Class Specialization
MultiSeed
Describes a seed with start and end position2 and diagonal upper and lower bounds. Additionaly diagonal segments between start and end position2 are stored.
Seed
MultiSeed
Seed<TPosition, MultiSeed>
Parameters
TPosition
The type of number that schuld be used. Must have negative numbers (e.g. int/long).
Specialization of
Metafunctions
SpecThe spec of a class. (Seed)
ValueType of the items in the container. (Seed)
Member Functions
SeedConstructor
Functions
addSeedAdds a seed to an existing set. (Seed)
appendDiag Adds diagonal to the seed.
bandedAlignmentCalculates a banded alignment around a Seed. (Seed)
endDiagonal Returns the diagonal of the end point. (Seed)
extendSeed Extends a seed. (Seed)
getAlignment Constructs a alignment from a MultiSeed.
leftDiagonal Returns the most left diagonal of the seed (maximum diagonal value). (Seed)
leftDim0 Returns the first position of the seed in the query. (Seed)
leftDim1 Returns the first position of the seed in the database. (Seed)
rightDiagonal Returns the most right diagonal of the seed (minimum diagonal value). (Seed)
rightDim0 Returns the last position of the seed in the query. (Seed)
rightDim1 Returns the last position of the seed in the database. (Seed)
scoreSeed Calculates the score of a seed.
setLeftDiagonal Sets a new value for the most left diagonal. (Seed)
setLeftDim0 Updates the start point of the seed. (Seed)
setLeftDim1 Updates the start point of the seed. (Seed)
setRightDiagonal Sets a new value for the most right diagonal. (Seed)
setRightDim0 Updates the end point of the seed. (Seed)
setRightDim1 Updates the end point of the seed. (Seed)
startDiagonal Returns the diagonal of the start point. (Seed)
SeqAn - Sequence Analysis Library - www.seqan.de