Safe Haskell	None
Language	Haskell2010

Biobase.Primary.Letter

Contents

Instances for Letter.

Description

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

Synopsis

newtype Letter (seqTy :: *) (nameTy :: k) = Letter {
- getLetter :: Int
}
changeNameTy :: Letter seqTy nameTy -> Letter seqTy newNameTy
letterDataType :: DataType
letterConstr :: Constr
type Primary t n = Vector (Letter t n)
class LetterChar t n where
- letterChar :: Letter t n -> Char
- charLetter :: Char -> Letter t n
class MkPrimary c t n where
- primary :: c -> Primary t n

Documentation

newtype Letter (seqTy :: *) (nameTy :: k) Source #

A Letter together with its phantom type seqTy encodes bio-sequences, while nameTy allows to specify a type-level name for a letter.

Constructors

Letter
Fields getLetter :: Int

Instances

BasepairConvert Basepair (Letter RNA n, Letter RNA n) Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: Basepair -> (Letter RNA n, Letter RNA n) Source #
BasepairConvert ViennaPair (Letter RNA n, Letter RNA n) Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: ViennaPair -> (Letter RNA n, Letter RNA n) Source #
Vector Vector (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) (Letter t n) -> m (Vector (Letter t n)) # basicUnsafeThaw :: PrimMonad m => Vector (Letter t n) -> m (Mutable Vector (PrimState m) (Letter t n)) # basicLength :: Vector (Letter t n) -> Int # basicUnsafeSlice :: Int -> Int -> Vector (Letter t n) -> Vector (Letter t n) # basicUnsafeIndexM :: Monad m => Vector (Letter t n) -> Int -> m (Letter t n) # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) (Letter t n) -> Vector (Letter t n) -> m () # elemseq :: Vector (Letter t n) -> Letter t n -> b -> b #
MVector MVector (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter Methods basicLength :: MVector s (Letter t n) -> Int # basicUnsafeSlice :: Int -> Int -> MVector s (Letter t n) -> MVector s (Letter t n) # basicOverlaps :: MVector s (Letter t n) -> MVector s (Letter t n) -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) (Letter t n)) # basicInitialize :: PrimMonad m => MVector (PrimState m) (Letter t n) -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> Letter t n -> m (MVector (PrimState m) (Letter t n)) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) (Letter t n) -> Int -> m (Letter t n) # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) (Letter t n) -> Int -> Letter t n -> m () # basicClear :: PrimMonad m => MVector (PrimState m) (Letter t n) -> m () # basicSet :: PrimMonad m => MVector (PrimState m) (Letter t n) -> Letter t n -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) (Letter t n) -> MVector (PrimState m) (Letter t n) -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) (Letter t n) -> MVector (PrimState m) (Letter t n) -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) (Letter t n) -> Int -> m (MVector (PrimState m) (Letter t n)) #
Eq (LimitType (Letter l n)) Source #
Instance details Defined in Biobase.Primary.Letter Methods (==) :: LimitType (Letter l n) -> LimitType (Letter l n) -> Bool # (/=) :: LimitType (Letter l n) -> LimitType (Letter l n) -> Bool #
Data (Letter l n) => Data (LimitType (Letter l n)) Source #
Instance details Defined in Biobase.Primary.Letter Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> LimitType (Letter l n) -> c (LimitType (Letter l n)) # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (LimitType (Letter l n)) # toConstr :: LimitType (Letter l n) -> Constr # dataTypeOf :: LimitType (Letter l n) -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c (LimitType (Letter l n))) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c (LimitType (Letter l n))) # gmapT :: (forall b. Data b => b -> b) -> LimitType (Letter l n) -> LimitType (Letter l n) # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> LimitType (Letter l n) -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> LimitType (Letter l n) -> r # gmapQ :: (forall d. Data d => d -> u) -> LimitType (Letter l n) -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> LimitType (Letter l n) -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> LimitType (Letter l n) -> m (LimitType (Letter l n)) # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> LimitType (Letter l n) -> m (LimitType (Letter l n)) # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> LimitType (Letter l n) -> m (LimitType (Letter l n)) #
