Biobase.Primary.Letter

A newtype with an attached phenotype which allows us to encode nucleotides and amino acids. Actual seqence-specific functions can be founds in the appropriate modules AA and Nuc.

Documentation

newtype Letter t

A Letter together with its phantom type t encodes bio-sequences.

Constructors

Letter

Fields

• getLetter :: Int

Instances

IsostericityLookup ExtPair

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

Methods

getClasses :: ExtPair -> [String]

inClass :: String -> [ExtPair]

IsostericityLookup Pair

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Methods

getClasses :: Pair -> [String]

inClass :: String -> [Pair]

Vector Vector (Letter a0)

Methods

basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) (Letter a0) -> m (Vector (Letter a0))

basicUnsafeThaw :: PrimMonad m => Vector (Letter a0) -> m (Mutable Vector (PrimState m) (Letter a0))

basicLength :: Vector (Letter a0) -> Int

basicUnsafeSlice :: Int -> Int -> Vector (Letter a0) -> Vector (Letter a0)

basicUnsafeIndexM :: Monad m => Vector (Letter a0) -> Int -> m (Letter a0)

basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) (Letter a0) -> Vector (Letter a0) -> m ()

elemseq :: Vector (Letter a0) -> Letter a0 -> b -> b

MVector MVector (Letter a0)

Methods

basicLength :: MVector s (Letter a0) -> Int

basicUnsafeSlice :: Int -> Int -> MVector s (Letter a0) -> MVector s (Letter a0)

basicOverlaps :: MVector s (Letter a0) -> MVector s (Letter a0) -> Bool

basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) (Letter a0))

basicInitialize :: PrimMonad m => MVector (PrimState m) (Letter a0) -> m ()

basicUnsafeReplicate :: PrimMonad m => Int -> Letter a0 -> m (MVector (PrimState m) (Letter a0))

basicUnsafeRead :: PrimMonad m => MVector (PrimState m) (Letter a0) -> Int -> m (Letter a0)

basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) (Letter a0) -> Int -> Letter a0 -> m ()

basicClear :: PrimMonad m => MVector (PrimState m) (Letter a0) -> m ()

basicSet :: PrimMonad m => MVector (PrimState m) (Letter a0) -> Letter a0 -> m ()

basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) (Letter a0) -> MVector (PrimState m) (Letter a0) -> m ()

basicUnsafeMove :: PrimMonad m => MVector (PrimState m) (Letter a0) -> MVector (PrimState m) (Letter a0) -> m ()

basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) (Letter a0) -> Int -> m (MVector (PrimState m) (Letter a0))

Bounded (Letter RNA)

Methods

minBound :: Letter RNA

maxBound :: Letter RNA

Bounded (Letter DNA)

Methods

minBound :: Letter DNA

maxBound :: Letter DNA

Bounded (Letter XNA)

Methods

minBound :: Letter XNA

maxBound :: Letter XNA

Bounded (Letter DEG)

Methods

minBound :: Letter DEG

maxBound :: Letter DEG

Enum (Letter Unknown)

Methods

succ :: Letter Unknown -> Letter Unknown

pred :: Letter Unknown -> Letter Unknown

toEnum :: Int -> Letter Unknown

fromEnum :: Letter Unknown -> Int

enumFrom :: Letter Unknown -> [Letter Unknown]

enumFromThen :: Letter Unknown -> Letter Unknown -> [Letter Unknown]

enumFromTo :: Letter Unknown -> Letter Unknown -> [Letter Unknown]

enumFromThenTo :: Letter Unknown -> Letter Unknown -> Letter Unknown -> [Letter Unknown]

Enum (Letter RNA)

Methods

succ :: Letter RNA -> Letter RNA

pred :: Letter RNA -> Letter RNA

toEnum :: Int -> Letter RNA

fromEnum :: Letter RNA -> Int

enumFrom :: Letter RNA -> [Letter RNA]

enumFromThen :: Letter RNA -> Letter RNA -> [Letter RNA]

enumFromTo :: Letter RNA -> Letter RNA -> [Letter RNA]

enumFromThenTo :: Letter RNA -> Letter RNA -> Letter RNA -> [Letter RNA]

Enum (Letter DNA)

Methods

succ :: Letter DNA -> Letter DNA

pred :: Letter DNA -> Letter DNA

toEnum :: Int -> Letter DNA

fromEnum :: Letter DNA -> Int

enumFrom :: Letter DNA -> [Letter DNA]

enumFromThen :: Letter DNA -> Letter DNA -> [Letter DNA]

enumFromTo :: Letter DNA -> Letter DNA -> [Letter DNA]

enumFromThenTo :: Letter DNA -> Letter DNA -> Letter DNA -> [Letter DNA]

Enum (Letter XNA)

