Safe Haskell	None
Language	Haskell2010

Biobase.Types.Index

Description

Biological sequence data is oftentimes indexed either 0- or 1-based. The Index type developed provides static guarantees that there is no confusion what index is in use.

This module does not export the ctor Index. If you want to (unsafely) use it, import Biobase.Types.Index.Type directly. Use fromInt0 to make clear that you count from 0 and transform to an Index t. I.e. fromInt0 0 :: Index 1 yields the lowest 1-base index.

Note that internally, every lowest index starts at 0 :: Int.

Synopsis

type I1 = Index 1
type I0 = Index 0
checkIndex :: forall t. KnownNat t => Index t -> Index t
reIndex :: Index n -> Index m
(+.) :: forall t. KnownNat t => Index t -> Int -> Index t
(-.) :: forall t. KnownNat t => Index t -> Int -> Index t
unsafePlus :: forall t. KnownNat t => Index t -> Int -> Index t
delta :: forall t. KnownNat t => Index t -> Index t -> Int
toInt :: forall t. KnownNat t => Index t -> Int
toInt0 :: forall t. KnownNat t => Index t -> Int
fromInt0 :: forall t. KnownNat t => Int -> Index t
getIndex :: Index t -> Int
index :: forall t. KnownNat t => Int -> Index t
maybeIndex :: forall t. KnownNat t => Int -> Maybe (Index t)
data Index (t :: Nat)

Documentation

type I1 = Index 1 Source #

One-based indices.

type I0 = Index 0 Source #

Zero-based indices.

checkIndex :: forall t. KnownNat t => Index t -> Index t Source #

Uses index to guarantee that the Index is ok.

reIndex :: Index n -> Index m Source #

Re-Index an index of type Index n as Index m. This is always safe, as 0 :: Index 0 gives 1 :: Index 1 for example. I.e. valid indices become valid indices.

(+.) :: forall t. KnownNat t => Index t -> Int -> Index t Source #

Helper function that allows addition of an Index and an Int, with the Int on the right.

(-.) :: forall t. KnownNat t => Index t -> Int -> Index t Source #

Helper function that allows subtraction of an Index and an Int, with the Int on the right.

unsafePlus :: forall t. KnownNat t => Index t -> Int -> Index t Source #

Unsafe plus.

delta :: forall t. KnownNat t => Index t -> Index t -> Int Source #

Delta between two Index points.

toInt :: forall t. KnownNat t => Index t -> Int Source #

toInt0 :: forall t. KnownNat t => Index t -> Int Source #

Return the index as an Int-style index that is zero-based.

fromInt0 :: forall t. KnownNat t => Int -> Index t Source #

As an index from an Int-style zero-based one.

TODO We might want to check that the argument is [0..].

getIndex :: Index t -> Int Source #

index :: forall t. KnownNat t => Int -> Index t Source #

Turn an Int into an Index safely.

maybeIndex :: forall t. KnownNat t => Int -> Maybe (Index t) Source #

Produce Just and Index or Nothing.

data Index (t :: Nat) Source #

A linear Int-based index type.