Read (Letter l n) => Read (LimitType (Letter l n)) Source #
Instance details Defined in Biobase.Primary.Letter Methods readsPrec :: Int -> ReadS (LimitType (Letter l n)) # readList :: ReadS [LimitType (Letter l n)] # readPrec :: ReadPrec (LimitType (Letter l n)) # readListPrec :: ReadPrec [LimitType (Letter l n)] #
Show (Letter l n) => Show (LimitType (Letter l n)) Source #
Instance details Defined in Biobase.Primary.Letter Methods showsPrec :: Int -> LimitType (Letter l n) -> ShowS # show :: LimitType (Letter l n) -> String # showList :: [LimitType (Letter l n)] -> ShowS #
IsString [Letter DNA n] Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods fromString :: String -> [Letter DNA n] #
IsString [Letter RNA n] Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods fromString :: String -> [Letter RNA n] #
IsString [Letter XNA n] Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods fromString :: String -> [Letter XNA n] #
IsString [Letter DEG n] Source #
Instance details Defined in Biobase.Primary.IUPAC Methods fromString :: String -> [Letter DEG n] #
(Unbox (Letter t n), IsString [Letter t n]) => IsString (Vector (Letter t n)) Source #
Instance details Defined in Biobase.Primary.Letter Methods fromString :: String -> Vector (Letter t n) #
Generic (LimitType (Letter l n)) Source #
Instance details Defined in Biobase.Primary.Letter Associated Types type Rep (LimitType (Letter l n)) :: Type -> Type # Methods from :: LimitType (Letter l n) -> Rep (LimitType (Letter l n)) x # to :: Rep (LimitType (Letter l n)) x -> LimitType (Letter l n) #
Translation (Codon (Letter DNA n)) Source #
Instance details Defined in Biobase.Primary.Trans Associated Types type TargetType (Codon (Letter DNA n)) :: Type # type CodonType (Codon (Letter DNA n)) :: Type # type AAType (Codon (Letter DNA n)) :: Type # Methods translate :: TranslationTable (CodonType (Codon (Letter DNA n))) (AAType (Codon (Letter DNA n))) -> Codon (Letter DNA n) -> TargetType (Codon (Letter DNA n)) #
IndexStream z => IndexStream (z :. Letter l n) Source #
Instance details Defined in Biobase.Primary.Letter Methods streamUp :: Monad m => LimitType (z :. Letter l n) -> LimitType (z :. Letter l n) -> Stream m (z :. Letter l n) # streamDown :: Monad m => LimitType (z :. Letter l n) -> LimitType (z :. Letter l n) -> Stream m (z :. Letter l n) #
IsostericityLookup (ExtPair n) Source #	For extended basepairs, we take the default mapping and go from there. TODO inClass missing
Instance details Defined in Biobase.Secondary.Isostericity Methods getClasses :: ExtPair n -> [String] Source # inClass :: String -> [ExtPair n] Source #
IsostericityLookup (Pair n) Source #	Normal basepairs are assumed to have cWW basepairing. TODO inClass missing
Instance details Defined in Biobase.Secondary.Isostericity Methods getClasses :: Pair n -> [String] Source # inClass :: String -> [Pair n] Source #
BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: (Letter RNA n, Letter RNA n) -> ViennaPair Source #
BasepairConvert (Letter RNA n, Letter RNA n) Basepair Source #
Instance details Defined in Biobase.Secondary.Convert Methods basepairConvert :: (Letter RNA n, Letter RNA n) -> Basepair Source #
Bounded (Letter AA n) Source #
Instance details Defined in Biobase.Primary.AA Methods minBound :: Letter AA n # maxBound :: Letter AA n #
Bounded (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods minBound :: Letter DNA n # maxBound :: Letter DNA n #
Bounded (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods minBound :: Letter RNA n # maxBound :: Letter RNA n #
Bounded (Letter XNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods minBound :: Letter XNA n # maxBound :: Letter XNA n #
Bounded (Letter DEG n) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods minBound :: Letter DEG n # maxBound :: Letter DEG n #
