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NCBI C++ ToolKit: src/algo/blast/api/blast_dbindex.cpp Source File

vector< CConstRef< CDbIndex::CSearchResults > >

;

( TSeqMap::size_type

= 0;

<

.size(); ++

) {

lut_options, word_options );

.start_oid <

.start_oid;

std::vector< SVolumeDescriptor >

;

TVolList::const_iterator

(

(

& indexname,

& partial );

(

<<

(multiple_threads ?

:

) );

(

<< n_threads );

( idb == 0 )

;

idb->

( queries, lut_options, word_options );

( idb == 0 )

;

( idbn == 0 )

;

( idb == 0 )

;

( idbn == 0 )

;

( idb == 0 )

;

*

=

;

string::size_type pos( 0 ), pos1( 0 );

( pos1 != string::npos ) {

pos1 = db_spec.find_first_of(

, pos );

db_names.push_back( db_spec.substr( pos, pos1 - pos ) );

idx_not_resolved(

);

<<

<< vol_name

<<

<< e.

() <<

);

idx_not_resolved =

;

( !idx_not_resolved && shdr->GetNumSeq() != dbnseq ) {

<<

<<

<< vol_name <<

);

idx_not_resolved =

;

( !idx_not_resolved ) {

curr_vols_size(

.size() );

total_idxvol_oids( 0 );

(

( 0 ), e( shdr->GetNumVol() );

< e; ++

) {

( name.empty() ) {

<<

<< name

<<

idx_not_resolved =

;

( !idx_not_resolved ) {

( idxvol_oids == 0 ) {

idx_not_resolved =

;

<<

<< name

<<

<<

<< vol_name );

total_idxvol_oids += idxvol_oids;

( idx_not_resolved ) {

( !idx_not_resolved && dbnseq != total_idxvol_oids ) {

<<

<< total_idxvol_oids <<

<<

<< dbnseq <<

idx_not_resolved =

;

partial = (partial || idx_not_resolved);

( idx_not_resolved ) {

: queries_( 0 ), multiple_threads_(

), n_threads_( 1 )

(

);

(

<< indexname );

(

);

(

);

has_index(

);

(

->has_index ) {

);

(

);

& vol_idx( *vol_idx_p );

find_volume(

);

( !find_volume )

;

TVolList::const_iterator vi(

( oid ) );

new_vol_idx = vi -

.begin();

( !vi->has_index ) { vol_idx = new_vol_idx;

; }

min_vol_idx( vol_idx == -1 ? 0 : vol_idx );

(

<< new_vol_idx <<

<< vi->name );

std::ostringstream os;

os <<

<< vi->name;

(

<< vi->name );

(

<< vi->name );

( ; min_vol_idx < new_vol_idx; ++min_vol_idx ) {

(

<<

vol_idx = new_vol_idx;

TVolList::const_iterator vi(

( oid ) );

TVolList::const_iterator vi(

.begin() + *last_vol_idx );

oid -= vi->start_oid;

TVolList::const_iterator vi(

( oid ) );

( vi->start_oid <= oid );

( vi->start_oid + vi->n_oids > oid );

oid -= vi->start_oid;

( (res = vr->

( oid, chunk )) != 0 ) {

(

<<

<< fname <<

<< rv);

( !indexnames.empty() ) {

vector< string > dbnames;

string::size_type start = 0, end = 0;

( start != string::npos ) {

end = indexnames.find_first_of(

, start );

dbnames.push_back( indexnames.substr( start, end - start ) );

start = indexnames.find_first_not_of(

, end );

dbni != dbnames.end(); ++dbni ) {

& indexname = *dbni;

start_vol = 0, stop_vol = 99;

end = indexname.find_first_of(

, start );

index_base = indexname.substr( start, end );

( start < indexname.length() && end != string::npos ) {

end = indexname.find_first_of(

, start );

( start < indexname.length() && end != string::npos ) {

end = indexname.find_first_of(

, start );

start_vol_str =

indexname.substr( start, end - start );

( !start_vol_str.empty() ) {

start_vol = atoi( start_vol_str.c_str() );

( start < indexname.length() && end != string::npos ) {

end = indexname.find_first_of(

, start );

stop_vol_str =

indexname.substr( start, end - start);

( !stop_vol_str.empty() ) {

stop_vol = atoi( stop_vol_str.c_str() );

( start_vol <= stop_vol ) {

(

= start_vol; (

long)

<= stop_vol; ++

) {

os << index_base <<

<< setw( 2 ) << setfill(

)

( !name.empty() ){

(

- last_i > 1 ) {

(

j = last_i + 1; j <

; ++j ) {

<< j <<

);

(

);

+= indexnames +

;

( vector< string >::size_type v = 0;

(

) +

( (res =

->GetResults( oid, chunk )) != 0 ) {

->GetWordSize();

(word_size < min_ws) {

rv =

;

rv =

;

rv =

;

& indexname,

old_style,

& partial,

word_size )

(

<<

;

(

<<

;

( init_hitlist != 0 );

oid, chunk, init_hitlist );

