Detailed Description

An Aligner is an object representing a specific alignment algorithm and its parameters, passed to Alignment functions to determine which algorithm to invoke. Three aligners are currently available:

- EditDistanceAligner
- SmithWatermanAligner
- GotohAligner

Classes
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 > >

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)

Function Documentation

template<AlignmentType TYPE>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE EditDistanceAligner<TYPE> nvbio::aln::make_edit_distance_aligner ( )

Definition at line 196 of file alignment_base.h.

template<AlignmentType TYPE, typename algorithm_tag >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE EditDistanceAligner<TYPE,algorithm_tag> nvbio::aln::make_edit_distance_aligner ( )

Definition at line 203 of file alignment_base.h.