src/algo/blast/api/blast_dbindex.cpp File Reference

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Detailed Description

Functionality for indexed databases.

Definition in file blast_dbindex.cpp.

#include <ncbi_pch.hpp>
#include <sstream>
#include <list>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbithr.hpp>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_util.h>
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <algo/blast/api/blast_dbindex.hpp>
#include <algo/blast/dbindex/dbindex.hpp>
#include "algo/blast/core/mb_indexed_lookup.h"

Include dependency graph for blast_dbindex.cpp:

Go to the source code of this file.

Classes
struct	SIndexedDbNewArgs
	This structure is used to transfer arguments to s_IDbSrcNew(). More...
class	CIndexedDb
	This class is responsible for loading indices and doing the actual seed search. More...
struct	CIndexedDb::SThreadLocal
	Data local to a running thread. More...
class	CPreSearchThread
	One thread of the indexed seed search. More...
Functions
static BlastSeqSrc *	s_IDbSrcNew (BlastSeqSrc *retval, void *args)
	Construct a new instance of index based subject sequence source.
static BlastSeqSrc *	s_CloneSrcNew (BlastSeqSrc *retval, void *args)
	Construct a copy of BlastSeqSrc structure.
static unsigned long	s_MB_IdbGetResults (void *idb_v, Int4 oid_i, Int4 chunk_i, BlastInitHitList *init_hitlist)
	Get the seed search results for a give subject id and chunk number.
	USING_SCOPE (ncbi::objects)
	USING_SCOPE (ncbi::blastdbindex)
int	MinIndexWordSize ()
	Get minimal word size accepted by indexing library.
static void	NullPreSearch (BlastSeqSrc *, LookupTableWrap *, BLAST_SequenceBlk *, BlastSeqLoc *, LookupTableOptions *, BlastInitialWordOptions *)
	No-op presearch function.
static void	NullSetQueryInfo (BlastSeqSrc *, LookupTableWrap *, CRef< CBlastSeqLocWrap >)
	No-op callback for setting query info.
static void	NullRunSearch (BlastSeqSrc *, BLAST_SequenceBlk *, LookupTableOptions *, BlastInitialWordOptions *)
	No-op callback to run indexed search.
static void	NullSetNumThreads (BlastSeqSrc *seq_src, size_t)
	No-op callback to set the number of threads for indexed search.
static void	IndexedDbSetNumThreads (BlastSeqSrc *seq_src, size_t n_threads)
	Set the number of treads for indexed search.
static void	IndexedDbRunSearch (BlastSeqSrc *seq_src, BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Run indexed search.
static void	IndexedDbSetQueryInfo (BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)
	Set information about unmasked query segments.
static void	IndexedDbPreSearch (BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Callback that is called for index based seed search.
BlastSeqSrc *	DbIndexSeqSrcInit (const string &indexname, BlastSeqSrc *db)
	Wrap a BlastSeqSrc object db by another object that provides index based seed searching.
BlastSeqSrc *	CloneSeqSrcInit (BlastSeqSrc *src)
	Creates a clone of a BlastSeqSrc structure.
void	CloneSeqSrc (BlastSeqSrc *dst, BlastSeqSrc *src)
	Copies the contents of src to dst.
DbIndexPreSearchFnType	GetDbIndexPreSearchFn ()
	Return the appropriate pre-search callback.
DbIndexSetQueryInfoFnType	GetDbIndexSetQueryInfoFn ()
	Return the appropriate callback to set query information in the index.
DbIndexRunSearchFnType	GetDbIndexRunSearchFn ()
	Return the appropriate callback to run indexed seed search.
DbIndexSetNumThreadsFnType	GetDbIndexSetNumThreadsFn ()
	Return the appropriate callback to set the number of threads for indexed seed search.
END_NCBI_SCOPE	USING_SCOPE (ncbi)
	USING_SCOPE (ncbi::blast)
static BlastSeqSrc *	s_GetForwardSeqSrc (void *handle)
	C language wrapper around CIndexedDb::GetDb().
static void *	s_GetForwardSeqDb (void *handle)
	C language wrapper around CIndexedDb::GetSeqDb().
static Int4	s_IDbGetNumSeqs (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetNumSeqsStats (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetMaxLength (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetAvgLength (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int8	s_IDbGetTotLen (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int8	s_IDbGetTotLenStats (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static const char *	s_IDbGetName (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Boolean	s_IDbGetIsProt (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int2	s_IDbGetSequence (void *handle, BlastSeqSrcGetSeqArg *seq_arg)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbGetSeqLen (void *handle, void *x)
	Forwards the call to CIndexedDb::db_.
static Int4	s_IDbIteratorNext (void *handle, BlastSeqSrcIterator *itr)
	Forwards the call to CIndexedDb::db_ but skip over the ones for which no results were poduces by pre-search.
static void	s_IDbReleaseSequence (void *handle, BlastSeqSrcGetSeqArg *getseq_arg)
	Forwards the call to CIndexedDb::db_.
static void	s_IDbResetChunkIterator (void *handle)
	Forwards the call to CIndexedDb::db_.
static BlastSeqSrc *	s_IDbSrcFree (BlastSeqSrc *seq_src)
	Destroy the sequence source.
static BlastSeqSrc *	s_IDbSrcCopy (BlastSeqSrc *seq_src)
	Fill the BlastSeqSrc data with a copy of its own contents.
static void	s_IDbSrcInit (BlastSeqSrc *retval, CIndexedDb::TThreadLocal *idb)
	Initialize the BlastSeqSrc data structure with the appropriate callbacks.
Variables
static DbIndexPreSearchFnType	PreSearchFn = &NullPreSearch
	Global pointer to the appropriate pre-search function, based on whether or not index search is enabled.
static DbIndexSetQueryInfoFnType	SetQueryInfoFn = &NullSetQueryInfo
	Global pointer to the appropriate callback to set query info, based on whether or not index search is enabled.
static DbIndexRunSearchFnType	RunSearchFn = &NullRunSearch
	Global pointer to the appropriate callback to run indexed search, based on whether or not index search is enabled.
static DbIndexSetNumThreadsFnType	SetNumThreadsFn = &NullSetNumThreads
	Global pointer to the appropriate to set number of threads for indexed search, based on whether or not index search is enabled.

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