NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Classes | Public Types | Public Methods | Public Members | List of all members
nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator > Struct Template Reference

Detailed description

template< typename t_aligner_type, typename pattern_set_type, typename qualities_set_type, typename text_set_type, typename sink_iterator>
struct nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >

Definition at line 863 of file batched_inl.h.

#include <batched_inl.h>

Classes

struct  context_type
 
struct  strings_type
 

Public Types

typedef t_aligner_type aligner_type
 
typedef
pattern_set_type::string_type 		input_pattern_string
 
typedef text_set_type::string_type input_text_string
 
typedef StringPrefetcher
< input_pattern_string,
lmem_cache_tag< 128 > > 		pattern_prefetcher_type
 
typedef
pattern_prefetcher_type::string_type 		pattern_string
 
typedef StringPrefetcher
< input_text_string,
lmem_cache_tag< 128 > > 		text_prefetcher_type
 
typedef
text_prefetcher_type::string_type 		text_string
 
typedef
qualities_set_type::string_type 		quals_string
 
typedef std::iterator_traits
< sink_iterator >::value_type 		sink_type
 

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE AlignmentStream (aligner_type _aligner, const uint32 _count, const pattern_set_type _patterns, const qualities_set_type _quals, const text_set_type _texts, sink_iterator _sinks, const uint32 _max_pattern_length, const uint32 _max_text_length)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE const
aligner_type & 		aligner () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 		max_pattern_length () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 		max_text_length () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 		size () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 		pattern_length (const uint32 i, context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 		text_length (const uint32 i, context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 		init_context (const uint32 i, context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		load_strings (const uint32 i, const uint32 window_begin, const uint32 window_end, const context_type *context, strings_type *strings) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		output (const uint32 i, const context_type *context) const
 

Public Members

aligner_type m_aligner
 
uint32 m_count
 
pattern_set_type m_patterns
 
qualities_set_type m_quals
 
text_set_type m_texts
 
sink_iterator m_sinks
 
const uint32 m_max_pattern_length
 
const uint32 m_max_text_length
 

Member Typedef Documentation

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef t_aligner_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::aligner_type

Definition at line 865 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef pattern_set_type::string_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::input_pattern_string

Definition at line 867 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef text_set_type::string_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::input_text_string

Definition at line 868 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef StringPrefetcher<input_pattern_string, lmem_cache_tag<128> > nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::pattern_prefetcher_type

Definition at line 869 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef pattern_prefetcher_type::string_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::pattern_string

Definition at line 870 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef qualities_set_type::string_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::quals_string

Definition at line 873 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef std::iterator_traits<sink_iterator>::value_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::sink_type

Definition at line 874 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef StringPrefetcher<input_text_string, lmem_cache_tag<128> > nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::text_prefetcher_type

Definition at line 871 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
typedef text_prefetcher_type::string_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::text_string

Definition at line 872 of file batched_inl.h.

Constructor & Destructor Documentation

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::AlignmentStream ( aligner_type  _aligner,
const uint32  _count,
const pattern_set_type  _patterns,
const qualities_set_type  _quals,
const text_set_type  _texts,
sink_iterator  _sinks,
const uint32  _max_pattern_length,
const uint32  _max_text_length 
)
inline

Definition at line 895 of file batched_inl.h.

Member Function Documentation

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const aligner_type& nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::aligner ( ) const
inline

Definition at line 915 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::init_context ( const uint32  i,
context_type *  context 
) const
inline

Definition at line 939 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::load_strings ( const uint32  i,
const uint32  window_begin,
const uint32  window_end,
const context_type *  context,
strings_type *  strings 
) const
inline

Definition at line 952 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::max_pattern_length ( ) const
inline

Definition at line 919 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::max_text_length ( ) const
inline

Definition at line 923 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::output ( const uint32  i,
const context_type *  context 
) const
inline

Definition at line 966 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::pattern_length ( const uint32  i,
context_type *  context 
) const
inline

Definition at line 931 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::size ( void  ) const
inline

Definition at line 927 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::text_length ( const uint32  i,
context_type *  context 
) const
inline

Definition at line 935 of file batched_inl.h.

Member Data Documentation

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
aligner_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_aligner

Definition at line 974 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_count

Definition at line 975 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
const uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_max_pattern_length

Definition at line 980 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
const uint32 nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_max_text_length

Definition at line 981 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
pattern_set_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_patterns

Definition at line 976 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
qualities_set_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_quals

Definition at line 977 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
sink_iterator nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_sinks

Definition at line 979 of file batched_inl.h.

template<typename t_aligner_type , typename pattern_set_type , typename qualities_set_type , typename text_set_type , typename sink_iterator >
text_set_type nvbio::aln::priv::AlignmentStream< t_aligner_type, pattern_set_type, qualities_set_type, text_set_type, sink_iterator >::m_texts

Definition at line 978 of file batched_inl.h.

The documentation for this struct was generated from the following file:
Generated on Wed Feb 25 2015 08:34:05 for NVBIO by   doxygen 1.8.4