Enum (Letter AA n) Source #
Instance details Defined in Biobase.Primary.AA Methods succ :: Letter AA n -> Letter AA n # pred :: Letter AA n -> Letter AA n # toEnum :: Int -> Letter AA n # fromEnum :: Letter AA n -> Int # enumFrom :: Letter AA n -> [Letter AA n] # enumFromThen :: Letter AA n -> Letter AA n -> [Letter AA n] # enumFromTo :: Letter AA n -> Letter AA n -> [Letter AA n] # enumFromThenTo :: Letter AA n -> Letter AA n -> Letter AA n -> [Letter AA n] #
Enum (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods succ :: Letter DNA n -> Letter DNA n # pred :: Letter DNA n -> Letter DNA n # toEnum :: Int -> Letter DNA n # fromEnum :: Letter DNA n -> Int # enumFrom :: Letter DNA n -> [Letter DNA n] # enumFromThen :: Letter DNA n -> Letter DNA n -> [Letter DNA n] # enumFromTo :: Letter DNA n -> Letter DNA n -> [Letter DNA n] # enumFromThenTo :: Letter DNA n -> Letter DNA n -> Letter DNA n -> [Letter DNA n] #
Enum (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods succ :: Letter RNA n -> Letter RNA n # pred :: Letter RNA n -> Letter RNA n # toEnum :: Int -> Letter RNA n # fromEnum :: Letter RNA n -> Int # enumFrom :: Letter RNA n -> [Letter RNA n] # enumFromThen :: Letter RNA n -> Letter RNA n -> [Letter RNA n] # enumFromTo :: Letter RNA n -> Letter RNA n -> [Letter RNA n] # enumFromThenTo :: Letter RNA n -> Letter RNA n -> Letter RNA n -> [Letter RNA n] #
Enum (Letter XNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods succ :: Letter XNA n -> Letter XNA n # pred :: Letter XNA n -> Letter XNA n # toEnum :: Int -> Letter XNA n # fromEnum :: Letter XNA n -> Int # enumFrom :: Letter XNA n -> [Letter XNA n] # enumFromThen :: Letter XNA n -> Letter XNA n -> [Letter XNA n] # enumFromTo :: Letter XNA n -> Letter XNA n -> [Letter XNA n] # enumFromThenTo :: Letter XNA n -> Letter XNA n -> Letter XNA n -> [Letter XNA n] #
Enum (Letter DEG n) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods succ :: Letter DEG n -> Letter DEG n # pred :: Letter DEG n -> Letter DEG n # toEnum :: Int -> Letter DEG n # fromEnum :: Letter DEG n -> Int # enumFrom :: Letter DEG n -> [Letter DEG n] # enumFromThen :: Letter DEG n -> Letter DEG n -> [Letter DEG n] # enumFromTo :: Letter DEG n -> Letter DEG n -> [Letter DEG n] # enumFromThenTo :: Letter DEG n -> Letter DEG n -> Letter DEG n -> [Letter DEG n] #
Enum (Letter Unknown n) Source #
Instance details Defined in Biobase.Primary.Unknown Methods succ :: Letter Unknown n -> Letter Unknown n # pred :: Letter Unknown n -> Letter Unknown n # toEnum :: Int -> Letter Unknown n # fromEnum :: Letter Unknown n -> Int # enumFrom :: Letter Unknown n -> [Letter Unknown n] # enumFromThen :: Letter Unknown n -> Letter Unknown n -> [Letter Unknown n] # enumFromTo :: Letter Unknown n -> Letter Unknown n -> [Letter Unknown n] # enumFromThenTo :: Letter Unknown n -> Letter Unknown n -> Letter Unknown n -> [Letter Unknown n] #
Eq (Letter seqTy nameTy) Source #
Instance details Defined in Biobase.Primary.Letter Methods (==) :: Letter seqTy nameTy -> Letter seqTy nameTy -> Bool # (/=) :: Letter seqTy nameTy -> Letter seqTy nameTy -> Bool #
(Typeable t, Typeable (Letter t n)) => Data (Letter t n) Source #	Manual `Data` instance because `Letter` should not show its implementation. This also allows for better use of generic programming downstream.
Instance details Defined in Biobase.Primary.Letter Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> Letter t n -> c (Letter t n) # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (Letter t n) # toConstr :: Letter t n -> Constr # dataTypeOf :: Letter t n -> DataType # dataCast1 :: Typeable t0 => (forall d. Data d => c (t0 d)) -> Maybe (c (Letter t n)) # dataCast2 :: Typeable t0 => (forall d e. (Data d, Data e) => c (t0 d e)) -> Maybe (c (Letter t n)) # gmapT :: (forall b. Data b => b -> b) -> Letter t n -> Letter t n # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> Letter t n -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> Letter t n -> r # gmapQ :: (forall d. Data d => d -> u) -> Letter t n -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> Letter t n -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> Letter t n -> m (Letter t n) # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> Letter t n -> m (Letter t n) # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> Letter t n -> m (Letter t n) #
