ELynx.Data.Character.NucleotideX

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)                      -

Documentation

data NucleotideX

Extended nucleotides.

Constructors

A

C

G

T

Gap

Instances

Bounded NucleotideX

Defined in ELynx.Data.Character.NucleotideX

Methods

minBound :: NucleotideX

maxBound :: NucleotideX

Enum NucleotideX

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

Defined in ELynx.Data.Character.NucleotideX

Methods

(==) :: NucleotideX -> NucleotideX -> Bool

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

Ord NucleotideX

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

Defined in ELynx.Data.Character.NucleotideX

Methods

readsPrec :: Int -> ReadS NucleotideX

readList :: ReadS [NucleotideX]

readPrec :: ReadPrec NucleotideX

readListPrec :: ReadPrec [NucleotideX]

Show NucleotideX

Defined in ELynx.Data.Character.NucleotideX

Methods

showsPrec :: Int -> NucleotideX -> ShowS

show :: NucleotideX -> String

showList :: [NucleotideX] -> ShowS

Unbox NucleotideX

Defined in ELynx.Data.Character.NucleotideX

CharacterX NucleotideX

Defined in ELynx.Data.Character.NucleotideX

Methods

gap :: NucleotideX

Character NucleotideX

Defined in ELynx.Data.Character.NucleotideX

Methods

toWord :: NucleotideX -> Word8

fromWord :: Word8 -> NucleotideX

Vector Vector NucleotideX

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

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

Defined in ELynx.Data.Character.NucleotideX

newtype Vector NucleotideX = V_NucleotideX (Vector Word8)

newtype MVector s NucleotideX

Defined in ELynx.Data.Character.NucleotideX

newtype MVector s NucleotideX = MV_NucleotideX (MVector s Word8)