Biobase.Types.Strand

Strand information. A newtyped version, complete with serialization, pattern synonyms, being a PrimitiveArray index type, etc.

TODO will be expanded to encode biological sense information more clearly: http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29.

Documentation

newtype Strand

Encode strand information. PlusStrand is defined as the strand encoded in, say, the FASTA file. MinusStrand hence is the reverse complement.

Constructors

Strand

Fields

• getStrand :: Int

Instances

Bounded Strand

Defined in Biobase.Types.Strand

Methods

minBound :: Strand

maxBound :: Strand

Enum Strand

Defined in Biobase.Types.Strand

Methods

succ :: Strand -> Strand

pred :: Strand -> Strand

toEnum :: Int -> Strand

fromEnum :: Strand -> Int

enumFrom :: Strand -> [Strand]

enumFromThen :: Strand -> Strand -> [Strand]

enumFromTo :: Strand -> Strand -> [Strand]

enumFromThenTo :: Strand -> Strand -> Strand -> [Strand]

Eq Strand

Defined in Biobase.Types.Strand

Methods

(==) :: Strand -> Strand -> Bool

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

Ord Strand

Defined in Biobase.Types.Strand

Methods

compare :: Strand -> Strand -> Ordering

(<) :: Strand -> Strand -> Bool

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

(>) :: Strand -> Strand -> Bool

(>=) :: Strand -> Strand -> Bool

max :: Strand -> Strand -> Strand

min :: Strand -> Strand -> Strand

Read Strand

Defined in Biobase.Types.Strand

Methods

readsPrec :: Int -> ReadS Strand

readList :: ReadS [Strand]

readPrec :: ReadPrec Strand

readListPrec :: ReadPrec [Strand]

Show Strand

Defined in Biobase.Types.Strand

Methods

showsPrec :: Int -> Strand -> ShowS

show :: Strand -> String

showList :: [Strand] -> ShowS

Generic Strand

Defined in Biobase.Types.Strand

Associated Types

type Rep Strand :: Type -> Type

Methods

from :: Strand -> Rep Strand x

to :: Rep Strand x -> Strand

Index Strand

Defined in Biobase.Types.Strand

Associated Types

data LimitType Strand :: Type

Methods

linearIndex :: LimitType Strand -> Strand -> Int

size :: LimitType Strand -> Int

inBounds :: LimitType Strand -> Strand -> Bool

zeroBound :: Strand

zeroBound' :: LimitType Strand

totalSize :: LimitType Strand -> [Integer]

IndexStream Strand

Defined in Biobase.Types.Strand

Methods

streamUp :: Monad m => LimitType Strand -> LimitType Strand -> Stream m Strand

streamDown :: Monad m => LimitType Strand -> LimitType Strand -> Stream m Strand

Arbitrary Strand

Defined in Biobase.Types.Strand

Methods

arbitrary :: Gen Strand

shrink :: Strand -> [Strand]

Hashable Strand

Defined in Biobase.Types.Strand

Methods

hashWithSalt :: Int -> Strand -> Int

hash :: Strand -> Int

ToJSON Strand

Defined in Biobase.Types.Strand

Methods

toJSON :: Strand -> Value

toEncoding :: Strand -> Encoding

toJSONList :: [Strand] -> Value

toEncodingList :: [Strand] -> Encoding

FromJSON Strand

Defined in Biobase.Types.Strand

Methods

parseJSON :: Value -> Parser Strand

parseJSONList :: Value -> Parser [Strand]

Binary Strand

Defined in Biobase.Types.Strand

Methods

put :: Strand -> Put

get :: Get Strand

putList :: [Strand] -> Put

Serialize Strand

Defined in Biobase.Types.Strand

Methods

put :: Putter Strand

get :: Get Strand

NFData Strand

Defined in Biobase.Types.Strand

Methods

rnf :: Strand -> ()

Unbox Strand

Defined in Biobase.Types.Strand

Vector Vector Strand

Defined in Biobase.Types.Strand

Methods

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

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

basicLength :: Vector Strand -> Int

basicUnsafeSlice :: Int -> Int -> Vector Strand -> Vector Strand

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

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

elemseq :: Vector Strand -> Strand -> b -> b

MVector MVector Strand

Defined in Biobase.Types.Strand

Methods

basicLength :: MVector s Strand -> Int

basicUnsafeSlice :: Int -> Int -> MVector s Strand -> MVector s Strand

basicOverlaps :: MVector s Strand -> MVector s Strand -> Bool

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

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

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

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

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

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

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

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

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

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

IndexStream z => IndexStream (z :. Strand)

Defined in Biobase.Types.Strand

Methods

streamUp :: Monad m => LimitType (z :. Strand) -> LimitType (z :. Strand) -> Stream m (z :. Strand)

streamDown :: Monad m => LimitType (z :. Strand) -> LimitType (z :. Strand) -> Stream m (z :. Strand)

type Rep Strand

Defined in Biobase.Types.Strand

type Rep Strand = D1 (MetaData "Strand" "Biobase.Types.Strand" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" True) (C1 (MetaCons "Strand" PrefixI True) (S1 (MetaSel (Just "getStrand") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))

data LimitType Strand

Defined in Biobase.Types.Strand

data LimitType Strand = LtStrand Strand

data Vector Strand

Defined in Biobase.Types.Strand

data Vector Strand = V_Strand (Vector Int)

data MVector s Strand

Defined in Biobase.Types.Strand

data MVector s Strand = MV_Strand (MVector s Int)

pattern PlusStrand :: Strand

pattern MinusStrand :: Strand