()
foreign import bpcall "Alphabet:" mkNumeric :: Int -> Alphabet
-- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
foreign import bpcall "Alphabet:" geneticCodeByNumber :: Int -> GeneticCode
foreign import bpcall "Alphabet:" geneticCodeRaw :: CPPString -> GeneticCode
geneticCode name = geneticCodeRaw (pack_cpp_string name)
standard_code = geneticCodeByNumber 1
foreign import bpcall "Alphabet:" sequenceToTextRaw :: Alphabet -> EVector Int -> CPPString
sequenceToText a s = T.fromCppString $ sequenceToTextRaw a s
class HasAlphabet x where
getAlphabet :: x -> Alphabet
gapCharIndex = -1 :: Int
missingCharIndex = -2 :: Int
type SMap = EVector Int
class HasAlphabet x => HasSMap x where
getSMap :: x -> SMap
instance Show Alphabet where
show a = show (getLetters a)
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