Biobase.Primary.Letter

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.

Documentation

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

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)

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: Basepair -> (Letter RNA n, Letter RNA n)

BasepairConvert ViennaPair (Letter RNA n, Letter RNA n)

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: ViennaPair -> (Letter RNA n, Letter RNA n)

Vector Vector (Letter t n)

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)

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))

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))

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))

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))

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]

Defined in Biobase.Primary.Nuc.DNA

Methods

fromString :: String -> [Letter DNA n]

IsString [Letter RNA n]

Defined in Biobase.Primary.Nuc.RNA

Methods

fromString :: String -> [Letter RNA n]

IsString [Letter XNA n]

Defined in Biobase.Primary.Nuc.XNA

Methods

fromString :: String -> [Letter XNA n]

IsString [Letter DEG n]

Defined in Biobase.Primary.IUPAC

Methods

fromString :: String -> [Letter DEG n]

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

Defined in Biobase.Primary.Letter

Methods

fromString :: String -> Vector (Letter t n)

Generic (LimitType (Letter l n))

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))

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)

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)

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

TODO inClass missing

Defined in Biobase.Secondary.Isostericity

Methods

getClasses :: ExtPair n -> [String]

inClass :: String -> [ExtPair n]

IsostericityLookup (Pair n)

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Defined in Biobase.Secondary.Isostericity

Methods

getClasses :: Pair n -> [String]

inClass :: String -> [Pair n]

BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: (Letter RNA n, Letter RNA n) -> ViennaPair

BasepairConvert (Letter RNA n, Letter RNA n) Basepair

Defined in Biobase.Secondary.Convert

Methods

basepairConvert :: (Letter RNA n, Letter RNA n) -> Basepair

Bounded (Letter AA n)

Defined in Biobase.Primary.AA

Methods

minBound :: Letter AA n

maxBound :: Letter AA n

Bounded (Letter DNA n)

Defined in Biobase.Primary.Nuc.DNA

Methods

minBound :: Letter DNA n

maxBound :: Letter DNA n

Bounded (Letter RNA n)

Defined in Biobase.Primary.Nuc.RNA

Methods

minBound :: Letter RNA n

maxBound :: Letter RNA n

Bounded (Letter XNA n)

Defined in Biobase.Primary.Nuc.XNA

Methods

minBound :: Letter XNA n

maxBound :: Letter XNA n

Bounded (Letter DEG n)

Defined in Biobase.Primary.IUPAC

Methods

minBound :: Letter DEG n

maxBound :: Letter DEG n

Enum (Letter AA n)

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)

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)

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)

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)

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)

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)

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)

Manual Data instance because Letter should not show its implementation. This also allows for better use of generic programming downstream.

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

TODO replace LtLetter Int with more specific limits? Maybe some constants?

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)

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)

Defined in Biobase.Primary.Letter

Methods

rnf :: Letter t n -> ()

Hashable (Letter t n)

Defined in Biobase.Primary.Letter

Methods

hashWithSalt :: Int -> Letter t n -> Int

hash :: Letter t n -> Int

ToJSON (Letter AA n)

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)

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)

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))

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))

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))

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))

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)

Defined in Biobase.Primary.AA

Methods

parseJSON :: Value -> Parser (Letter AA n)

parseJSONList :: Value -> Parser [Letter AA n]

FromJSON (Letter RNA n)

Defined in Biobase.Primary.Nuc.RNA

Methods

parseJSON :: Value -> Parser (Letter RNA n)

parseJSONList :: Value -> Parser [Letter RNA n]

FromJSON (Letter Unknown n)

Defined in Biobase.Primary.Unknown

Methods

parseJSON :: Value -> Parser (Letter Unknown n)

parseJSONList :: Value -> Parser [Letter Unknown n]

Binary (Letter t n)

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)

Defined in Biobase.Primary.Letter

Methods

put :: Putter (Letter t n)

get :: Get (Letter t n)

Unbox (Letter t n)

Defined in Biobase.Primary.Letter

Degenerate (Letter XNA n)

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter XNA n]

toDegenerate :: [Letter XNA n] -> Maybe Char

Degenerate (Letter DNA n)

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter DNA n]

toDegenerate :: [Letter DNA n] -> Maybe Char

Degenerate (Letter RNA n)

Defined in Biobase.Primary.IUPAC

Methods

fromDegenerate :: Char -> [Letter RNA n]

toDegenerate :: [Letter RNA n] -> Maybe Char

newtype MVector s (Letter t n)

Defined in Biobase.Primary.Letter

newtype MVector s (Letter t n) = MV_Letter (MVector s Int)

type Rep (LimitType (Letter l n))

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))

Defined in Biobase.Primary.Trans

type AAType (Codon (Letter DNA n)) = Letter AA n

type CodonType (Codon (Letter DNA n))

