seqan3::detail::simd_global_alignment_state< simd_t > Struct Template Reference

A state that is only used for global alignments. More...

#include <seqan3/alignment/pairwise/policy/simd_find_optimum_policy.hpp>

Inheritance diagram for seqan3::detail::simd_global_alignment_state< simd_t >:

Public Attributes
simd_t	coordinate_offset {}
	A coordinate offset that needs to be subtracted for every alignment to get the correct end position.
simd_t	last_column_mask {}
	A mask vector storing the row indices for alignments that end in the last column of the global matrix.
simd_t	last_row_mask {}
	A mask vector storing the column indices for alignments that end in the last row of the global matrix.
simd_t	score_offset {}
	The score offset that needs to be subtracted for every alignment to get the correct result.

Detailed Description

template<simd::simd_concept simd_t>
struct seqan3::detail::simd_global_alignment_state< simd_t >

A state that is only used for global alignments.

Template Parameters

simd_t

The simd vector score type; must model seqan3::simd::simd_concept.

This state is only used for the global alignment to compute the correct optimum for every sequence pair. If the sequences have different lengths the respective cells in the alignment matrix need to be queried to check for the global optimum. In addition, the final scores and coordinates must be corrected as they are based on the outer matrix defined by the longest sequence in the first and second collection.

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The documentation for this struct was generated from the following file:

• simd_find_optimum_policy.hpp