gotoh_inl.h File Reference

#include <nvbio/alignment/sink.h>
#include <nvbio/alignment/utils.h>
#include <nvbio/alignment/alignment_base_inl.h>
#include <nvbio/basic/iterator.h>
#include <nvbio/strings/vectorized_string.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::priv::gotoh_use_vectorization< string_type >
struct	nvbio::aln::priv::gotoh_use_vectorization< vector_view< T * > >
struct	nvbio::aln::priv::gotoh_use_vectorization< vector_view< const T * > >
struct	nvbio::aln::priv::GotohScoringContext< BAND_LEN, TYPE, algorithm_tag >
struct	nvbio::aln::priv::GotohCheckpointedScoringContext< BAND_LEN, TYPE, algorithm_tag, checkpoint_type >
struct	nvbio::aln::priv::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >
struct	nvbio::aln::priv::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >
struct	nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, algorithm_tag, symbol_type >
struct	nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >
struct	nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type >
struct	nvbio::aln::priv::gotoh_bandlen_selector< TYPE, DIM, symbol_type >
struct	nvbio::aln::priv::gotoh_bandlen_selector< TYPE, DIM, simd4u8 >
struct	nvbio::aln::priv::alignment_score_dispatch< GotohAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >
struct	nvbio::aln::priv::alignment_checkpointed_dispatch< CHECKPOINTS, GotohAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type >

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::aln
	nvbio::aln::priv

Macros
#define	NVBIO_SW_VECTOR_LOADING

Functions
template<uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename checkpoint_type , typename submatrix_type , typename backtracer_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::alignment_traceback (const GotohAligner< TYPE, scoring_type > aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_width, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)

Macro Definition Documentation

#define NVBIO_SW_VECTOR_LOADING

Definition at line 41 of file gotoh_inl.h.