Copyright	2021 Dominik Schrempf
License	GPL-3.0-or-later
Maintainer	[email protected]
Stability	unstable
Portability	portable
Safe Haskell	None
Language	Haskell2010

ELynx.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.Character.NucleotideX Methods minBound :: NucleotideX # maxBound :: NucleotideX #
Enum NucleotideX Source #
Instance details Defined in ELynx.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] #
Read NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX Methods readsPrec :: Int -> ReadS NucleotideX # readList :: ReadS [NucleotideX] # readPrec :: ReadPrec NucleotideX # readListPrec :: ReadPrec [NucleotideX] #
Show NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX Methods showsPrec :: Int -> NucleotideX -> ShowS # show :: NucleotideX -> String # showList :: [NucleotideX] -> ShowS #
Character NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX Methods toWord :: NucleotideX -> Word8 Source # fromWord :: Word8 -> NucleotideX Source #
CharacterX NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX Methods gap :: NucleotideX Source #
Eq NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX Methods (==) :: NucleotideX -> NucleotideX -> Bool # (/=) :: NucleotideX -> NucleotideX -> Bool #
Ord NucleotideX Source #
Instance details Defined in ELynx.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 #
Unbox NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX
Vector Vector NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX Methods basicUnsafeFreeze :: Mutable Vector s NucleotideX -> ST s (Vector NucleotideX) basicUnsafeThaw :: Vector NucleotideX -> ST s (Mutable Vector s NucleotideX) basicLength :: Vector NucleotideX -> Int basicUnsafeSlice :: Int -> Int -> Vector NucleotideX -> Vector NucleotideX basicUnsafeIndexM :: Vector NucleotideX -> Int -> Box NucleotideX basicUnsafeCopy :: Mutable Vector s NucleotideX -> Vector NucleotideX -> ST s () elemseq :: Vector NucleotideX -> NucleotideX -> b -> b
MVector MVector NucleotideX Source #
Instance details Defined in ELynx.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 :: Int -> ST s (MVector s NucleotideX) basicInitialize :: MVector s NucleotideX -> ST s () basicUnsafeReplicate :: Int -> NucleotideX -> ST s (MVector s NucleotideX) basicUnsafeRead :: MVector s NucleotideX -> Int -> ST s NucleotideX basicUnsafeWrite :: MVector s NucleotideX -> Int -> NucleotideX -> ST s () basicClear :: MVector s NucleotideX -> ST s () basicSet :: MVector s NucleotideX -> NucleotideX -> ST s () basicUnsafeCopy :: MVector s NucleotideX -> MVector s NucleotideX -> ST s () basicUnsafeMove :: MVector s NucleotideX -> MVector s NucleotideX -> ST s () basicUnsafeGrow :: MVector s NucleotideX -> Int -> ST s (MVector s NucleotideX)
newtype Vector NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX newtype Vector NucleotideX = V_NucleotideX (Vector Word8)
newtype MVector s NucleotideX Source #
Instance details Defined in ELynx.Character.NucleotideX newtype MVector s NucleotideX = MV_NucleotideX (MVector s Word8)