BitMagic-C++
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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... | |
Collection of sequences and k-mer fingerprint vectors.
Definition at line 130 of file xsample07a.cpp.
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Definition at line 180 of file xsample07a.cpp.
Referenced by compute_group(), compute_jaccard_clusters(), and main().
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.
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().
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Get k-mer BLOB pointer.
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().
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Get k-mer vector BLOB size.
Definition at line 183 of file xsample07a.cpp.
Referenced by save_kmer_buffers().
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Definition at line 167 of file xsample07a.cpp.
Referenced by generate_k_mers().
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Definition at line 169 of file xsample07a.cpp.
Referenced by generate_k_mers_parallel(), and total_seq_size().
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Definition at line 146 of file xsample07a.cpp.
Referenced by generate_k_mers(), and load_kmer_buffers().
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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().
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Definition at line 158 of file xsample07a.cpp.
References size().
Referenced by main().
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Definition at line 171 of file xsample07a.cpp.
References seq_size().
Referenced by generate_k_mers_parallel().