Data structures for computing banded sequence alignments. More...

Collaboration diagram for Band:

Classes
struct	seqan3::lower_bound< value_t >
	Type for a lower boundary. More...

class	seqan3::static_band
	Data structure for a static band. More...

struct	seqan3::upper_bound< value_t >
	Type for an upper boundary. More...

Detailed Description

Data structures for computing banded sequence alignments.

See also: Alignment

SeqAn offers the computation of banded alignments to reduce the running time of the algorithm. This can be helpful if the region in which the optimal alignment exists is known a priori. To specify the banded alignment the developer can use the seqan3::align_cfg::band_fixed_size option. This band configuration is initialised with a seqan3::align_cfg::lower_diagonal and a seqan3::align_cfg::upper_diagonal. The upper diagonal must always be greater than or equal to the lower diagonal. To choose the correct band parameters, imagine a matrix with the first sequence written on top and the second sequence along the left vertical side. A negative value reflects a start of the diagonal within the vertical part, while a positive value implies a start within the top part of this matrix at the respective position.

See also: seqan3::align_cfg::band_fixed_size

Classes

Detailed Description