Biobase.Types.Index

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.

Documentation

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

Uses index to guarantee that the Index is ok.

reIndex :: forall n m. (KnownNat n, KnownNat m) => Index n -> Index m

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

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

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

Unsafe plus.

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

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

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

Delta between two Index points.

unsafeMinus :: forall t. KnownNat t => Index t -> Int -> Index t

Unsafe minus.

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

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

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

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

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

type I0 = Index 0

Zero-based indices.

type I1 = Index 1

One-based indices.

getIndex :: Index t -> Int

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

Turn an Int into an Index safely.

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

Produce Just and Index or Nothing.

data Index t

A linear Int-based index type.

Instances

Vector Vector (Index t0)

Methods

basicUnsafeFreeze :: PrimMonad m => Mutable Vector (PrimState m) (Index t0) -> m (Vector (Index t0))

basicUnsafeThaw :: PrimMonad m => Vector (Index t0) -> m (Mutable Vector (PrimState m) (Index t0))

basicLength :: Vector (Index t0) -> Int

basicUnsafeSlice :: Int -> Int -> Vector (Index t0) -> Vector (Index t0)

basicUnsafeIndexM :: Monad m => Vector (Index t0) -> Int -> m (Index t0)

basicUnsafeCopy :: PrimMonad m => Mutable Vector (PrimState m) (Index t0) -> Vector (Index t0) -> m ()

elemseq :: Vector (Index t0) -> Index t0 -> b -> b

MVector MVector (Index t0)

Methods

basicLength :: MVector s (Index t0) -> Int

basicUnsafeSlice :: Int -> Int -> MVector s (Index t0) -> MVector s (Index t0)

basicOverlaps :: MVector s (Index t0) -> MVector s (Index t0) -> Bool

basicUnsafeNew :: PrimMonad m => Int -> m (MVector (PrimState m) (Index t0))

basicInitialize :: PrimMonad m => MVector (PrimState m) (Index t0) -> m ()

basicUnsafeReplicate :: PrimMonad m => Int -> Index t0 -> m (MVector (PrimState m) (Index t0))

basicUnsafeRead :: PrimMonad m => MVector (PrimState m) (Index t0) -> Int -> m (Index t0)

basicUnsafeWrite :: PrimMonad m => MVector (PrimState m) (Index t0) -> Int -> Index t0 -> m ()

basicClear :: PrimMonad m => MVector (PrimState m) (Index t0) -> m ()

basicSet :: PrimMonad m => MVector (PrimState m) (Index t0) -> Index t0 -> m ()

basicUnsafeCopy :: PrimMonad m => MVector (PrimState m) (Index t0) -> MVector (PrimState m) (Index t0) -> m ()

basicUnsafeMove :: PrimMonad m => MVector (PrimState m) (Index t0) -> MVector (PrimState m) (Index t0) -> m ()

basicUnsafeGrow :: PrimMonad m => MVector (PrimState m) (Index t0) -> Int -> m (MVector (PrimState m) (Index t0))

Eq (Index t)

Methods

(==) :: Index t -> Index t -> Bool

(/=) :: Index t -> Index t -> Bool

KnownNat t => Num (Index t)

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)

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)

Methods

readsPrec :: Int -> ReadS (Index t)

readList :: ReadS [Index t]

readPrec :: ReadPrec (Index t)

readListPrec :: ReadPrec [Index t]

Show (Index t)

Methods

showsPrec :: Int -> Index t -> ShowS

show :: Index t -> String

showList :: [Index t] -> ShowS

Ix (Index t)

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)

Associated Types

type Rep (Index t) :: * -> *

Methods

from :: Index t -> Rep (Index t) x

to :: Rep (Index t) x -> Index t

KnownNat t => Index (Index t)

Methods

linearIndex :: Index t -> Index t -> Index t -> Int

smallestLinearIndex :: Index t -> Int

largestLinearIndex :: Index t -> Int

size :: Index t -> Index t -> Int

inBounds :: Index t -> Index t -> Index t -> Bool

IndexStream (Index t)

Methods

streamUp :: Monad m => Index t -> Index t -> Stream m (Index t)

streamDown :: Monad m => Index t -> Index t -> Stream m (Index t)

Arbitrary (Index t)

Methods

arbitrary :: Gen (Index t)

shrink :: Index t -> [Index t]

Hashable (Index t)

Methods

hashWithSalt :: Int -> Index t -> Int

hash :: Index t -> Int

ToJSON (Index t)

Methods

toJSON :: Index t -> Value

toEncoding :: Index t -> Encoding

toJSONList :: [Index t] -> Value

toEncodingList :: [Index t] -> Encoding

FromJSON (Index t)

Methods

parseJSON :: Value -> Parser (Index t)

parseJSONList :: Value -> Parser [Index t]

Binary (Index t)

Methods

put :: Index t -> Put

get :: Get (Index t)

putList :: [Index t] -> Put

Serialize (Index t)

Methods

put :: Putter (Index t)

get :: Get (Index t)

NFData (Index t)

Methods

rnf :: Index t -> ()

Unbox (Index t0)

IndexStream z => IndexStream ((:.) z (Index t))

Methods

streamUp :: Monad m => (z :. Index t) -> (z :. Index t) -> Stream m (z :. Index t)

streamDown :: Monad m => (z :. Index t) -> (z :. Index t) -> Stream m (z :. Index t)

data MVector s (Index t0)

data MVector s (Index t0) = MV_Index (MVector s Int)

type Rep (Index t)

type Rep (Index t) = D1 (MetaData "Index" "Biobase.Types.Index.Type" "BiobaseTypes-0.1.2.1-1LTYzU1e5OWItpBBqXiV1g" True) (C1 (MetaCons "Index" PrefixI True) (S1 (MetaSel (Just Symbol "getIndex") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 Int)))

data Vector (Index t0)

data Vector (Index t0) = V_Index (Vector Int)