Ord (Letter seqTy nameTy) Source #
Instance details Defined in Biobase.Primary.Letter Methods compare :: Letter seqTy nameTy -> Letter seqTy nameTy -> Ordering # (<) :: Letter seqTy nameTy -> Letter seqTy nameTy -> Bool # (<=) :: Letter seqTy nameTy -> Letter seqTy nameTy -> Bool # (>) :: Letter seqTy nameTy -> Letter seqTy nameTy -> Bool # (>=) :: Letter seqTy nameTy -> Letter seqTy nameTy -> Bool # max :: Letter seqTy nameTy -> Letter seqTy nameTy -> Letter seqTy nameTy # min :: Letter seqTy nameTy -> Letter seqTy nameTy -> Letter seqTy nameTy #
Read (Letter AA n) Source #
Instance details Defined in Biobase.Primary.AA Methods readsPrec :: Int -> ReadS (Letter AA n) # readList :: ReadS [Letter AA n] # readPrec :: ReadPrec (Letter AA n) # readListPrec :: ReadPrec [Letter AA n] #
Read (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods readsPrec :: Int -> ReadS (Letter DNA n) # readList :: ReadS [Letter DNA n] # readPrec :: ReadPrec (Letter DNA n) # readListPrec :: ReadPrec [Letter DNA n] #
Read (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods readsPrec :: Int -> ReadS (Letter RNA n) # readList :: ReadS [Letter RNA n] # readPrec :: ReadPrec (Letter RNA n) # readListPrec :: ReadPrec [Letter RNA n] #
Read (Letter XNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods readsPrec :: Int -> ReadS (Letter XNA n) # readList :: ReadS [Letter XNA n] # readPrec :: ReadPrec (Letter XNA n) # readListPrec :: ReadPrec [Letter XNA n] #
Read (Letter Unknown n) Source #
Instance details Defined in Biobase.Primary.Unknown Methods readsPrec :: Int -> ReadS (Letter Unknown n) # readList :: ReadS [Letter Unknown n] # readPrec :: ReadPrec (Letter Unknown n) # readListPrec :: ReadPrec [Letter Unknown n] #
Show (Letter AA n) Source #
Instance details Defined in Biobase.Primary.AA Methods showsPrec :: Int -> Letter AA n -> ShowS # show :: Letter AA n -> String # showList :: [Letter AA n] -> ShowS #
Show (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods showsPrec :: Int -> Letter DNA n -> ShowS # show :: Letter DNA n -> String # showList :: [Letter DNA n] -> ShowS #
Show (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods showsPrec :: Int -> Letter RNA n -> ShowS # show :: Letter RNA n -> String # showList :: [Letter RNA n] -> ShowS #
Show (Letter XNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods showsPrec :: Int -> Letter XNA n -> ShowS # show :: Letter XNA n -> String # showList :: [Letter XNA n] -> ShowS #
Show (Letter DEG n) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods showsPrec :: Int -> Letter DEG n -> ShowS # show :: Letter DEG n -> String # showList :: [Letter DEG n] -> ShowS #
Show (Letter Unknown n) Source #
Instance details Defined in Biobase.Primary.Unknown Methods showsPrec :: Int -> Letter Unknown n -> ShowS # show :: Letter Unknown n -> String # showList :: [Letter Unknown n] -> ShowS #
Ix (Letter seqTy nameTy) Source #
Instance details Defined in Biobase.Primary.Letter Methods range :: (Letter seqTy nameTy, Letter seqTy nameTy) -> [Letter seqTy nameTy] # index :: (Letter seqTy nameTy, Letter seqTy nameTy) -> Letter seqTy nameTy -> Int # unsafeIndex :: (Letter seqTy nameTy, Letter seqTy nameTy) -> Letter seqTy nameTy -> Int inRange :: (Letter seqTy nameTy, Letter seqTy nameTy) -> Letter seqTy nameTy -> Bool # rangeSize :: (Letter seqTy nameTy, Letter seqTy nameTy) -> Int # unsafeRangeSize :: (Letter seqTy nameTy, Letter seqTy nameTy) -> Int
Generic (Letter seqTy nameTy) Source #
Instance details Defined in Biobase.Primary.Letter Associated Types type Rep (Letter seqTy nameTy) :: Type -> Type # Methods from :: Letter seqTy nameTy -> Rep (Letter seqTy nameTy) x # to :: Rep (Letter seqTy nameTy) x -> Letter seqTy nameTy #
Translation (Primary DNA n) Source #