Instances

Vector Vector (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) (Index t) -> m (Vector (Index t)) # basicUnsafeThaw :: PrimMonad m => Vector (Index t) -> m (Mutable Vector (PrimState m) (Index t)) # basicLength :: Vector (Index t) -> Int # basicUnsafeSlice :: Int -> Int -> Vector (Index t) -> Vector (Index t) # basicUnsafeIndexM :: Monad m => Vector (Index t) -> Int -> m (Index t) # basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) (Index t) -> Vector (Index t) -> m () # elemseq :: Vector (Index t) -> Index t -> b -> b #
MVector MVector (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods basicLength :: MVector s (Index t) -> Int # basicUnsafeSlice :: Int -> Int -> MVector s (Index t) -> MVector s (Index t) # basicOverlaps :: MVector s (Index t) -> MVector s (Index t) -> Bool # basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) (Index t)) # basicInitialize :: PrimMonad m => MVector (PrimState m) (Index t) -> m () # basicUnsafeReplicate :: PrimMonad m => Int -> Index t -> m (MVector (PrimState m) (Index t)) # basicUnsafeRead :: PrimMonad m => MVector (PrimState m) (Index t) -> Int -> m (Index t) # basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) (Index t) -> Int -> Index t -> m () # basicClear :: PrimMonad m => MVector (PrimState m) (Index t) -> m () # basicSet :: PrimMonad m => MVector (PrimState m) (Index t) -> Index t -> m () # basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) (Index t) -> MVector (PrimState m) (Index t) -> m () # basicUnsafeMove :: PrimMonad m => MVector (PrimState m) (Index t) -> MVector (PrimState m) (Index t) -> m () # basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) (Index t) -> Int -> m (MVector (PrimState m) (Index t)) #
Eq (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods (==) :: Index t -> Index t -> Bool # (/=) :: Index t -> Index t -> Bool #
KnownNat t => Data (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> Index t -> c (Index t) # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (Index t) # toConstr :: Index t -> Constr # dataTypeOf :: Index t -> DataType # dataCast1 :: Typeable t0 => (forall d. Data d => c (t0 d)) -> Maybe (c (Index t)) # dataCast2 :: Typeable t0 => (forall d e. (Data d, Data e) => c (t0 d e)) -> Maybe (c (Index t)) # gmapT :: (forall b. Data b => b -> b) -> Index t -> Index t # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> Index t -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> Index t -> r # gmapQ :: (forall d. Data d => d -> u) -> Index t -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> Index t -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> Index t -> m (Index t) # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> Index t -> m (Index t) # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> Index t -> m (Index t) #
KnownNat t => Num (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods (+) :: Index t -> Index t -> Index t # (-) :: Index t -> Index t -> Index t # (*) :: Index t -> Index t -> Index t # negate :: Index t -> Index t # abs :: Index t -> Index t # signum :: Index t -> Index t # fromInteger :: Integer -> Index t #
Ord (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods compare :: Index t -> Index t -> Ordering # (<) :: Index t -> Index t -> Bool # (<=) :: Index t -> Index t -> Bool # (>) :: Index t -> Index t -> Bool # (>=) :: Index t -> Index t -> Bool # max :: Index t -> Index t -> Index t # min :: Index t -> Index t -> Index t #
Read (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods readsPrec :: Int -> ReadS (Index t) # readList :: ReadS [Index t] # readPrec :: ReadPrec (Index t) # readListPrec :: ReadPrec [Index t] #
Show (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods showsPrec :: Int -> Index t -> ShowS # show :: Index t -> String # showList :: [Index t] -> ShowS #
Ix (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods range :: (Index t, Index t) -> [Index t] # index :: (Index t, Index t) -> Index t -> Int # unsafeIndex :: (Index t, Index t) -> Index t -> Int inRange :: (Index t, Index t) -> Index t -> Bool # rangeSize :: (Index t, Index t) -> Int # unsafeRangeSize :: (Index t, Index t) -> Int
Generic (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Associated Types type Rep (Index t) :: Type -> Type # Methods from :: Index t -> Rep (Index t) x # to :: Rep (Index t) x -> Index t #
KnownNat t => Index (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Associated Types data LimitType (Index t) :: Type # Methods linearIndex :: LimitType (Index t) -> Index t -> Int # size :: LimitType (Index t) -> Int # inBounds :: LimitType (Index t) -> Index t -> Bool # zeroBound :: Index t # zeroBound' :: LimitType (Index t) # totalSize :: LimitType (Index t) -> [Integer] #
KnownNat t => IndexStream (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods streamUp :: Monad m => LimitType (Index t) -> LimitType (Index t) -> Stream m (Index t) # streamDown :: Monad m => LimitType (Index t) -> LimitType (Index t) -> Stream m (Index t) #
Arbitrary (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods arbitrary :: Gen (Index t) # shrink :: Index t -> [Index t] #
NFData (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods rnf :: Index t -> () #
Hashable (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods hashWithSalt :: Int -> Index t -> Int # hash :: Index t -> Int #
ToJSON (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods toJSON :: Index t -> Value # toEncoding :: Index t -> Encoding # toJSONList :: [Index t] -> Value # toEncodingList :: [Index t] -> Encoding #
FromJSON (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods parseJSON :: Value -> Parser (Index t) # parseJSONList :: Value -> Parser [Index t] #
Binary (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods put :: Index t -> Put # get :: Get (Index t) # putList :: [Index t] -> Put #
Serialize (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods put :: Putter (Index t) # get :: Get (Index t) #
Unbox (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type
(KnownNat t, IndexStream z) => IndexStream (z :. Index t) Source #
Instance details Defined in Biobase.Types.Index.Type Methods streamUp :: Monad m => LimitType (z :. Index t) -> LimitType (z :. Index t) -> Stream m (z :. Index t) # streamDown :: Monad m => LimitType (z :. Index t) -> LimitType (z :. Index t) -> Stream m (z :. Index t) #
newtype MVector s (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type newtype MVector s (Index t) = MV_Index (MVector s Int)
type Rep (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type type Rep (Index t) = D1 (MetaData "Index" "Biobase.Types.Index.Type" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "Index" PrefixI True) (S1 (MetaSel (Just "getIndex") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))
newtype LimitType (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type newtype LimitType (Index t) = LtIndex Int
newtype Vector (Index t) Source #
Instance details Defined in Biobase.Types.Index.Type newtype Vector (Index t) = V_Index (Vector Int)