bio-0.4: A bioinformatics librarySource codeContentsIndex
Bio.Location.LocMap
Contents
Constructing location lookup maps
Searching for target locations
Modifying location lookup maps
Utilities
Description

Efficient lookup of sequence positions and locations in a large map of target locations. For example, target locations might represent a collection of genes annotated on a chromosome. The LocMap would efficiently find which gene(s) overlapped a sequence position on that chromosome.

Target locations are assigned to one or more zones based on bounds. Query locations are then tested only against the target locations in the relevant zones.

Synopsis
data LocMap a
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]
Constructing location lookup maps
data LocMap a Source
Data structure allowing efficient lookup of target sequence locations that overlap a query location. Target locations can be paired with an arbitrary object.
show/hide Instances
fromList :: Offset -> [(Loc, a)] -> LocMap aSource
Create a LocMap from an association list of target locations.
Searching for target locations
lookupWithin :: Pos -> LocMap a -> [(Loc, a)]Source
Find the (possibly empty) list of target locations and associated objects that contain a sequence position, in the sense of isWithin
lookupOverlaps :: Loc -> LocMap a -> [(Loc, a)]Source
Find the (possibly empty) list of target locations and associated objects that overlap a sequence location, in the sense of overlaps
Modifying location lookup maps
delete :: Eq a => (Loc, a) -> LocMap a -> LocMap aSource
Remove a target location and 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 aSource
Generalized version of delete that removes the first target location / object association that satisfies a predicate function.
insert :: Loc -> a -> LocMap a -> LocMap aSource
Insert a new target association into a target location map.
Utilities
checkInvariants :: LocMap a -> [String]Source
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