alignment_base.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/alignment/utils.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::PatternBlockingTag
	block along the pattern More...
struct	nvbio::aln::TextBlockingTag
	block along the text (at the moment, this is only supported for scoring) More...
struct	nvbio::aln::MyersTag< ALPHABET_SIZE_T >
	Myers bit-vector algorithm. More...
struct	nvbio::aln::transpose_tag< T >
struct	nvbio::aln::transpose_tag< PatternBlockingTag >
struct	nvbio::aln::transpose_tag< TextBlockingTag >
struct	nvbio::aln::transpose_aligner< T >
struct	nvbio::aln::SmithWatermanTag
	the Smith-Waterman aligner tag More...
struct	nvbio::aln::GotohTag
	the Gotoh aligner tag More...
struct	nvbio::aln::EditDistanceTag
	the Edit Distance aligner tag More...
struct	nvbio::aln::HammingDistanceTag
	the Hamming Distance aligner tag More...
struct	nvbio::aln::aligner_tag< aligner_type >
struct	nvbio::aln::Alignment< ScoreType >
struct	nvbio::aln::EditDistanceAligner< T_TYPE, AlgorithmType >
struct	nvbio::aln::transpose_aligner< EditDistanceAligner< T_TYPE, AlgorithmTag > >
struct	nvbio::aln::GotohAligner< T_TYPE, scoring_scheme_type, AlgorithmType >
struct	nvbio::aln::transpose_aligner< GotohAligner< T_TYPE, scoring_scheme_type, AlgorithmTag > >
struct	nvbio::aln::SmithWatermanAligner< T_TYPE, scoring_scheme_type, AlgorithmType >
struct	nvbio::aln::transpose_aligner< SmithWatermanAligner< T_TYPE, scoring_scheme_type, AlgorithmTag > >
struct	nvbio::aln::HammingDistanceAligner< T_TYPE, scoring_scheme_type, AlgorithmType >
struct	nvbio::aln::transpose_aligner< HammingDistanceAligner< T_TYPE, scoring_scheme_type, AlgorithmTag > >

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

Enumerations
enum	nvbio::aln::AlignmentType { nvbio::aln::GLOBAL, nvbio::aln::LOCAL, nvbio::aln::SEMI_GLOBAL }
enum	nvbio::aln::DirectionVector {   nvbio::aln::SUBSTITUTION = 0u, nvbio::aln::INSERTION = 1u, nvbio::aln::DELETION = 2u, nvbio::aln::SINK = 3u,   nvbio::aln::INSERTION_EXT = 4u, nvbio::aln::DELETION_EXT = 8u, nvbio::aln::HMASK = 3u, nvbio::aln::EMASK = 4u,   nvbio::aln::FMASK = 8u }
enum	nvbio::aln::State { nvbio::aln::HSTATE = 0, nvbio::aln::ESTATE = 1, nvbio::aln::FSTATE = 2 }

Functions
template<AlignmentType TYPE>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE EditDistanceAligner< TYPE >	nvbio::aln::make_edit_distance_aligner ()
template<AlignmentType TYPE, typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE EditDistanceAligner< TYPE, algorithm_tag >	nvbio::aln::make_edit_distance_aligner ()
template<AlignmentType TYPE>
EditDistanceAligner< TYPE, TextBlockingTag >	nvbio::aln::transpose (const EditDistanceAligner< TYPE, PatternBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
EditDistanceAligner< TYPE, PatternBlockingTag >	nvbio::aln::transpose (const EditDistanceAligner< TYPE, TextBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE GotohAligner < TYPE, scoring_scheme_type >	nvbio::aln::make_gotoh_aligner (const scoring_scheme_type &scheme)
template<AlignmentType TYPE, typename algorithm_tag , typename scoring_scheme_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE GotohAligner < TYPE, scoring_scheme_type, algorithm_tag >	nvbio::aln::make_gotoh_aligner (const scoring_scheme_type &scheme)
template<AlignmentType TYPE, typename scoring_scheme_type >
GotohAligner< TYPE, scoring_scheme_type, TextBlockingTag >	nvbio::aln::transpose (const GotohAligner< TYPE, scoring_scheme_type, PatternBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
GotohAligner< TYPE, scoring_scheme_type, PatternBlockingTag >	nvbio::aln::transpose (const GotohAligner< TYPE, scoring_scheme_type, TextBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SmithWatermanAligner< TYPE, scoring_scheme_type >	nvbio::aln::make_smith_waterman_aligner (const scoring_scheme_type &scheme)
template<AlignmentType TYPE, typename scoring_scheme_type >
SmithWatermanAligner< TYPE, scoring_scheme_type, TextBlockingTag >	nvbio::aln::transpose (const SmithWatermanAligner< TYPE, scoring_scheme_type, PatternBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
SmithWatermanAligner< TYPE, scoring_scheme_type, PatternBlockingTag >	nvbio::aln::transpose (const SmithWatermanAligner< TYPE, scoring_scheme_type, TextBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HammingDistanceAligner< TYPE, scoring_scheme_type >	nvbio::aln::make_hamming_distance_aligner (const scoring_scheme_type &scheme)
template<AlignmentType TYPE, typename scoring_scheme_type , typename algorithm_tag >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE HammingDistanceAligner< TYPE, scoring_scheme_type, algorithm_tag >	nvbio::aln::make_hamming_distance_aligner (const scoring_scheme_type &scheme)
template<AlignmentType TYPE, typename scoring_scheme_type >
HammingDistanceAligner< TYPE, scoring_scheme_type, TextBlockingTag >	nvbio::aln::transpose (const HammingDistanceAligner< TYPE, scoring_scheme_type, PatternBlockingTag > &aligner)
template<AlignmentType TYPE, typename scoring_scheme_type >
HammingDistanceAligner< TYPE, scoring_scheme_type, PatternBlockingTag >	nvbio::aln::transpose (const HammingDistanceAligner< TYPE, scoring_scheme_type, TextBlockingTag > &aligner)