Instance details Defined in Biobase.Primary.Trans Associated Types type TargetType (Primary DNA n) :: Type # type CodonType (Primary DNA n) :: Type # type AAType (Primary DNA n) :: Type # Methods translate :: TranslationTable (CodonType (Primary DNA n)) (AAType (Primary DNA n)) -> Primary DNA n -> TargetType (Primary DNA n) #
Transcribe (Primary DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion Associated Types type TranscribeTo (Primary DNA n) :: Type # Methods transcribe :: Iso' (Primary DNA n) (TranscribeTo (Primary DNA n)) #
Transcribe (Primary RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion Associated Types type TranscribeTo (Primary RNA n) :: Type # Methods transcribe :: Iso' (Primary RNA n) (TranscribeTo (Primary RNA n)) #
Transcribe (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion Associated Types type TranscribeTo (Letter DNA n) :: Type # Methods transcribe :: Iso' (Letter DNA n) (TranscribeTo (Letter DNA n)) #
Transcribe (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion Associated Types type TranscribeTo (Letter RNA n) :: Type # Methods transcribe :: Iso' (Letter RNA n) (TranscribeTo (Letter RNA n)) #
Index (Letter l n) Source #	TODO replace `LtLetter Int` with more specific limits? Maybe some constants?
Instance details Defined in Biobase.Primary.Letter Associated Types data LimitType (Letter l n) :: Type # Methods linearIndex :: LimitType (Letter l n) -> Letter l n -> Int # size :: LimitType (Letter l n) -> Int # inBounds :: LimitType (Letter l n) -> Letter l n -> Bool # zeroBound :: Letter l n # zeroBound' :: LimitType (Letter l n) # totalSize :: LimitType (Letter l n) -> [Integer] #
IndexStream (Letter l n) Source #
Instance details Defined in Biobase.Primary.Letter Methods streamUp :: Monad m => LimitType (Letter l n) -> LimitType (Letter l n) -> Stream m (Letter l n) # streamDown :: Monad m => LimitType (Letter l n) -> LimitType (Letter l n) -> Stream m (Letter l n) #
NFData (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter Methods rnf :: Letter t n -> () #
Hashable (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter Methods hashWithSalt :: Int -> Letter t n -> Int # hash :: Letter t n -> Int #
ToJSON (Letter AA n) Source #
Instance details Defined in Biobase.Primary.AA Methods toJSON :: Letter AA n -> Value # toEncoding :: Letter AA n -> Encoding # toJSONList :: [Letter AA n] -> Value # toEncodingList :: [Letter AA n] -> Encoding #
ToJSON (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods toJSON :: Letter RNA n -> Value # toEncoding :: Letter RNA n -> Encoding # toJSONList :: [Letter RNA n] -> Value # toEncodingList :: [Letter RNA n] -> Encoding #
ToJSON (Letter Unknown n) Source #
Instance details Defined in Biobase.Primary.Unknown Methods toJSON :: Letter Unknown n -> Value # toEncoding :: Letter Unknown n -> Encoding # toJSONList :: [Letter Unknown n] -> Value # toEncodingList :: [Letter Unknown n] -> Encoding #
LetterChar x n => ToJSON (Pretty [] (Letter x n)) Source #
Instance details Defined in Biobase.Primary.Pretty Methods toJSON :: Pretty [] (Letter x n) -> Value # toEncoding :: Pretty [] (Letter x n) -> Encoding # toJSONList :: [Pretty [] (Letter x n)] -> Value # toEncodingList :: [Pretty [] (Letter x n)] -> Encoding #
LetterChar x n => ToJSON (Pretty Vector (Letter x n)) Source #
Instance details Defined in Biobase.Primary.Pretty Methods toJSON :: Pretty Vector (Letter x n) -> Value # toEncoding :: Pretty Vector (Letter x n) -> Encoding # toJSONList :: [Pretty Vector (Letter x n)] -> Value # toEncodingList :: [Pretty Vector (Letter x n)] -> Encoding #
LetterChar x n => ToJSON (Pretty Vector (Letter x n)) Source #
Instance details Defined in Biobase.Primary.Pretty Methods toJSON :: Pretty Vector (Letter x n) -> Value # toEncoding :: Pretty Vector (Letter x n) -> Encoding # toJSONList :: [Pretty Vector (Letter x n)] -> Value # toEncodingList :: [Pretty Vector (Letter x n)] -> Encoding #
(LetterChar x n, Storable (Letter x n)) => ToJSON (Pretty Vector (Letter x n)) Source #
