NCBI C++ ToolKit
Classes | Functions | Variables
vdbblast_local.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbiapp.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/psiblast_options.hpp>
#include <algo/blast/api/psiblast.hpp>
#include <corelib/ncbithr.hpp>
#include <corelib/ncbitime.hpp>
#include <corelib/ncbimtx.hpp>
#include <corelib/ncbiexpt.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/tblastn_options.hpp>
#include <algo/blast/vdb/vdb2blast_util.hpp>
#include <algo/blast/vdb/vdbblast_local.hpp>
+ Include dependency graph for vdbblast_local.cpp:

Go to the source code of this file.

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Classes

struct  SVDBThreadResult
 
class  CVDBThread
 
struct  SSortStruct
 

Functions

const string k_NOT_CSRA_DB ("NOT_CSRA")
 
const string k_CSRA_CHUNK ("CSRA_CHUNK: ")
 
static void s_MergeAlignSet (CSeq_align_set &final_set, const CSeq_align_set &input_set, const int list_size)
 
static CRef< CSearchResultSets_CombineSearchSets (vector< CRef< CSearchResultSet > > &t, unsigned int num_of_threads, const int list_size)
 
CRef< CSearchResultSets_RunLocalVDBSearch (const string &dbs, CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opt_handle, Int4 &num_extensions, bool include_filtered_reads)
 
CRef< CSearchResultSets_RunPsiVDBSearch (const string &dbs, CRef< CPssmWithParameters > pssm, CRef< CBlastOptionsHandle > opt_handle, bool include_filtered_reads)
 
static bool s_SortDbSize (const SSortStruct &a, const SSortStruct &b)
 
static void s_DivideDBsForThread (unsigned int num_threads, vector< SSortStruct > &in_list, vector< vector< SSortStruct > > &out_list, vector< Uint8 > &acc_size)
 
static void s_RemoveNonCSRAEntry (vector< SSortStruct > &in_list)
 
static void s_GetChunksForThread (vector< SSortStruct > &in_list, vector< string > &chunks, const unsigned int dbs_per_chunk, const string tag)
 
static unsigned int s_GetNumDbsPerChunk (unsigned int num_threads, unsigned int num_dbs)
 
void s_TrimResults (CSearchResultSet &rs, int hit_list_size)
 
static int s_GetModifiedHitlistSize (const int orig_size)
 
CRef< CBlastQueryVectors_CloneBlastQueryVector (const CBlastQueryVector &orig)
 

Variables

static const unsigned int DEFAULT_MAX_DBS_OPEN = 8000
 
static const unsigned int DEFAULT_MAX_DBS_PER_CHUNK = 1500
 

Function Documentation

◆ k_CSRA_CHUNK()

const string k_CSRA_CHUNK ( "CSRA_CHUNK: "  )

◆ k_NOT_CSRA_DB()

const string k_NOT_CSRA_DB ( "NOT_CSRA"  )

◆ s_CloneBlastQueryVector()

CRef<CBlastQueryVector> s_CloneBlastQueryVector ( const CBlastQueryVector orig)

Definition at line 767 of file vdbblast_local.cpp.

References GetScope(), i, orig, and CBlastQueryVector::push_back().

Referenced by CLocalVDBBlast::x_PrepareQuery().

◆ s_CombineSearchSets()

static CRef<CSearchResultSet> s_CombineSearchSets ( vector< CRef< CSearchResultSet > > &  t,
unsigned int  num_of_threads,
const int  list_size 
)
static

◆ s_DivideDBsForThread()

static void s_DivideDBsForThread ( unsigned int  num_threads,
vector< SSortStruct > &  in_list,
vector< vector< SSortStruct > > &  out_list,
vector< Uint8 > &  acc_size 
)
static

Definition at line 410 of file vdbblast_local.cpp.

References i, in_list(), s_SortDbSize(), and ct::sort().

Referenced by CLocalVDBBlast::PreprocessDBs().

◆ s_GetChunksForThread()

static void s_GetChunksForThread ( vector< SSortStruct > &  in_list,
vector< string > &  chunks,
const unsigned int  dbs_per_chunk,
const string  tag 
)
static

Definition at line 441 of file vdbblast_local.cpp.

References _TRACE, i, in_list(), kEmptyStr, kMax_I4, and tag.

Referenced by CLocalVDBBlast::PreprocessDBs().

◆ s_GetModifiedHitlistSize()

static int s_GetModifiedHitlistSize ( const int  orig_size)
static

Definition at line 682 of file vdbblast_local.cpp.

Referenced by CLocalVDBBlast::Run().

◆ s_GetNumDbsPerChunk()

static unsigned int s_GetNumDbsPerChunk ( unsigned int  num_threads,
unsigned int  num_dbs 
)
static

◆ s_MergeAlignSet()

static void s_MergeAlignSet ( CSeq_align_set final_set,
const CSeq_align_set input_set,
const int  list_size 
)
static

◆ s_RemoveNonCSRAEntry()

static void s_RemoveNonCSRAEntry ( vector< SSortStruct > &  in_list)
static

Definition at line 428 of file vdbblast_local.cpp.

References i, in_list(), and k_NOT_CSRA_DB().

Referenced by CLocalVDBBlast::PreprocessDBs().

◆ s_RunLocalVDBSearch()

CRef<CSearchResultSet> s_RunLocalVDBSearch ( const string dbs,
CRef< IQueryFactory query_factory,
CRef< CBlastOptionsHandle opt_handle,
Int4 num_extensions,
bool  include_filtered_reads 
)

◆ s_RunPsiVDBSearch()

CRef<CSearchResultSet> s_RunPsiVDBSearch ( const string dbs,
CRef< CPssmWithParameters pssm,
CRef< CBlastOptionsHandle opt_handle,
bool  include_filtered_reads 
)

◆ s_SortDbSize()

static bool s_SortDbSize ( const SSortStruct a,
const SSortStruct b 
)
static

Definition at line 404 of file vdbblast_local.cpp.

References a, and b.

Referenced by s_DivideDBsForThread().

◆ s_TrimResults()

void s_TrimResults ( CSearchResultSet rs,
int  hit_list_size 
)

Definition at line 674 of file vdbblast_local.cpp.

References i, and CSearchResultSet::size().

Referenced by CLocalVDBBlast::Run().

Variable Documentation

◆ DEFAULT_MAX_DBS_OPEN

const unsigned int DEFAULT_MAX_DBS_OPEN = 8000
static

Definition at line 473 of file vdbblast_local.cpp.

Referenced by s_GetNumDbsPerChunk().

◆ DEFAULT_MAX_DBS_PER_CHUNK

const unsigned int DEFAULT_MAX_DBS_PER_CHUNK = 1500
static

Definition at line 474 of file vdbblast_local.cpp.

Referenced by s_GetNumDbsPerChunk().

Modified on Fri Mar 01 10:07:20 2024 by modify_doxy.py rev. 669887