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NCBI C++ ToolKit: include/algo/blast/proteinkmer/blastkmerutils.hpp File Reference

USING_SCOPE (blast) set< uint32_t > BlastKmerGetKmerSet (const string &query_sequence, bool do_seg, TSeqRange &range, int kmerNum, int alphabetChoice) Get KMERs for a given sequence using a compressed alphabet. More...
set< uint32_t > BlastKmerGetKmerSet2 (const string &query_sequence, TSeqRange &range, int kmerNum, int alphabetChoice, vector< int > badMers) Get KMERs for a given sequence using a compressed alphabet. More...
set< uint32_t > BlastKmerGetKmerSetStats (const string &query_sequence, int kmerNum, map< string, int > &kmerCount, map< string, int > &kmerCountPlus, int alphabetChoice, bool perQuery) Simplified version of BlastKmerGetKmerSet. More...
int BlastKmerBreakUpSequence (int length, vector< TSeqRange > &range_v, int chunkSize) Breaks a sequences up into chunks if the sequences is above a certain length. More...
void BlastKmerGetCompressedTranslationTable (vector< Uint1 > &trans_table, int alphabetChoice) Creates translation table for compressed alphabets. More...
int BlastKmerGetDistance (const vector< uint32_t > &minhash1, const vector< uint32_t > &minhash2) Calculates the number of differences between two minhash arrays. More...
bool minhash_query (const string &query, vector< vector< uint32_t > > &seq_hash, int num_hashes, uint32_t *a, uint32_t *b, int do_seg, int kmerNum, int alphabetChoice, int chunkSize) bool minhash_query2 (const string &query, vector< vector< uint32_t > > &seq_hash, int kmerNum, int numHashes, int alphabetChoice, vector< int > badMers, int chunkSize) Hash the query for the minimum values;. More...
void get_LSH_match_from_hash (const vector< vector< uint32_t > > &lsh_hash_vec, const uint64_t *lsh_array, vector< set< uint32_t > > &candidates) void get_LSH_hashes (vector< vector< uint32_t > > &query_hash, vector< vector< uint32_t > > &lsh_hash_vec, int num_bands, int rows_per_band) void get_LSH_hashes5 (vector< vector< uint32_t > > &query_hash, vector< vector< uint32_t > > &lsh_hash_vec, int numHashes, int numRows) Gets the LSH hash for one hash function. More...
void neighbor_query (const vector< vector< uint32_t > > &query_hash, const uint64_t *lsh, vector< set< uint32_t > > &candidates, CMinHashFile &mhfile, int num_hashes, int min_hits, double thresh, TBlastKmerPrelimScoreVector &score_vector, BlastKmerStats &kmer_stats, int kmerVersion) void GetRandomNumbers (uint32_t *a, uint32_t *b, int numHashes) Get the random numbers for the hash function. More...
void GetKValues (vector< vector< int > > &kvector, int k_value, int l_value, int array_size) Function to get the k sites to compare for Buhler LSH. More...
void get_LSH_hashes2 (vector< vector< uint32_t > > &query_hash, vector< vector< uint32_t > > &lsh_hash_vec, int num_k, int num_l, vector< vector< int > > &kValues) int BlastKmerVerifyIndex (CRef< CSeqDB > seqdb, string &error_msg) ◆ PKMER_PRIME ◆ TBlastKmerPrelimScoreVector

Vector of pairs of database OIDs and scores.

ONLY for use during KMER search, not presentation of results or communication with other modules (BLAST or not).

Definition at line 122 of file blastkmerutils.hpp.

◆ BlastKmerBreakUpSequence() ◆ BlastKmerGetCompressedTranslationTable() void BlastKmerGetCompressedTranslationTable ( vector< Uint1 > & trans_table, int alphabetChoice ) ◆ BlastKmerGetDistance()

Calculates the number of differences between two minhash arrays.

Used to decide whether two arrays are similar enough. The assumption is made that both arrays are of the same size.

Parameters: minhash1 First array [in] minhash2 Second array [in]

Returns: distance.

Definition at line 399 of file blastkmerutils.cpp.

Referenced by s_MinhashSequences(), and s_MinhashSequences2().

