#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 SVN repository for this file.

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

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

CRef< CSearchResultSet >	s_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< CBlastQueryVector >	s_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: " )

Referenced by CLocalVDBBlast::PreprocessDBs(), s_RunLocalVDBSearch(), and s_RunPsiVDBSearch().

◆ k_NOT_CSRA_DB()

const string k_NOT_CSRA_DB ( "NOT_CSRA" )

Referenced by CLocalVDBBlast::PreprocessDBs(), and s_RemoveNonCSRAEntry().

◆ 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

Definition at line 139 of file vdbblast_local.cpp.

References CSearchResultSet::clear(), TQueryMessages::Combine(), CSeq_align_set_Base::Get(), GetSeqId(), i, CSeq_align_set::IsEmpty(), CSearchResultSet::push_back(), s_MergeAlignSet(), CSeq_align_set_Base::Set(), and t.

Referenced by CLocalVDBBlast::Run(), CVDBThread::RunTandemSearches(), and CLocalVDBBlast::RunThreadedSearch().

◆ 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

Definition at line 476 of file vdbblast_local.cpp.

References DEFAULT_MAX_DBS_OPEN, DEFAULT_MAX_DBS_PER_CHUNK, env, kEmptyStr, min(), and NStr::StringToUInt().

Referenced by CLocalVDBBlast::PreprocessDBs().

◆ s_MergeAlignSet()

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

static

Definition at line 57 of file vdbblast_local.cpp.

References CSeq_align::eScore_BitScore, CSeq_align::eScore_EValue, kMax_UI8, and CSeq_id::Match().

Referenced by s_CombineSearchSets().

◆ 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
	)

Definition at line 191 of file vdbblast_local.cpp.

References ERR_POST, exit(), CLocalBlast::GetNumExtensions(), CVDBBlastUtil::GetSRASeqInfoSrc(), CVDBBlastUtil::GetSRASeqSrc(), k_CSRA_CHUNK(), kEmptyStr, CThreadable::kMinNumThreads, results, CLocalBlast::Run(), CThreadable::SetNumberOfThreads(), and CException::what().

Referenced by CVDBThread::Main(), CLocalVDBBlast::Run(), and CVDBThread::RunTandemSearches().

◆ s_RunPsiVDBSearch()

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