Instance details Defined in Biobase.Primary.Pretty Methods toJSON :: Pretty Vector (Letter x n) -> Value # toEncoding :: Pretty Vector (Letter x n) -> Encoding # toJSONList :: [Pretty Vector (Letter x n)] -> Value # toEncodingList :: [Pretty Vector (Letter x n)] -> Encoding #
FromJSON (Letter AA n) Source #
Instance details Defined in Biobase.Primary.AA Methods parseJSON :: Value -> Parser (Letter AA n) # parseJSONList :: Value -> Parser [Letter AA n] #
FromJSON (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods parseJSON :: Value -> Parser (Letter RNA n) # parseJSONList :: Value -> Parser [Letter RNA n] #
FromJSON (Letter Unknown n) Source #
Instance details Defined in Biobase.Primary.Unknown Methods parseJSON :: Value -> Parser (Letter Unknown n) # parseJSONList :: Value -> Parser [Letter Unknown n] #
Binary (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter Methods put :: Letter t n -> Put # get :: Get (Letter t n) # putList :: [Letter t n] -> Put #
Serialize (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter Methods put :: Putter (Letter t n) # get :: Get (Letter t n) #
Unbox (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter
Degenerate (Letter XNA n) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods fromDegenerate :: Char -> [Letter XNA n] Source # toDegenerate :: [Letter XNA n] -> Maybe Char Source #
Degenerate (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods fromDegenerate :: Char -> [Letter DNA n] Source # toDegenerate :: [Letter DNA n] -> Maybe Char Source #
Degenerate (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods fromDegenerate :: Char -> [Letter RNA n] Source # toDegenerate :: [Letter RNA n] -> Maybe Char Source #
newtype MVector s (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter newtype MVector s (Letter t n) = MV_Letter (MVector s Int)
type Rep (LimitType (Letter l n)) Source #
Instance details Defined in Biobase.Primary.Letter type Rep (LimitType (Letter l n)) = D1 (MetaData "LimitType" "Biobase.Primary.Letter" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "LtLetter" PrefixI False) (S1 (MetaSel (Nothing :: Maybe Symbol) NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 (Letter l n))))
type AAType (Codon (Letter DNA n)) Source #
Instance details Defined in Biobase.Primary.Trans type AAType (Codon (Letter DNA n)) = Letter AA n
type CodonType (Codon (Letter DNA n)) Source #
Instance details Defined in Biobase.Primary.Trans type CodonType (Codon (Letter DNA n)) = Letter DNA n
type TargetType (Codon (Letter DNA n)) Source #
Instance details Defined in Biobase.Primary.Trans type TargetType (Codon (Letter DNA n)) = Letter AA n
type Rep (Letter seqTy nameTy) Source #
Instance details Defined in Biobase.Primary.Letter type Rep (Letter seqTy nameTy) = D1 (MetaData "Letter" "Biobase.Primary.Letter" "BiobaseXNA-0.11.0.0-6sSV7wA2ZNJ62zYFxZDZpd" True) (C1 (MetaCons "Letter" PrefixI True) (S1 (MetaSel (Just "getLetter") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
type AAType (Primary DNA n) Source #
Instance details Defined in Biobase.Primary.Trans type AAType (Primary DNA n) = Letter AA n
type CodonType (Primary DNA n) Source #
Instance details Defined in Biobase.Primary.Trans type CodonType (Primary DNA n) = Letter DNA n
type TargetType (Primary DNA n) Source #
Instance details Defined in Biobase.Primary.Trans type TargetType (Primary DNA n) = Primary AA n
newtype LimitType (Letter l n) Source #
Instance details Defined in Biobase.Primary.Letter newtype LimitType (Letter l n) = LtLetter (Letter l n)
newtype Vector (Letter t n) Source #
Instance details Defined in Biobase.Primary.Letter newtype Vector (Letter t n) = V_Letter (Vector Int)
type TranscribeTo (Primary DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion type TranscribeTo (Primary DNA n) = Primary RNA n
type TranscribeTo (Primary RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion type TranscribeTo (Primary RNA n) = Primary DNA n
type TranscribeTo (Letter DNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion type TranscribeTo (Letter DNA n) = Letter RNA n
type TranscribeTo (Letter RNA n) Source #
Instance details Defined in Biobase.Primary.Nuc.Conversion type TranscribeTo (Letter RNA n) = Letter DNA n