Defined in Biobase.Primary.Trans

type CodonType (Codon (Letter DNA n)) = Letter DNA n

type TargetType (Codon (Letter DNA n))

Defined in Biobase.Primary.Trans

type TargetType (Codon (Letter DNA n)) = Letter AA n

type Rep (Letter seqTy nameTy)

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)

Defined in Biobase.Primary.Trans

type AAType (Primary DNA n) = Letter AA n

type CodonType (Primary DNA n)

Defined in Biobase.Primary.Trans

type CodonType (Primary DNA n) = Letter DNA n

type TargetType (Primary DNA n)

Defined in Biobase.Primary.Trans

type TargetType (Primary DNA n) = Primary AA n

newtype LimitType (Letter l n)

Defined in Biobase.Primary.Letter

newtype LimitType (Letter l n) = LtLetter (Letter l n)

newtype Vector (Letter t n)

Defined in Biobase.Primary.Letter

newtype Vector (Letter t n) = V_Letter (Vector Int)

type TranscribeTo (Primary DNA n)

Defined in Biobase.Primary.Nuc.Conversion

type TranscribeTo (Primary DNA n) = Primary RNA n

type TranscribeTo (Primary RNA n)

Defined in Biobase.Primary.Nuc.Conversion

type TranscribeTo (Primary RNA n) = Primary DNA n

type TranscribeTo (Letter DNA n)

Defined in Biobase.Primary.Nuc.Conversion

type TranscribeTo (Letter DNA n) = Letter RNA n

type TranscribeTo (Letter RNA n)

Defined in Biobase.Primary.Nuc.Conversion

type TranscribeTo (Letter RNA n) = Letter DNA n

changeNameTy :: Letter seqTy nameTy -> Letter seqTy newNameTy

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

letterDataType :: DataType

letterConstr :: Constr

type Primary t n = Vector (Letter t n)

class LetterChar t n 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.

Methods

letterChar :: Letter t n -> Char

charLetter :: Char -> Letter t n

Instances

LetterChar AA (n :: k)

Defined in Biobase.Primary.AA

Methods

letterChar :: Letter AA n -> Char

charLetter :: Char -> Letter AA n

LetterChar DNA (n :: k)

Defined in Biobase.Primary.Nuc.DNA

Methods

letterChar :: Letter DNA n -> Char

charLetter :: Char -> Letter DNA n

LetterChar RNA (n :: k)

Defined in Biobase.Primary.Nuc.RNA

Methods

letterChar :: Letter RNA n -> Char

charLetter :: Char -> Letter RNA n

LetterChar XNA (n :: k)

Defined in Biobase.Primary.Nuc.XNA

Methods

letterChar :: Letter XNA n -> Char

charLetter :: Char -> Letter XNA n

class MkPrimary c t n where

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

Methods

primary :: c -> Primary t n

Instances

MkPrimary (Vector Char) t n => MkPrimary ByteString t (n :: k)

Defined in Biobase.Primary.Letter

Methods

primary :: ByteString -> Primary t n

MkPrimary (Vector Char) t n => MkPrimary ByteString t (n :: k)

Defined in Biobase.Primary.Letter

Methods

primary :: ByteString -> Primary t n

MkPrimary (Vector Char) t n => MkPrimary Text t (n :: k)

Defined in Biobase.Primary.Letter

Methods

primary :: Text -> Primary t n

MkPrimary (Vector Char) t n => MkPrimary Text t (n :: k)

Defined in Biobase.Primary.Letter

Methods

primary :: Text -> Primary t n

MkPrimary (Vector Char) t n => MkPrimary String t (n :: k)

Defined in Biobase.Primary.Letter

Methods

primary :: String -> Primary t n

MkPrimary (Vector Char) AA (n :: k)

Defined in Biobase.Primary.AA

Methods

primary :: Vector Char -> Primary AA n

MkPrimary (Vector Char) DNA (n :: k)

Defined in Biobase.Primary.Nuc.DNA

Methods

primary :: Vector Char -> Primary DNA n

MkPrimary (Vector Char) RNA (n :: k)

Defined in Biobase.Primary.Nuc.RNA

Methods

primary :: Vector Char -> Primary RNA n

MkPrimary (Vector Char) XNA (n :: k)

Defined in Biobase.Primary.Nuc.XNA

Methods

primary :: Vector Char -> Primary XNA n

MkPrimary (Vector Char) DEG (n :: k)

Defined in Biobase.Primary.IUPAC

Methods

primary :: Vector Char -> Primary DEG n

MkPrimary (Vector Int) Unknown (n :: k)

Defined in Biobase.Primary.Unknown

Methods

primary :: Vector Int -> Primary Unknown n

Instances for Letter.