bio-0.3.5: A bioinformatics library Source code Contents Index

Bio.Location.LocMap

Description

A structure to allow fast lookup of objects whose sequence location lines up with a give position.

Synopsis

data LocMap a mkLocMap :: Offset -> LocMap a defaultZonesize :: Offset fromList :: Offset -> [(Loc, a)] -> LocMap a lookupWithin :: Pos -> LocMap a -> [(Loc, a)] lookupOverlaps :: Loc -> LocMap a -> [(Loc, a)] delete :: Eq a => (Loc, a) -> LocMap a -> LocMap a deleteBy :: ((Loc, a) -> Bool) -> LocMap a -> LocMap a insert :: Loc -> a -> LocMap a -> LocMap a checkInvariants :: LocMap a -> [String]

Documentation

data LocMap a Source

Collection mapping a collection of Loc locations, possibly overlapping, binned for efficient lookup by position. Instances Monoid (LocMap a)

mkLocMap :: Offset -> LocMap a Source

Create an empty LocMap with a specified position bin size

defaultZonesize :: Offset Source

fromList :: Offset -> [(Loc, a)] -> LocMap a Source

Create a LocMap from an associated list.

lookupWithin :: Pos -> LocMap a -> [(Loc, a)] Source

Find the (possibly empty) list of sequence regions and associated objects that contain a Pos position, in the sense of withinLoc

lookupOverlaps :: Loc -> LocMap a -> [(Loc, a)] Source

Find the (possibly empty) list of sequence regions and associated objects that overlap a Loc region, in the sense of overlapsLoc

delete :: Eq a => (Loc, a) -> LocMap a -> LocMap a Source

Remove a region / object association from the map, if it is present. If it is present multiple times, only the first occurrence will be deleted.

deleteBy :: ((Loc, a) -> Bool) -> LocMap a -> LocMap a Source

Remove the first region / object association satisfying a predicate function.

insert :: Loc -> a -> LocMap a -> LocMap a Source

Add an object with an associated Loc sequence region

checkInvariants :: LocMap a -> [String] Source

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