gotoh_banded_inl.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::priv::banded::GotohScoringContext< BAND_LEN, TYPE >
struct	nvbio::aln::priv::banded::GotohCheckpointedScoringContext< BAND_LEN, TYPE, checkpoint_type >
struct	nvbio::aln::priv::banded::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >
struct	nvbio::aln::priv::banded::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >
struct	nvbio::aln::priv::banded::gotoh_alignment_score_dispatch< BAND_LEN, TYPE >

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

Macros
#define	SW_F_INITIALIZED_TO_INF

Functions
template<uint32 BAND_LEN, AlignmentType TYPE, typename H_band_type , typename F_band_type , typename scoring_type , typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::priv::banded::init_row_zero (H_band_type &H_band, F_band_type &F_band, const scoring_type &scoring, const score_type infimum)
template<uint32 BAND_LEN, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_score (const GotohAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink)
template<uint32 BAND_LEN, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_score (const GotohAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename pattern_type , typename qual_type , typename text_type , typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	nvbio::aln::priv::banded_alignment_checkpoints (const GotohAligner< TYPE, scoring_type > &aligner, pattern_type pattern, qual_type quals, text_type text, const int32 min_score, sink_type &sink, checkpoint_type checkpoints)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, AlignmentType TYPE, typename scoring_type , typename pattern_string , typename qual_string , typename text_string , typename checkpoint_type , typename submatrix_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::aln::priv::banded_alignment_submatrix (const GotohAligner< TYPE, scoring_type > &aligner, pattern_string pattern, qual_string quals, text_string text, const int32 min_score, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
template<uint32 BAND_LEN, 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::banded_alignment_traceback (const GotohAligner< TYPE, scoring_type > &aligner, checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix, const uint32 submatrix_height, uint8 &state, uint2 &sink, backtracer_type &backtracer)