NCBI C++ ToolKit
Functions
blastkmerindex.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/blast/proteinkmer/blastkmerindex.hpp>
#include <algo/blast/proteinkmer/blastkmerutils.hpp>
#include <algo/blast/proteinkmer/mhfile.hpp>
#include <corelib/ncbifile.hpp>
#include "pearson.hpp"
+ Include dependency graph for blastkmerindex.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions

uint32_t uhash (uint64_t x, uint64_t a, uint64_t b)
 
static Uint4 FNV_hash (uint32_t num)
 FNV Hash. See http://www.isthe.com/chongo/tech/comp/fnv/index.html. More...
 
void s_MinhashSequences (uint32_t q_oid, CSeqDB &db, vector< vector< vector< uint32_t > > > &seq_hash, uint32_t *dead, int num_hashes, const uint32_t *a, const uint32_t *b, bool do_seg, int kmerNum, int oidOffset, int alphabetChoice, int version, int chunkSize)
 
void s_MinhashSequences2 (uint32_t q_oid, CSeqDB &db, vector< vector< vector< uint32_t > > > &seq_hash, uint32_t *dead, int num_hashes, int kmerNum, int oidOffset, int alphabetChoice, int version, vector< int > badMers, int chunkSize)
 
static void s_Get_LSH_index_hashes (vector< vector< vector< uint32_t > > > &seq_hash, vector< vector< uint32_t > > &lsh, int q_oid, int numBands, int numRows, int &total_chunks, uint8_t *uniqueHash)
 
static void s_Get_LSH_index_hashes2 (vector< vector< vector< uint32_t > > > &seq_hash, vector< vector< uint32_t > > &lsh, int q_oid, int num_k, int num_l, int array_size, int &total_chunks, uint8_t *uniqueHash, vector< vector< int > > &kvector)
 
static void s_Get_LSH_index_hashes5 (vector< vector< vector< uint32_t > > > &seq_hash, vector< vector< uint32_t > > &lsh, int q_oid, int numHashes, int numRows, int &total_chunks, uint8_t *uniqueHash)
 
vector< ints_BlastKmerLoadBadMers (int alphabet)
 

Function Documentation

◆ FNV_hash()

static Uint4 FNV_hash ( uint32_t  num)
static

◆ s_BlastKmerLoadBadMers()

vector<int> s_BlastKmerLoadBadMers ( int  alphabet)

Definition at line 497 of file blastkmerindex.cpp.

References in().

Referenced by CBlastKmerBuildIndex::x_BuildIndex().

◆ s_Get_LSH_index_hashes()

static void s_Get_LSH_index_hashes ( vector< vector< vector< uint32_t > > > &  seq_hash,
vector< vector< uint32_t > > &  lsh,
int  q_oid,
int  numBands,
int  numRows,
int total_chunks,
uint8_t uniqueHash 
)
static

◆ s_Get_LSH_index_hashes2()

static void s_Get_LSH_index_hashes2 ( vector< vector< vector< uint32_t > > > &  seq_hash,
vector< vector< uint32_t > > &  lsh,
int  q_oid,
int  num_k,
int  num_l,
int  array_size,
int total_chunks,
uint8_t uniqueHash,
vector< vector< int > > &  kvector 
)
static

◆ s_Get_LSH_index_hashes5()

static void s_Get_LSH_index_hashes5 ( vector< vector< vector< uint32_t > > > &  seq_hash,
vector< vector< uint32_t > > &  lsh,
int  q_oid,
int  numHashes,
int  numRows,
int total_chunks,
uint8_t uniqueHash 
)
static

◆ s_MinhashSequences()

void s_MinhashSequences ( uint32_t  q_oid,
CSeqDB db,
vector< vector< vector< uint32_t > > > &  seq_hash,
uint32_t dead,
int  num_hashes,
const uint32_t a,
const uint32_t b,
bool  do_seg,
int  kmerNum,
int  oidOffset,
int  alphabetChoice,
int  version,
int  chunkSize 
)

◆ s_MinhashSequences2()

void s_MinhashSequences2 ( uint32_t  q_oid,
CSeqDB db,
vector< vector< vector< uint32_t > > > &  seq_hash,
uint32_t dead,
int  num_hashes,
int  kmerNum,
int  oidOffset,
int  alphabetChoice,
int  version,
vector< int badMers,
int  chunkSize 
)

◆ uhash()

uint32_t uhash ( uint64_t  x,
uint64_t  a,
uint64_t  b 
)
inline

Definition at line 138 of file blastkmerindex.cpp.

References a, b, and PKMER_PRIME.

Referenced by s_MinhashSequences().

Modified on Mon Jul 22 05:05:20 2024 by modify_doxy.py rev. 669887