BiobaseTypes-0.2.0.1: Collection of types for bioinformatics

Safe HaskellNone
LanguageHaskell2010

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

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

Instances
Bounded Strand Source # 
Instance details

Defined in Biobase.Types.Strand

Enum Strand Source # 
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Defined in Biobase.Types.Strand

Eq Strand Source # 
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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

Read Strand Source # 
Instance details

Defined in Biobase.Types.Strand

Show Strand Source # 
Instance details

Defined in Biobase.Types.Strand

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 #

Arbitrary Strand Source # 
Instance details

Defined in Biobase.Types.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

FromJSON Strand Source # 
Instance details

Defined in Biobase.Types.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

Unbox Strand Source # 
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Defined in Biobase.Types.Strand

Reversing Strand Source # 
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Defined in Biobase.Types.Strand

Methods

reversing :: Strand -> Strand #

Vector Vector Strand Source # 
Instance details

Defined in Biobase.Types.Strand

MVector MVector Strand Source # 
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Defined in Biobase.Types.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 Vector Strand Source # 
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Defined in Biobase.Types.Strand

newtype MVector s Strand Source # 
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Defined in Biobase.Types.Strand