Methods

succ :: Letter XNA -> Letter XNA

pred :: Letter XNA -> Letter XNA

toEnum :: Int -> Letter XNA

fromEnum :: Letter XNA -> Int

enumFrom :: Letter XNA -> [Letter XNA]

enumFromThen :: Letter XNA -> Letter XNA -> [Letter XNA]

enumFromTo :: Letter XNA -> Letter XNA -> [Letter XNA]

enumFromThenTo :: Letter XNA -> Letter XNA -> Letter XNA -> [Letter XNA]

Enum (Letter DEG)

Methods

succ :: Letter DEG -> Letter DEG

pred :: Letter DEG -> Letter DEG

toEnum :: Int -> Letter DEG

fromEnum :: Letter DEG -> Int

enumFrom :: Letter DEG -> [Letter DEG]

enumFromThen :: Letter DEG -> Letter DEG -> [Letter DEG]

enumFromTo :: Letter DEG -> Letter DEG -> [Letter DEG]

enumFromThenTo :: Letter DEG -> Letter DEG -> Letter DEG -> [Letter DEG]

Enum (Letter AA)

Methods

succ :: Letter AA -> Letter AA

pred :: Letter AA -> Letter AA

toEnum :: Int -> Letter AA

fromEnum :: Letter AA -> Int

enumFrom :: Letter AA -> [Letter AA]

enumFromThen :: Letter AA -> Letter AA -> [Letter AA]

enumFromTo :: Letter AA -> Letter AA -> [Letter AA]

enumFromThenTo :: Letter AA -> Letter AA -> Letter AA -> [Letter AA]

Eq (Letter t)

Methods

(==) :: Letter t -> Letter t -> Bool

(/=) :: Letter t -> Letter t -> Bool

Ord (Letter t)

Methods

compare :: Letter t -> Letter t -> Ordering

(<) :: Letter t -> Letter t -> Bool

(<=) :: Letter t -> Letter t -> Bool

(>) :: Letter t -> Letter t -> Bool

(>=) :: Letter t -> Letter t -> Bool

max :: Letter t -> Letter t -> Letter t

min :: Letter t -> Letter t -> Letter t

Read (Letter Unknown)

Methods

readsPrec :: Int -> ReadS (Letter Unknown)

readList :: ReadS [Letter Unknown]

readPrec :: ReadPrec (Letter Unknown)

readListPrec :: ReadPrec [Letter Unknown]

Read (Letter RNA)

Methods

readsPrec :: Int -> ReadS (Letter RNA)

readList :: ReadS [Letter RNA]

readPrec :: ReadPrec (Letter RNA)

readListPrec :: ReadPrec [Letter RNA]

Read (Letter DNA)

Methods

readsPrec :: Int -> ReadS (Letter DNA)

readList :: ReadS [Letter DNA]

readPrec :: ReadPrec (Letter DNA)

readListPrec :: ReadPrec [Letter DNA]

Read (Letter XNA)

Methods

readsPrec :: Int -> ReadS (Letter XNA)

readList :: ReadS [Letter XNA]

readPrec :: ReadPrec (Letter XNA)

readListPrec :: ReadPrec [Letter XNA]

Read (Letter AA)

Methods

readsPrec :: Int -> ReadS (Letter AA)

readList :: ReadS [Letter AA]

readPrec :: ReadPrec (Letter AA)

readListPrec :: ReadPrec [Letter AA]

Show (Letter Unknown)

Methods

showsPrec :: Int -> Letter Unknown -> ShowS

show :: Letter Unknown -> String

showList :: [Letter Unknown] -> ShowS

Show (Letter RNA)

Methods

showsPrec :: Int -> Letter RNA -> ShowS

show :: Letter RNA -> String

showList :: [Letter RNA] -> ShowS

Show (Letter DNA)

Methods

showsPrec :: Int -> Letter DNA -> ShowS

show :: Letter DNA -> String

showList :: [Letter DNA] -> ShowS

Show (Letter XNA)

Methods

showsPrec :: Int -> Letter XNA -> ShowS

show :: Letter XNA -> String

showList :: [Letter XNA] -> ShowS

Show (Letter DEG)

Methods

showsPrec :: Int -> Letter DEG -> ShowS

show :: Letter DEG -> String

showList :: [Letter DEG] -> ShowS

Show (Letter AA)

Methods

showsPrec :: Int -> Letter AA -> ShowS

show :: Letter AA -> String

showList :: [Letter AA] -> ShowS

Ix (Letter t)

Methods

range :: (Letter t, Letter t) -> [Letter t]

index :: (Letter t, Letter t) -> Letter t -> Int

unsafeIndex :: (Letter t, Letter t) -> Letter t -> Int

inRange :: (Letter t, Letter t) -> Letter t -> Bool

rangeSize :: (Letter t, Letter t) -> Int

unsafeRangeSize :: (Letter t, Letter t) -> Int

IsString [Letter RNA]