changeNameTy :: Letter seqTy nameTy -> Letter seqTy newNameTy Source #

While coerce will always work, this way restricts the change to just the nameTy.

letterDataType :: DataType Source #

letterConstr :: Constr Source #

type Primary t n = Vector (Letter t n) Source #

class LetterChar t n where Source #

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.

Methods

letterChar :: Letter t n -> Char Source #

charLetter :: Char -> Letter t n Source #

Instances

LetterChar AA (n :: k) Source #
Instance details Defined in Biobase.Primary.AA Methods letterChar :: Letter AA n -> Char Source # charLetter :: Char -> Letter AA n Source #
LetterChar DNA (n :: k) Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods letterChar :: Letter DNA n -> Char Source # charLetter :: Char -> Letter DNA n Source #
LetterChar RNA (n :: k) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods letterChar :: Letter RNA n -> Char Source # charLetter :: Char -> Letter RNA n Source #
LetterChar XNA (n :: k) Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods letterChar :: Letter XNA n -> Char Source # charLetter :: Char -> Letter XNA n Source #

class MkPrimary c t n where Source #

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

Methods

primary :: c -> Primary t n Source #

Instances

MkPrimary (Vector Char) t n => MkPrimary ByteString t (n :: k) Source #
Instance details Defined in Biobase.Primary.Letter Methods primary :: ByteString -> Primary t n Source #
MkPrimary (Vector Char) t n => MkPrimary ByteString t (n :: k) Source #
Instance details Defined in Biobase.Primary.Letter Methods primary :: ByteString -> Primary t n Source #
MkPrimary (Vector Char) t n => MkPrimary Text t (n :: k) Source #
Instance details Defined in Biobase.Primary.Letter Methods primary :: Text -> Primary t n Source #
MkPrimary (Vector Char) t n => MkPrimary Text t (n :: k) Source #
Instance details Defined in Biobase.Primary.Letter Methods primary :: Text -> Primary t n Source #
MkPrimary (Vector Char) t n => MkPrimary String t (n :: k) Source #
Instance details Defined in Biobase.Primary.Letter Methods primary :: String -> Primary t n Source #
MkPrimary (Vector Char) AA (n :: k) Source #
Instance details Defined in Biobase.Primary.AA Methods primary :: Vector Char -> Primary AA n Source #
MkPrimary (Vector Char) DNA (n :: k) Source #
Instance details Defined in Biobase.Primary.Nuc.DNA Methods primary :: Vector Char -> Primary DNA n Source #
MkPrimary (Vector Char) RNA (n :: k) Source #
Instance details Defined in Biobase.Primary.Nuc.RNA Methods primary :: Vector Char -> Primary RNA n Source #
MkPrimary (Vector Char) XNA (n :: k) Source #
Instance details Defined in Biobase.Primary.Nuc.XNA Methods primary :: Vector Char -> Primary XNA n Source #
MkPrimary (Vector Char) DEG (n :: k) Source #
Instance details Defined in Biobase.Primary.IUPAC Methods primary :: Vector Char -> Primary DEG n Source #
MkPrimary (Vector Int) Unknown (n :: k) Source #
Instance details Defined in Biobase.Primary.Unknown Methods primary :: Vector Int -> Primary Unknown n Source #

Documentation

Instances for Letter.

Instances for `Letter`.