nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type > Struct Template Reference

Detailed description

template< uint32 BAND_LEN, AlignmentType TYPE, typename symbol_type>
struct nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >

Definition at line 460 of file gotoh_inl.h.

#include <gotoh_inl.h>

Static Public Methods
template<bool CHECK_M, typename context_type , typename query_cache , typename score_type , typename temp_iterator , typename sink_type , typename scoring_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE void	update_row (context_type &context, const uint32 block, const uint32 M, const uint32 i, const uint32 N, const symbol_type r_i, const query_cache q_cache, temp_iterator temp, score_type &temp_i, score_type *H_band, score_type *F_band, sink_type &sink, const score_type min_score, score_type &max_score, const score_type G_o, const score_type G_e, const score_type zero, const scoring_type scoring)
template<typename context_type , typename query_type , typename qual_type , typename ref_type , typename scoring_type , typename sink_type , typename column_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool	run (const scoring_type &scoring, context_type &context, query_type query, qual_type quals, ref_type ref, const int32 min_score, sink_type &sink, const uint32 window_begin, const uint32 window_end, column_type temp)
template<uint32 MAX_REF_LEN, typename context_type , typename query_type , typename qual_type , typename ref_type , typename scoring_type , typename sink_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool	run (const scoring_type &scoring, context_type &context, query_type query, qual_type quals, ref_type ref, const int32 min_score, sink_type &sink, const uint32 window_begin, const uint32 window_end)

Member Function Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, typename symbol_type >

template<typename context_type , typename query_type , typename qual_type , typename ref_type , typename scoring_type , typename sink_type , typename column_type >

NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >::run ( const scoring_type &  scoring, context_type &  context, query_type  query, qual_type  quals, ref_type  ref, const int32  min_score, sink_type &  sink, const uint32  window_begin, const uint32  window_end, column_type  temp  )

inlinestatic

Definition at line 629 of file gotoh_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, typename symbol_type >

template<uint32 MAX_REF_LEN, typename context_type , typename query_type , typename qual_type , typename ref_type , typename scoring_type , typename sink_type >

NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >::run ( const scoring_type &  scoring, context_type &  context, query_type  query, qual_type  quals, ref_type  ref, const int32  min_score, sink_type &  sink, const uint32  window_begin, const uint32  window_end  )

inlinestatic

Definition at line 936 of file gotoh_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, typename symbol_type >

template<bool CHECK_M, typename context_type , typename query_cache , typename score_type , typename temp_iterator , typename sink_type , typename scoring_type >

NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE void nvbio::aln::priv::gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type >::update_row ( context_type &  context, const uint32  block, const uint32  M, const uint32  i, const uint32  N, const symbol_type  r_i, const query_cache  q_cache, temp_iterator  temp, score_type &  temp_i, score_type *  H_band, score_type *  F_band, sink_type &  sink, const score_type  min_score, score_type &  max_score, const score_type  G_o, const score_type  G_e, const score_type  zero, const scoring_type  scoring  )

inlinestatic

Definition at line 473 of file gotoh_inl.h.

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvbio/alignment/gotoh/gotoh_inl.h