Methods

fromString :: String -> [Letter RNA]

IsString [Letter DNA]

Methods

fromString :: String -> [Letter DNA]

IsString [Letter XNA]

Methods

fromString :: String -> [Letter XNA]

IsString [Letter DEG]

Methods

fromString :: String -> [Letter DEG]

(Unbox (Letter t), IsString [Letter t]) => IsString (Vector (Letter t))

Methods

fromString :: String -> Vector (Letter t)

Generic (Letter t)

Associated Types

type Rep (Letter t) :: * -> *

Methods

from :: Letter t -> Rep (Letter t) x

to :: Rep (Letter t) x -> Letter t

Index (Letter l)

Methods

linearIndex :: Letter l -> Letter l -> Letter l -> Int

smallestLinearIndex :: Letter l -> Int

largestLinearIndex :: Letter l -> Int

size :: Letter l -> Letter l -> Int

inBounds :: Letter l -> Letter l -> Letter l -> Bool

IndexStream (Letter l)

Methods

streamUp :: Monad m => Letter l -> Letter l -> Stream m (Letter l)

streamDown :: Monad m => Letter l -> Letter l -> Stream m (Letter l)

Hashable (Letter t)

Methods

hashWithSalt :: Int -> Letter t -> Int

hash :: Letter t -> Int

MkPrimary (Vector Char) DNA => FromJSON (Primary DNA)

Methods

parseJSON :: Value -> Parser (Primary DNA)

parseJSONList :: Value -> Parser [Primary DNA]

MkPrimary (Vector Char) XNA => FromJSON (Primary XNA)

Methods

parseJSON :: Value -> Parser (Primary XNA)

parseJSONList :: Value -> Parser [Primary XNA]

FromJSON (Letter Unknown)

Methods

parseJSON :: Value -> Parser (Letter Unknown)

parseJSONList :: Value -> Parser [Letter Unknown]

FromJSON (Letter RNA)

Methods

parseJSON :: Value -> Parser (Letter RNA)

parseJSONList :: Value -> Parser [Letter RNA]

FromJSON (Letter AA)

Methods

parseJSON :: Value -> Parser (Letter AA)

parseJSONList :: Value -> Parser [Letter AA]

LetterChar DNA => ToJSON (Primary DNA)

Methods

toJSON :: Primary DNA -> Value

toEncoding :: Primary DNA -> Encoding

toJSONList :: [Primary DNA] -> Value

toEncodingList :: [Primary DNA] -> Encoding

LetterChar XNA => ToJSON (Primary XNA)

Methods

toJSON :: Primary XNA -> Value

toEncoding :: Primary XNA -> Encoding

toJSONList :: [Primary XNA] -> Value

toEncodingList :: [Primary XNA] -> Encoding

ToJSON (Letter Unknown)

Methods

toJSON :: Letter Unknown -> Value

toEncoding :: Letter Unknown -> Encoding

toJSONList :: [Letter Unknown] -> Value

toEncodingList :: [Letter Unknown] -> Encoding

ToJSON (Letter RNA)

Methods

toJSON :: Letter RNA -> Value

toEncoding :: Letter RNA -> Encoding

toJSONList :: [Letter RNA] -> Value

toEncodingList :: [Letter RNA] -> Encoding

ToJSON (Letter AA)

Methods

toJSON :: Letter AA -> Value

toEncoding :: Letter AA -> Encoding

toJSONList :: [Letter AA] -> Value

toEncodingList :: [Letter AA] -> Encoding

Binary (Letter t)

Methods

put :: Letter t -> Put

get :: Get (Letter t)

Serialize (Letter t)

Methods

put :: Putter (Letter t)

get :: Get (Letter t)

NFData (Letter t)

Methods

rnf :: Letter t -> ()

Unbox (Letter a0)

Degenerate (Letter RNA)

Methods

fromDegenerate :: Char -> [Letter RNA]

toDegenerate :: [Letter RNA] -> Maybe Char

Degenerate (Letter DNA)

Methods

fromDegenerate :: Char -> [Letter DNA]

toDegenerate :: [Letter DNA] -> Maybe Char

Degenerate (Letter XNA)

Methods

fromDegenerate :: Char -> [Letter XNA]

toDegenerate :: [Letter XNA] -> Maybe Char

Complement (Letter RNA) (Letter RNA)

Methods

complement :: Letter RNA -> Letter RNA

Complement (Letter RNA) (Letter DNA)

Methods

complement :: Letter RNA -> Letter DNA

Complement (Letter DNA) (Letter RNA)

