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.NucleotideX

Description

See header of Alphabet.

Extended nucleotides with gaps. See also https://www.bioinformatics.org/sms/iupac.html or https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry.

Symbol  Description  Bases represented  Complement
------  -----------  -----------------  ----------
A       Adenine      A                  T
C       Cytosine        C               G
G       Guanine            G            C
T       Thymine               T         A
------  -----------  -----------------  ----------
- or .  Gap (Zero)                      -

Synopsis

data NucleotideX
- = A
- | C
- | G
- | T
- | Gap

Documentation

data NucleotideX Source #

Extended nucleotides.

Constructors

A
C
G
T
Gap

Instances

Instances details

Bounded NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods minBound :: NucleotideX # maxBound :: NucleotideX #
Enum NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods succ :: NucleotideX -> NucleotideX # pred :: NucleotideX -> NucleotideX # toEnum :: Int -> NucleotideX # fromEnum :: NucleotideX -> Int # enumFrom :: NucleotideX -> [NucleotideX] # enumFromThen :: NucleotideX -> NucleotideX -> [NucleotideX] # enumFromTo :: NucleotideX -> NucleotideX -> [NucleotideX] # enumFromThenTo :: NucleotideX -> NucleotideX -> NucleotideX -> [NucleotideX] #
Eq NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods (==) :: NucleotideX -> NucleotideX -> Bool # (/=) :: NucleotideX -> NucleotideX -> Bool #
Ord NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods compare :: NucleotideX -> NucleotideX -> Ordering # (<) :: NucleotideX -> NucleotideX -> Bool # (<=) :: NucleotideX -> NucleotideX -> Bool # (>) :: NucleotideX -> NucleotideX -> Bool # (>=) :: NucleotideX -> NucleotideX -> Bool # max :: NucleotideX -> NucleotideX -> NucleotideX # min :: NucleotideX -> NucleotideX -> NucleotideX #
Read NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods readsPrec :: Int -> ReadS NucleotideX # readList :: ReadS [NucleotideX] # readPrec :: ReadPrec NucleotideX # readListPrec :: ReadPrec [NucleotideX] #
Show NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods showsPrec :: Int -> NucleotideX -> ShowS # show :: NucleotideX -> String # showList :: [NucleotideX] -> ShowS #
Unbox NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX
CharacterX NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods gap :: NucleotideX Source #
Character NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods toWord :: NucleotideX -> Word8 Source # fromWord :: Word8 -> NucleotideX Source #
Vector Vector NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) NucleotideX -> m (Vector NucleotideX) # basicUnsafeThaw :: PrimMonad m => Vector NucleotideX -> m (Mutable Vector (PrimState m) NucleotideX) # basicLength :: Vector NucleotideX -> Int # basicUnsafeSlice :: Int -> Int -> Vector NucleotideX -> Vector NucleotideX # basicUnsafeIndexM :: Monad m => Vector NucleotideX -> Int -> m NucleotideX # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) NucleotideX -> Vector NucleotideX -> m () # elemseq :: Vector NucleotideX -> NucleotideX -> b -> b #
MVector MVector NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX Methods basicLength :: MVector s NucleotideX -> Int # basicUnsafeSlice :: Int -> Int -> MVector s NucleotideX -> MVector s NucleotideX # basicOverlaps :: MVector s NucleotideX -> MVector s NucleotideX -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) NucleotideX) # basicInitialize :: PrimMonad m => MVector (PrimState m) NucleotideX -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> NucleotideX -> m (MVector (PrimState m) NucleotideX) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) NucleotideX -> Int -> m NucleotideX # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) NucleotideX -> Int -> NucleotideX -> m () # basicClear :: PrimMonad m => MVector (PrimState m) NucleotideX -> m () # basicSet :: PrimMonad m => MVector (PrimState m) NucleotideX -> NucleotideX -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) NucleotideX -> MVector (PrimState m) NucleotideX -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) NucleotideX -> MVector (PrimState m) NucleotideX -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) NucleotideX -> Int -> m (MVector (PrimState m) NucleotideX) #
newtype Vector NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX newtype Vector NucleotideX = V_NucleotideX (Vector Word8)
newtype MVector s NucleotideX Source #
Instance details Defined in ELynx.Data.Character.NucleotideX newtype MVector s NucleotideX = MV_NucleotideX (MVector s Word8)