◆ BlastKmerGetKmerSet()

Get KMERs for a given sequence using a compressed alphabet.

Parameters: query_sequence string with one sequence [in] do_seg Should the sequence be segged (not recommended) [in] range portion of sequence to be processed [in] kmerNum size of kmer [in] alphabetChoice 0 is 15 letter, 1 is 10 letter alphabet [in]

Returns: set of unsigned ints for the kmers.

Definition at line 206 of file blastkmerutils.cpp.

References BlastKmerGetCompressedTranslationTable(), BlastSeqLocFree(), free(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), i, set< Key, Compare >::insert(), malloc(), BlastSeqLoc::next, NULL, query, SegParametersFree(), SegParametersNewAa(), and SeqBufferSeg().

Referenced by minhash_query(), and s_MinhashSequences().

◆ BlastKmerGetKmerSet2()

Get KMERs for a given sequence using a compressed alphabet.

This version can read in overrepresented KMERs and extend them by one.

Parameters: query_sequence string with one sequence [in] range portion of sequence to be processed [in] kmerNum size of kmer [in] alphabetChoice 0 is 15 letter, 1 is 10 letter alphabet [in] badMers Overrepresented KMERs [in]

Returns: set of unsigned ints for the kmers.

Definition at line 270 of file blastkmerutils.cpp.

References BlastKmerGetCompressedTranslationTable(), free(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), i, set< Key, Compare >::insert(), malloc(), and query.

Referenced by minhash_query2(), and s_MinhashSequences2().

◆ BlastKmerGetKmerSetStats() ◆ BlastKmerVerifyIndex() ◆ get_LSH_hashes() void get_LSH_hashes ( vector< vector< uint32_t > > & query_hash, vector< vector< uint32_t > > & lsh_hash_vec, int num_bands, int rows_per_band ) ◆ get_LSH_hashes2() void get_LSH_hashes2 ( vector< vector< uint32_t > > & query_hash, vector< vector< uint32_t > > & lsh_hash_vec, int num_k, int num_l, vector< vector< int > > & kValues ) ◆ get_LSH_hashes5() void get_LSH_hashes5 ( vector< vector< uint32_t > > & query_hash, vector< vector< uint32_t > > & lsh_hash_vec, int numHashes, int numRows ) ◆ get_LSH_match_from_hash() ◆ GetKValues() void GetKValues ( vector< vector< int > > & kvector, int k_value, int l_value, int array_size ) ◆ GetRandomNumbers() ◆ minhash_query()

Definition at line 415 of file blastkmerutils.cpp.

References a, b, set< Key, Compare >::begin(), BlastKmerBreakUpSequence(), BlastKmerGetKmerSet(), set< Key, Compare >::empty(), set< Key, Compare >::end(), i, query, and uhash().

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmer::x_ProcessQuery().

◆ minhash_query2()

Hash the query for the minimum values;.

Parameters: query as a ASCII string [in] seq_hash hash values for all kmers [out] kmerNum number of letters in a KMER [in] numHashes number of hashes in a signature [in] alphabetChoice 15 or 10 letters [in] badMers Overrepresented KMERS [in]

Definition at line 479 of file blastkmerutils.cpp.

References set< Key, Compare >::begin(), BlastKmerBreakUpSequence(), BlastKmerGetKmerSet2(), set< Key, Compare >::empty(), set< Key, Compare >::end(), FNV_hash(), i, query, and ct::sort().

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmer::x_ProcessQuery().

◆ neighbor_query()

Definition at line 744 of file blastkmerutils.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), estimate_jaccard(), estimate_jaccard2(), CMinHashFile::GetDataWidth(), CMinHashFile::GetHits(), CMinHashFile::GetMinHits(), CMinHashFile::GetVersion(), BlastKmerStats::hit_count, i, map_checker< Container >::insert(), int, BlastKmerStats::jd_count, BlastKmerStats::jd_oid_count, n, offset, BlastKmerStats::oids_considered, read_size(), s_HashHashQuery(), ct::sort(), and BlastKmerStats::total_matches.

Referenced by CBlastKmer::x_RunKmerFile().

◆ USING_SCOPE()

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