-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Initial project template from stack
--   
--   Please see README.md
@package bio-sequence
@version 0.1.0.0

module Bio.Sequence.AminoAcid
data AminoAcid
Alanine :: AminoAcid
Glycine :: AminoAcid
Valine :: AminoAcid
Isoleucine :: AminoAcid
Leucine :: AminoAcid
Methionine :: AminoAcid
Phenylalanine :: AminoAcid
Tyrosine :: AminoAcid
Tryptophan :: AminoAcid
Serine :: AminoAcid
Threonine :: AminoAcid
Asparagine :: AminoAcid
Glutamine :: AminoAcid
Cysteine :: AminoAcid
Proline :: AminoAcid
Arginine :: AminoAcid
Histidine :: AminoAcid
Lysine :: AminoAcid
AsparticAcid :: AminoAcid
GlutamicAcid :: AminoAcid
AcetylGroup :: AminoAcid
MetilAmine :: AminoAcid
shortName3 :: AminoAcid -> String
shortName :: AminoAcid -> Char
fromChar :: Char -> AminoAcid
fromShortCode :: String -> AminoAcid

module Bio.Sequence.Alignment.Matrix
class ScoringMatrix a
scoring :: ScoringMatrix a => a -> Substitution Char
data BLOSUM62
BLOSUM62 :: BLOSUM62
data PAM250
PAM250 :: PAM250
data NUC44
NUC44 :: NUC44
blosum62 :: Substitution Char
pam250 :: Substitution Char
nuc44 :: Substitution Char
matrix :: QuasiQuoter
instance GHC.Classes.Eq Bio.Sequence.Alignment.Matrix.NUC44
instance GHC.Show.Show Bio.Sequence.Alignment.Matrix.NUC44
instance GHC.Classes.Eq Bio.Sequence.Alignment.Matrix.PAM250
instance GHC.Show.Show Bio.Sequence.Alignment.Matrix.PAM250
instance GHC.Classes.Eq Bio.Sequence.Alignment.Matrix.BLOSUM62
instance GHC.Show.Show Bio.Sequence.Alignment.Matrix.BLOSUM62
instance Bio.Sequence.Alignment.Internal.Matrix.Scoring.ScoringMatrix Bio.Sequence.Alignment.Matrix.BLOSUM62
instance Bio.Sequence.Alignment.Internal.Matrix.Scoring.ScoringMatrix Bio.Sequence.Alignment.Matrix.PAM250
instance Bio.Sequence.Alignment.Internal.Matrix.Scoring.ScoringMatrix Bio.Sequence.Alignment.Matrix.NUC44

module Bio.Sequence.Alignment

-- | Substitution function for <tt>a</tt> values comparison
type Substitution a = a -> a -> Int

-- | Gap type
type Gap = Int

-- | Introduces all useful methods to create an alignment
class Alignment a
gap :: Alignment a => a -> Gap
substitution :: Alignment a => a -> Substitution Char
conditions :: Alignment a => a -> Conditions
inits :: Alignment a => a -> Int -> Int
selector :: Alignment a => a -> StartSelector
additional :: Alignment a => a -> Int
alignment :: Alignment a => a -> ByteString -> ByteString -> (Int, (ByteString, ByteString))
mkGlobal :: Substitution Char -> Gap -> SimpleAlignment
mkLocal :: Substitution Char -> Gap -> SimpleAlignment
mkSemiglobal :: Substitution Char -> Gap -> SimpleAlignment
mkEditDistance :: EditDistance

module Bio.Sequence.Alignment.Scoring
similarity :: ByteString -> ByteString -> Float
hamming :: ByteString -> ByteString -> Int
relativeHamming :: ByteString -> ByteString -> Float
alignmentScore :: Substitution Char -> ByteString -> ByteString -> Int
alignmentSemiglobalScore :: Substitution Char -> ByteString -> ByteString -> Int

module Bio.Macro
data MacroMolecule a r
MacroMolecule :: !String -> ![Chain a r] -> MacroMolecule a r
[mmName] :: MacroMolecule a r -> !String
[mmChains] :: MacroMolecule a r -> ![Chain a r]
data Chain t r
Chain :: !t -> ![r] -> Chain t r
[chainType] :: Chain t r -> !t
[chainResidues] :: Chain t r -> ![r]

module Bio.Sequence
type Sequence = Chain Text
data Chain t r
Chain :: !t -> ![r] -> Chain t r
[chainType] :: Chain t r -> !t
[chainResidues] :: Chain t r -> ![r]

module Bio.Sequence.Parser.Fasta
fastaParser :: Parser [Sequence Char]
aminoParser :: Parser [Sequence AminoAcid]