CSequenceColl Class Reference

Collection of sequences and k-mer fingerprint vectors. More...

Public Types
typedef std::vector< unsigned char >	buffer_type

Public Member Functions
	CSequenceColl ()
	CSequenceColl (const CSequenceColl &)=delete
void	add_sequence (const string &acc, vector_char_type *seq_ptr)
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void	set_buffer (size_t i, const buffer_type &buf)
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void	sync_buffers_size ()
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size_t	size () const
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const string &	get_acc (size_t i) const
const vector_char_type &	get_sequence (size_t i) const
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size_t	seq_size (size_t i) const
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size_t	total_seq_size () const
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size_t	buf_size () const
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size_t	get_buf_size (size_t i) const
	Get k-mer vector BLOB size. More...
const unsigned char *	get_buf (size_t i) const
	Get k-mer BLOB pointer. More...
void	deserialize_k_mers (bvector_ptr_vector_type &k_mers_vect, const bm::bvector<> &bv_req, bm::bvector<>::size_type bv_req_count) const
	Deserialize group of k-mer fingerprint vectors. More...

Detailed Description

Collection of sequences and k-mer fingerprint vectors.

Examples

xsample07a.cpp.

Definition at line 130 of file xsample07a.cpp.

Member Function Documentation

add_sequence()

void CSequenceColl::add_sequence ( const string &  acc, vector_char_type *  seq_ptr  )

inline

Examples

xsample07a.cpp.

Definition at line 140 of file xsample07a.cpp.

Referenced by load_FASTA().

buf_size()

size_t CSequenceColl::buf_size ( ) const

inline

Examples

xsample07a.cpp.

Definition at line 180 of file xsample07a.cpp.

Referenced by compute_group(), compute_jaccard_clusters(), and main().

deserialize_k_mers()

void CSequenceColl::deserialize_k_mers	(	bvector_ptr_vector_type &	k_mers_vect,
		const bm::bvector<> &	bv_req,
		bm::bvector<>::size_type	bv_req_count
	)		const

Deserialize group of k-mer fingerprint vectors.

Examples

xsample07a.cpp.

Definition at line 208 of file xsample07a.cpp.

References BM_DECLARE_TEMP_BLOCK, bm::deserialize(), bm::bvector< Alloc >::first(), get_buf(), and bm::bvector< Alloc >::iterator_base::valid().

Referenced by compute_and_sim().

get_buf()

const unsigned char* CSequenceColl::get_buf ( size_t  i ) const

inline

Get k-mer BLOB pointer.

Examples

xsample07a.cpp.

Definition at line 186 of file xsample07a.cpp.

Referenced by assign_to_best_cluster(), assign_to_best_cluster_union(), compute_group(), compute_seq_group_union(), deserialize_k_mers(), CSeqClusters::elect_leaders(), resolve_duplicates(), and save_kmer_buffers().

get_buf_size()

size_t CSequenceColl::get_buf_size ( size_t  i ) const

inline

Get k-mer vector BLOB size.

Examples

xsample07a.cpp.

Definition at line 183 of file xsample07a.cpp.

Referenced by save_kmer_buffers().

get_sequence()

const vector_char_type& CSequenceColl::get_sequence ( size_t  i ) const

inline

Examples

xsample07a.cpp.

Definition at line 167 of file xsample07a.cpp.

Referenced by generate_k_mers().

seq_size()

size_t CSequenceColl::seq_size ( size_t  i ) const

inline

Examples

xsample07a.cpp.

Definition at line 169 of file xsample07a.cpp.

Referenced by generate_k_mers_parallel(), and total_seq_size().

set_buffer()

void CSequenceColl::set_buffer ( size_t  i, const buffer_type &  buf  )

inline

Examples

xsample07a.cpp.

Definition at line 146 of file xsample07a.cpp.

Referenced by generate_k_mers(), and load_kmer_buffers().

size()

size_t CSequenceColl::size ( ) const

inline

Examples

xsample07a.cpp.

Definition at line 163 of file xsample07a.cpp.

Referenced by generate_k_mers(), generate_k_mers_parallel(), main(), save_kmer_buffers(), and sync_buffers_size().

sync_buffers_size()

void CSequenceColl::sync_buffers_size ( )

inline

Examples

xsample07a.cpp.

Definition at line 158 of file xsample07a.cpp.

References size().

Referenced by main().

total_seq_size()

size_t CSequenceColl::total_seq_size ( ) const

inline

Examples

xsample07a.cpp.

Definition at line 171 of file xsample07a.cpp.

References seq_size().

Referenced by generate_k_mers_parallel().

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

• xsample07a.cpp