batched.h File Reference

#include <nvbio/alignment/alignment.h>
#include <nvbio/alignment/batched_inl.h>
#include <nvbio/alignment/batched_banded_inl.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::HostThreadScheduler
struct	nvbio::aln::DeviceThreadBlockScheduler< BLOCKDIM_T, MINBLOCKS_T >
struct	nvbio::aln::DeviceStagedThreadScheduler
struct	nvbio::aln::DeviceWarpScheduler
struct	nvbio::aln::supports_scheduler< T, Scheduler >
struct	nvbio::aln::supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, HostThreadScheduler >
struct	nvbio::aln::supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, DeviceThreadScheduler >
struct	nvbio::aln::supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, DeviceStagedThreadScheduler >
struct	nvbio::aln::supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, DeviceWarpScheduler >
struct	nvbio::aln::supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, HostThreadScheduler >
struct	nvbio::aln::supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceThreadScheduler >
struct	nvbio::aln::supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceStagedThreadScheduler >
struct	nvbio::aln::supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceWarpScheduler >
struct	nvbio::aln::supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, HostThreadScheduler >
struct	nvbio::aln::supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceThreadScheduler >
struct	nvbio::aln::supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceStagedThreadScheduler >
struct	nvbio::aln::supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceWarpScheduler >
struct	nvbio::aln::supports_scheduler< HammingDistanceAligner< TYPE, ScoringScheme, AlgorithmTag >, HostThreadScheduler >
struct	nvbio::aln::supports_scheduler< HammingDistanceAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceThreadScheduler >
struct	nvbio::aln::supports_scheduler< HammingDistanceAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceStagedThreadScheduler >
struct	nvbio::aln::BatchedAlignmentScore< stream_type, algorithm_type >
struct	nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, algorithm_type >
struct	nvbio::aln::BatchedAlignmentTraceback< CHECKPOINTS, stream_type, algorithm_type >
struct	nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, algorithm_type >

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

Typedefs
typedef DeviceThreadBlockScheduler< 128, 1 >	nvbio::aln::DeviceThreadScheduler

Functions
template<typename aligner_type , typename pattern_set_type , typename text_set_type , typename sink_iterator , typename scheduler_type >
void	nvbio::aln::batch_alignment_score (const aligner_type aligner, const pattern_set_type patterns, const text_set_type texts, sink_iterator sinks, const scheduler_type scheduler, const uint32 max_pattern_length=1000, const uint32 max_text_length=1000)
template<typename aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator , typename scheduler_type >
void	nvbio::aln::batch_alignment_score (const aligner_type aligner, const pattern_set_type patterns, const qualities_set_type quals, const text_set_type texts, sink_iterator sinks, const scheduler_type scheduler, const uint32 max_pattern_length=1000, const uint32 max_text_length=1000)
template<uint32 BAND_LEN, typename aligner_type , typename pattern_set_type , typename text_set_type , typename sink_iterator , typename scheduler_type >
void	nvbio::aln::batch_banded_alignment_score (const aligner_type aligner, const pattern_set_type patterns, const text_set_type texts, sink_iterator sinks, const scheduler_type scheduler, const uint32 max_pattern_length, const uint32 max_text_length)