BitMagic-C++: CSequenceColl Class Reference

BitMagic-C++

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)
void	set_buffer (size_t i, const buffer_type &buf)
void	sync_buffers_size ()
size_t	size () const
const string &	get_acc (size_t i) const
const vector_char_type &	get_sequence (size_t i) const
size_t	seq_size (size_t i) const
size_t	total_seq_size () const
size_t	buf_size () const
size_t	get_buf_size (size_t i) const
	Get k-mer vector BLOB size.
const unsigned char *	get_buf (size_t i) const
	Get k-mer BLOB pointer.
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.

Detailed Description

Collection of sequences and k-mer fingerprint vectors.

Examples: xsample07a.cpp.

Definition at line 130 of file xsample07a.cpp.

Member Typedef Documentation

◆ buffer_type

typedef std::vector<unsigned char> CSequenceColl::buffer_type

Examples: xsample07a.cpp.

Definition at line 133 of file xsample07a.cpp.

Constructor & Destructor Documentation

◆ CSequenceColl() [1/2]

CSequenceColl::CSequenceColl ( )

inline

Examples: xsample07a.cpp.

Definition at line 136 of file xsample07a.cpp.

Referenced by CSequenceColl().

◆ CSequenceColl() [2/2]

CSequenceColl::CSequenceColl ( const CSequenceColl & )

delete

References CSequenceColl().

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_acc()

const string & CSequenceColl::get_acc ( size_t i ) const

inline

Examples: xsample07a.cpp.

Definition at line 166 of file xsample07a.cpp.

◆ 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().

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

xsample07a.cpp