| Class Specialization 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.
Seed
ChainedSeed
Seed<TPosition, ChainedSeed> Parameters
TPosition | The type of number that schuld be used. Must have negative numbers (e.g. int/long).
Specialization of Seed Metafunctions
Spec | The spec of a class. (Seed)
Value | Type of the items in the container. (Seed)
Member Functions
Seed | Constructor
Functions
addSeed | Adds a seed to an existing set. (Seed)
appendDiag | Adds diagonal to the seed.
bandedAlignment | Calculates a banded alignment around a Seed. (Seed)
dimension | Dimension of a seed. (Seed)
endDiagonal | Returns the diagonal of the end point. (Seed)
extendSeed | Extends a seed. (Seed)
extendSeedScore | Extends a seed and increases the score. (Seed)
getAlignment | Constructs a alignment from a ChainedSeed.
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)
leftPosition | The begin position of segment in a seed. (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)
rightPosition | The end position of segment in a seed. (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)
setLeftPosition | Sets begin position of segment in a 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)
setRightPosition | Sets end position of segment in a seed. (Seed)
startDiagonal | Returns the diagonal of the start point. (Seed)
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