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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.
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Synopsis |
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Constructing location lookup maps
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Data structure allowing efficient lookup of target sequence
locations that overlap a query location. Target locations can be
paired with an arbitrary object.
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Create a LocMap from an association list of target locations.
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Searching for target locations
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Find the (possibly empty) list of target locations and associated
objects that contain a sequence position, in the sense of
isWithin
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Find the (possibly empty) list of target locations and associated
objects that overlap a sequence location, in the sense of overlaps
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Modifying location lookup maps
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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.
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Generalized version of delete that removes the first target
location / object association that satisfies a predicate function.
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Insert a new target association into a target location map.
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Utilities
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Produced by Haddock version 2.4.2 |