ELynx.Data.Character.NucleotideI

Creation date: Thu Oct 4 18:26:35 2018.

See header of Alphabet.

Nucleotide IUPAC code. See also https://www.bioinformatics.org/sms/iupac.html or https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry.

Remarks:

• Question marks (?) are interpreted as unknowns (same as N). However, when a sequence is printed/exported, Ns will be used.
• Full stops (.) are interpreted as gaps (same as -). However, when a sequence is printed/exported, -s will be used

Symbol  Description  Bases represented  Complement
------  -----------  -----------------  ----------
A       Adenine      A                  T
C       Cytosine        C               G
G       Guanine            G            C
T       Thymine               T         A
------  -----------  -----------------  ----------
U       Uracil                U         A
W       Weak         A        T         W
S       Strong          C  G            S
M       aMino        A  C               K
K       Keto               G  T         M
R       puRine       A     G            Y
Y       pYrimidine      C     T         R
B       not A           C  G  T         V
D       not C        A     G  T         H
H       not G        A  C     T         D
V       not T        A  C  G            B
------  -----------  -----------------  ----------
N       any          A  C  G  T         N           (preferred)
?       any          A  C  G  T         N
------  -----------  -----------------  ----------
-       Gap (Zero)                      -           (preferred)
.       Gap (Zero)                      -

Documentation

data NucleotideI

NucleotideIs.

Constructors

A

C

G

T

U

W

S

M

K

R

Y

B

D

H

V

N

Gap

Instances

Bounded NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

minBound :: NucleotideI

maxBound :: NucleotideI

Enum NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

succ :: NucleotideI -> NucleotideI

pred :: NucleotideI -> NucleotideI

toEnum :: Int -> NucleotideI

fromEnum :: NucleotideI -> Int

enumFrom :: NucleotideI -> [NucleotideI]

enumFromThen :: NucleotideI -> NucleotideI -> [NucleotideI]

enumFromTo :: NucleotideI -> NucleotideI -> [NucleotideI]

enumFromThenTo :: NucleotideI -> NucleotideI -> NucleotideI -> [NucleotideI]

Eq NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

(==) :: NucleotideI -> NucleotideI -> Bool

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

Ord NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

compare :: NucleotideI -> NucleotideI -> Ordering

(<) :: NucleotideI -> NucleotideI -> Bool

(<=) :: NucleotideI -> NucleotideI -> Bool

(>) :: NucleotideI -> NucleotideI -> Bool

(>=) :: NucleotideI -> NucleotideI -> Bool

max :: NucleotideI -> NucleotideI -> NucleotideI

min :: NucleotideI -> NucleotideI -> NucleotideI

Read NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

readsPrec :: Int -> ReadS NucleotideI

readList :: ReadS [NucleotideI]

readPrec :: ReadPrec NucleotideI

readListPrec :: ReadPrec [NucleotideI]

Show NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

showsPrec :: Int -> NucleotideI -> ShowS

show :: NucleotideI -> String

showList :: [NucleotideI] -> ShowS

Unbox NucleotideI

Defined in ELynx.Data.Character.NucleotideI

CharacterI NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

unknown :: NucleotideI

iupac :: [NucleotideI]

toStandard :: NucleotideI -> [NucleotideI]

CharacterX NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

gap :: NucleotideI

Character NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

toWord :: NucleotideI -> Word8

fromWord :: Word8 -> NucleotideI

Vector Vector NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) NucleotideI -> m (Vector NucleotideI)

basicUnsafeThaw :: PrimMonad m => Vector NucleotideI -> m (Mutable Vector (PrimState m) NucleotideI)

basicLength :: Vector NucleotideI -> Int

basicUnsafeSlice :: Int -> Int -> Vector NucleotideI -> Vector NucleotideI

basicUnsafeIndexM :: Monad m => Vector NucleotideI -> Int -> m NucleotideI

basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) NucleotideI -> Vector NucleotideI -> m ()

elemseq :: Vector NucleotideI -> NucleotideI -> b -> b

MVector MVector NucleotideI

Defined in ELynx.Data.Character.NucleotideI

Methods

basicLength :: MVector s NucleotideI -> Int

basicUnsafeSlice :: Int -> Int -> MVector s NucleotideI -> MVector s NucleotideI

basicOverlaps :: MVector s NucleotideI -> MVector s NucleotideI -> Bool

basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) NucleotideI)

basicInitialize :: PrimMonad m => MVector (PrimState m) NucleotideI -> m ()

basicUnsafeReplicate :: PrimMonad m => Int -> NucleotideI -> m (MVector (PrimState m) NucleotideI)

basicUnsafeRead :: PrimMonad m => MVector (PrimState m) NucleotideI -> Int -> m NucleotideI

basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) NucleotideI -> Int -> NucleotideI -> m ()

basicClear :: PrimMonad m => MVector (PrimState m) NucleotideI -> m ()

basicSet :: PrimMonad m => MVector (PrimState m) NucleotideI -> NucleotideI -> m ()

basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) NucleotideI -> MVector (PrimState m) NucleotideI -> m ()

basicUnsafeMove :: PrimMonad m => MVector (PrimState m) NucleotideI -> MVector (PrimState m) NucleotideI -> m ()

basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) NucleotideI -> Int -> m (MVector (PrimState m) NucleotideI)

newtype Vector NucleotideI

Defined in ELynx.Data.Character.NucleotideI

newtype Vector NucleotideI = V_NucleotideI (Vector Word8)

newtype MVector s NucleotideI

Defined in ELynx.Data.Character.NucleotideI

newtype MVector s NucleotideI = MV_NucleotideI (MVector s Word8)