extract_non_overlapped_repeats< string_set_type > Struct Template Reference

Detailed description

template< typename string_set_type>
struct extract_non_overlapped_repeats< string_set_type >

Definition at line 812 of file kmers_inl.h.

#include <kmers_inl.h>

Public Types
typedef string_set_type::string_type	sequence

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	extract_non_overlapped_repeats (const string_set_type _string_set, const SequenceSetKmerCoord *_chain_coords, const uint32 *_chain_pref_gids, const uint32 *_chain_suffix_gids, const uint32 *_chain_offsets, const uint32 *_adj_extraction_offsets, const uint32 *_chain_overlaps, const uint32 _kmer_size, const uint32 _uid_offset, SequenceSetKmerCoord *_kmers_out, uint32 *_prefix_uids, uint32 *_suffix_uids)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	operator() (const uint32 idx) const

Public Members
const string_set_type	string_set
const SequenceSetKmerCoord *	super_coords
const uint32 *	super_prefix_global_ids
const uint32 *	super_suffix_global_ids
const uint32 *	chain_offsets
const uint32 *	adj_extraction_offsets
const uint32 *	chain_overlaps
const uint32	kmer_size
const uint32	uid_offset
const uniform_seeds_functor	seeder
SequenceSetKmerCoord *	kmers_out
uint32 *	prefix_uids
uint32 *	suffix_uids

Member Typedef Documentation

template<typename string_set_type >

typedef string_set_type::string_type extract_non_overlapped_repeats< string_set_type >::sequence

Definition at line 814 of file kmers_inl.h.

Constructor & Destructor Documentation

template<typename string_set_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE extract_non_overlapped_repeats< string_set_type >::extract_non_overlapped_repeats ( const string_set_type  _string_set, const SequenceSetKmerCoord *  _chain_coords, const uint32 *  _chain_pref_gids, const uint32 *  _chain_suffix_gids, const uint32 *  _chain_offsets, const uint32 *  _adj_extraction_offsets, const uint32 *  _chain_overlaps, const uint32  _kmer_size, const uint32  _uid_offset, SequenceSetKmerCoord *  _kmers_out, uint32 *  _prefix_uids, uint32 *  _suffix_uids  )

inline

Definition at line 831 of file kmers_inl.h.

Member Function Documentation

template<typename string_set_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void extract_non_overlapped_repeats< string_set_type >::operator() ( const uint32  idx) const

inline

Definition at line 852 of file kmers_inl.h.

Member Data Documentation

template<typename string_set_type >

const uint32* extract_non_overlapped_repeats< string_set_type >::adj_extraction_offsets

Definition at line 820 of file kmers_inl.h.

template<typename string_set_type >

const uint32* extract_non_overlapped_repeats< string_set_type >::chain_offsets

Definition at line 819 of file kmers_inl.h.

template<typename string_set_type >

const uint32* extract_non_overlapped_repeats< string_set_type >::chain_overlaps

Definition at line 821 of file kmers_inl.h.

template<typename string_set_type >

const uint32 extract_non_overlapped_repeats< string_set_type >::kmer_size

Definition at line 822 of file kmers_inl.h.

template<typename string_set_type >

SequenceSetKmerCoord* extract_non_overlapped_repeats< string_set_type >::kmers_out

Definition at line 826 of file kmers_inl.h.

template<typename string_set_type >

uint32* extract_non_overlapped_repeats< string_set_type >::prefix_uids

Definition at line 827 of file kmers_inl.h.

template<typename string_set_type >

const uniform_seeds_functor extract_non_overlapped_repeats< string_set_type >::seeder

Definition at line 824 of file kmers_inl.h.

template<typename string_set_type >

const string_set_type extract_non_overlapped_repeats< string_set_type >::string_set

Definition at line 815 of file kmers_inl.h.

template<typename string_set_type >

uint32* extract_non_overlapped_repeats< string_set_type >::suffix_uids

Definition at line 828 of file kmers_inl.h.

template<typename string_set_type >

const SequenceSetKmerCoord* extract_non_overlapped_repeats< string_set_type >::super_coords

Definition at line 816 of file kmers_inl.h.

template<typename string_set_type >

const uint32* extract_non_overlapped_repeats< string_set_type >::super_prefix_global_ids

Definition at line 817 of file kmers_inl.h.

template<typename string_set_type >

const uint32* extract_non_overlapped_repeats< string_set_type >::super_suffix_global_ids

Definition at line 818 of file kmers_inl.h.

template<typename string_set_type >

const uint32 extract_non_overlapped_repeats< string_set_type >::uid_offset

Definition at line 823 of file kmers_inl.h.

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

• E:/git/nvbio/nvMicroAssembly/kmers_inl.h