Class
Seed
Describes a seed.

Seed

ChainedSeed | MultiSeed | SimpleSeed

Seed<TPosition, TSpecSeed>
Include Headers
seqan/seeds.h
Parameters

TPosition | The type number that schuld be used. Must have negative numbers (e.g. int/long).
TSpec | The seed type used.

Specializations

ChainedSeed | Describes a seed with start and end position2 and diagonal upper and lower bounds. Additionaly diagonal segments between start and end position2 are stored.
MultiSeed | Data structure which represents a seed of multiple sequences.
SimpleSeed | Describes a seed with start and end position and diagonal upper and lower bounds.

Metafunctions

Spec | The spec of a class.
Value | Type of the items in the container.

Functions

addSeed | Adds a seed to an existing set.
bandedAlignment | Calculates a banded alignment around a Seed.
dimension | Dimension of a seed.
endDiagonal | Returns the diagonal of the end point.
extendSeed | Extends a seed.
extendSeedScore | Extends a seed and increases the score.
leftDiagonal | Returns the most left diagonal of the seed (maximum diagonal value).
leftDim0 | Returns the first position of the seed in the query.
leftDim1 | Returns the first position of the seed in the database.
leftPosition | The begin position of segment in a seed.
rightDiagonal | Returns the most right diagonal of the seed (minimum diagonal value).
rightDim0 | Returns the last position of the seed in the query.
rightDim1 | Returns the last position of the seed in the database.
rightPosition | The end position of segment in a seed.
setLeftDiagonal | Sets a new value for the most left diagonal.
setLeftDim0 | Updates the start point of the seed.
setLeftDim1 | Updates the start point of the seed.
setLeftPosition | Sets begin position of segment in a seed.
setRightDiagonal | Sets a new value for the most right diagonal.
setRightDim0 | Updates the end point of the seed.
setRightDim1 | Updates the end point of the seed.
setRightPosition | Sets end position of segment in a seed.
startDiagonal | Returns the diagonal of the start point.

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