Class
SeedSet
Manages seeds for local chaining and merging algorithms.
SeedSet<TPosition, TSeedSpec, TScoringScheme, TSpec>
Include Headers
seqan/seeds.h
Parameters
TPosition
Type that saves the positions and upper/lower bounds.
Remarks: Positive and negative values are needed.
TSeedSpec
The Seed specialization.
TScoringScheme
The scoring sheme to use.
Specializations
NonScored SeedSetSeedSet that uses seeds without scores.
Scored SeedSetSeedSet that uses scored Seeds.
Metafunctions
IteratorType of iterator objects that are used to traverse the container.
SpecThe spec of a class.
ValueType of the items in the container.
ValueType of the items in the container.
Member Functions
SeedSetConstructor
Functions
addSeedAdds a seed to an existing set.
addSeedsAdds several seeds to an existing set. If a merging or chaining algorithm is used seeds are added if the merging or chaining fails.
beginThe begin of a container.
beginThe begin of a container.
endThe end of a container.
endThe end of a container.
maximumDistanceSets the maximal distance between two seed during a chaining process.
qualityValueSets the minimum length for a seed to be saved permanently.
setMaximumDistanceSets the maximal distance between two seed during a chaining process.
setQualityValueSets the minimum length for a seed to be saved permanently.
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