Safe Haskell	None
Language	Haskell2010

Biobase.Types.Strand

Description

Strand information. A newtyped version, complete with serialization, pattern synonyms, being a PrimitiveArray index type, etc. The strand information includes +, -, as well as the (GFF3) . not stranded, and ? for unknown strand information.

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

Synopsis

newtype Strand = Strand {
- getStrand :: Int
}
pattern PlusStrand :: Strand
pattern MinusStrand :: Strand
pattern NotStranded :: Strand
pattern UnknownStrand :: Strand

Documentation

newtype Strand Source #

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 Source #
Instance details Defined in Biobase.Types.Strand Methods minBound :: Strand # maxBound :: Strand #
Enum Strand Source #
Instance details 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 Source #
Instance details Defined in Biobase.Types.Strand Methods (==) :: Strand -> Strand -> Bool # (/=) :: Strand -> Strand -> Bool #
Data Strand Source #
Instance details Defined in Biobase.Types.Strand Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> Strand -> c Strand # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c Strand # toConstr :: Strand -> Constr # dataTypeOf :: Strand -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c Strand) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c Strand) # gmapT :: (forall b. Data b => b -> b) -> Strand -> Strand # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> Strand -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> Strand -> r # gmapQ :: (forall d. Data d => d -> u) -> Strand -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> Strand -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> Strand -> m Strand # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> Strand -> m Strand # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> Strand -> m Strand #
Ord Strand Source #
Instance details 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 Source #
Instance details Defined in Biobase.Types.Strand Methods readsPrec :: Int -> ReadS Strand # readList :: ReadS [Strand] # readPrec :: ReadPrec Strand # readListPrec :: ReadPrec [Strand] #
Show Strand Source #
Instance details Defined in Biobase.Types.Strand Methods showsPrec :: Int -> Strand -> ShowS # show :: Strand -> String # showList :: [Strand] -> ShowS #
Generic Strand Source #
Instance details 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 Source #
Instance details 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] #
Arbitrary Strand Source #
Instance details Defined in Biobase.Types.Strand Methods arbitrary :: Gen Strand # shrink :: Strand -> [Strand] #
NFData Strand Source #
Instance details Defined in Biobase.Types.Strand Methods rnf :: Strand -> () #
Hashable Strand Source #
Instance details Defined in Biobase.Types.Strand Methods hashWithSalt :: Int -> Strand -> Int # hash :: Strand -> Int #
ToJSON Strand Source #
Instance details Defined in Biobase.Types.Strand Methods toJSON :: Strand -> Value # toEncoding :: Strand -> Encoding # toJSONList :: [Strand] -> Value # toEncodingList :: [Strand] -> Encoding #
FromJSON Strand Source #
Instance details Defined in Biobase.Types.Strand Methods parseJSON :: Value -> Parser Strand # parseJSONList :: Value -> Parser [Strand] #
Binary Strand Source #
Instance details Defined in Biobase.Types.Strand Methods put :: Strand -> Put # get :: Get Strand # putList :: [Strand] -> Put #
Serialize Strand Source #
Instance details Defined in Biobase.Types.Strand Methods put :: Putter Strand # get :: Get Strand #
Unbox Strand Source #
Instance details Defined in Biobase.Types.Strand
Reversing Strand Source #
Instance details Defined in Biobase.Types.Strand Methods reversing :: Strand -> Strand #
Vector Vector Strand Source #
Instance details 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 Source #
Instance details 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) Source #
Instance details 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 Source #
Instance details Defined in Biobase.Types.Strand type Rep Strand = D1 (MetaData "Strand" "Biobase.Types.Strand" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "Strand" PrefixI True) (S1 (MetaSel (Just "getStrand") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
newtype LimitType Strand Source #
Instance details Defined in Biobase.Types.Strand newtype LimitType Strand = LtStrand Strand
newtype Vector Strand Source #
Instance details Defined in Biobase.Types.Strand newtype Vector Strand = V_Strand (Vector Int)
newtype MVector s Strand Source #
Instance details Defined in Biobase.Types.Strand newtype MVector s Strand = MV_Strand (MVector s Int)

pattern PlusStrand :: Strand Source #

pattern MinusStrand :: Strand Source #

pattern NotStranded :: Strand Source #

pattern UnknownStrand :: Strand Source #