Methods

complement :: Letter DNA -> Letter RNA

Complement (Letter DNA) (Letter DNA)

Methods

complement :: Letter DNA -> Letter DNA

IndexStream z => IndexStream ((:.) z (Letter l))

Methods

streamUp :: Monad m => (z :. Letter l) -> (z :. Letter l) -> Stream m (z :. Letter l)

streamDown :: Monad m => (z :. Letter l) -> (z :. Letter l) -> Stream m (z :. Letter l)

LetterChar x => ToJSON (Pretty [] (Letter x))

Methods

toJSON :: Pretty [] (Letter x) -> Value

toEncoding :: Pretty [] (Letter x) -> Encoding

toJSONList :: [Pretty [] (Letter x)] -> Value

toEncodingList :: [Pretty [] (Letter x)] -> Encoding

LetterChar x => ToJSON (Pretty Vector (Letter x))

Methods

toJSON :: Pretty Vector (Letter x) -> Value

toEncoding :: Pretty Vector (Letter x) -> Encoding

toJSONList :: [Pretty Vector (Letter x)] -> Value

toEncodingList :: [Pretty Vector (Letter x)] -> Encoding

LetterChar x => ToJSON (Pretty Vector (Letter x))

Methods

toJSON :: Pretty Vector (Letter x) -> Value

toEncoding :: Pretty Vector (Letter x) -> Encoding

toJSONList :: [Pretty Vector (Letter x)] -> Value

toEncodingList :: [Pretty Vector (Letter x)] -> Encoding

(LetterChar x, Storable (Letter x)) => ToJSON (Pretty Vector (Letter x))

Methods

toJSON :: Pretty Vector (Letter x) -> Value

toEncoding :: Pretty Vector (Letter x) -> Encoding

toJSONList :: [Pretty Vector (Letter x)] -> Value

toEncodingList :: [Pretty Vector (Letter x)] -> Encoding

MkViennaPair (Letter RNA, Letter RNA)

Methods

mkViennaPair :: (Letter RNA, Letter RNA) -> ViennaPair

fromViennaPair :: ViennaPair -> (Letter RNA, Letter RNA)

data MVector s (Letter a0)

data MVector s (Letter a0) = MV_Letter (MVector s Int)

type Rep (Letter t)

type Rep (Letter t) = D1 (MetaData "Letter" "Biobase.Primary.Letter" "BiobaseXNA-0.9.3.0-8oUGCIbMbYx8TN6nAPRU1W" True) (C1 (MetaCons "Letter" PrefixI True) (S1 (MetaSel (Just Symbol "getLetter") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))

data Vector (Letter a0)

data Vector (Letter a0) = V_Letter (Vector Int)

type Primary t = Vector (Letter t)

class LetterChar t where

Convert Letter types into character forms. DNA, RNA, and amino acid sequences can make use of this. Other Letter types only if they have single-char representations.

Minimal complete definition

letterChar, charLetter

Methods

letterChar :: Letter t -> Char

charLetter :: Char -> Letter t

Instances

LetterChar RNA

Methods

letterChar :: Letter RNA -> Char

charLetter :: Char -> Letter RNA

LetterChar DNA

Methods

letterChar :: Letter DNA -> Char

charLetter :: Char -> Letter DNA

LetterChar XNA

Methods

letterChar :: Letter XNA -> Char

charLetter :: Char -> Letter XNA

LetterChar AA

Methods

letterChar :: Letter AA -> Char

charLetter :: Char -> Letter AA

class MkPrimary n t where

Conversion from a large number of sequence-like inputs to primary sequences.

Minimal complete definition

primary

Methods

primary :: n -> Primary t

Instances

MkPrimary (Vector Char) t => MkPrimary ByteString t

Methods

primary :: ByteString -> Primary t

MkPrimary (Vector Char) t => MkPrimary ByteString t

Methods

primary :: ByteString -> Primary t

MkPrimary (Vector Char) t => MkPrimary String t

Methods

primary :: String -> Primary t

MkPrimary (Vector Char) t => MkPrimary Text t

Methods

primary :: Text -> Primary t

MkPrimary (Vector Char) t => MkPrimary Text t

Methods

primary :: Text -> Primary t

MkPrimary (Vector Char) RNA

Methods

primary :: Vector Char -> Primary RNA

MkPrimary (Vector Char) DNA

Methods

primary :: Vector Char -> Primary DNA

MkPrimary (Vector Char) XNA

Methods

primary :: Vector Char -> Primary XNA

MkPrimary (Vector Char) DEG

Methods

primary :: Vector Char -> Primary DEG

MkPrimary (Vector Char) AA

Methods

primary :: Vector Char -> Primary AA

MkPrimary (Vector Int) Unknown

Methods

primary :: Vector Int -> Primary Unknown

Instances for Letter.