Declarations for indexed blast databases.

void(* DbIndexSetUsingThreadsFnType)(bool multiple_threads)

Type of a callback to set the concurrency state in the index structure.

void(* DbIndexRunSearchFnType)(BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Type of a callback to run the indexed seed search.

void(* DbIndexSetNumThreadsFnType)(size_t n_threads)

Type of a callback to provide the number of threads to the indexing library, when multi-threaded sear...

void(* DbIndexSetQueryInfoFnType)(LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)

Type of a callback to set the query information in the index structure.

void BlastInitHitListReset(BlastInitHitList *init_hitlist)

Free the ungapped data substructures and reset initial HSP count to 0.

void BlastInitHitListMove(BlastInitHitList *dst, BlastInitHitList *src)

Move the contents of a BlastInitHitList structure.

Structures and functions prototypes used for BLAST gapped extension.

Structures and API used for saving BLAST hits.

Various auxiliary BLAST utility functions.

BlastSeqLoc * getLocs() const

Get access to the held object.

unsigned long GetWordSize() const

Get the search word size.

BlastInitHitList * GetResults(TSeqNum seq) const

Get the result set for a particular logical subject.

Types of exception the indexing library can throw.

TSeqNum StartSeq() const

Get the OID of the first sequence in the index.

CConstRef< CSearchResults > Search(const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const SSearchOptions &search_options)

Search the index.

static CRef< CDbIndex > Load(const std::string &fname, bool nomap=false)

Load index.

CSequenceIStream::TStreamPos TSeqNum

Type used to enumerate sequences in the index.

TSeqNum StopSeq() const

Get the OID of the last sequence in the index.

Index wrapper exceptions.

Index wrapper for new style MegaBLAST indexing functionality.

Index wrapper for old style MegaBLAST indexing functionality.

This class is responsible for loading indices and doing the actual seed search.

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

int GetNumOIDs() const

Returns the size of the (possibly sparse) OID range.

Include a standard set of the NCBI C++ Toolkit most basic headers.

const SIndexHeader ReadIndexHeader< false >(void *map)

CRef< CIndexSuperHeader_Base > GetIndexSuperHeader(const std::string &fname)

Read superheader structure from the file.

size_t GetIdxVolNumOIDs(const std::string &fname)

Read the index header information from the given file.

static const struct name_t names[]

std::string name

Fully qualified name of the volume.

virtual int MinIndexWordSize()=0

int ref_count

How many threads still need the result set.

virtual unsigned long GetResults(CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const

Return results corresponding to a given subject sequence and chunk.

void TraceVolumes(void)

This is only used for debugging output.

DbIndexSetQueryInfoFnType GetDbIndexSetQueryInfoFn()

Return the appropriate callback to set query information in the index.

void ClearDbIndexCallbacks(void)

static DbIndexSetNumThreadsFnType SetNumThreadsFn

Global pointer to the appropriate callback to set the number of threads.

virtual ~CIndexedDb()

Object destructor.

static void IndexedDbSetUsingThreads(bool multiple_threads)

Set state of concurrency in the index structure.

vector< CConstRef< CDbIndex::CSearchResults > > TResultSet

Type used to represent collections of search result sets.

friend bool operator<(const SVolumeDescriptor &a, const SVolumeDescriptor &b)

Volumes are compared by their starting ordinal ids.

static void ParseDBNames(const std::string db_spec, TStrVec &db_names)

Generate a list of BLAST database names from a single string.

virtual int CheckOid(Int4 oid, Int4 *last_vol_id)

Check whether any results were reported for a given subject sequence.

friend std::ostream & operator<<(std::ostream &os, const SVolumeDescriptor &vd)

This is only used for debug tracing.

bool multiple_threads_

flag indicating that multithreading is in effect

CDbIndex::SSearchOptions sopt_

common search parameters

virtual ~CIndexedDb_New()

Object destructor.

virtual int CheckOid(Int4 oid, Int4 *last_vol_id)=0

Check whether any results were reported for a given subject sequence.

virtual void EndSearchIndication(Int4)

Not used.

virtual void DoPreSearch(BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Run preliminary indexed search functionality.

std::vector< std::string > TStrVec

Alias for a vector os strings.

virtual void DoPreSearch(BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Wrapper around PreSearch().

USING_SCOPE(ncbi::objects)

static DbIndexSetUsingThreadsFnType SetUsingThreadsFn

Global pointer to the appropriate callback to set the state of concurrency.

virtual void EndSearchIndication(Int4 last_vol_id)=0

Function used by threads to indicate that they are done with iterating over the database sequences.

void SetQueryInfo(CRef< CBlastSeqLocWrap > locs_wrap)

Set the current set of unmasked query segments.

void UpdateIndex(Int4 oid, Int4 *vol_idx)

Update the seed sets, if necessary.

virtual void EndSearchIndication(Int4 last_vol_id)

Function used by threads to indicate that they are done with iterating over the database sequences.

bool has_index

'true' if the volume is indexed.

static void TraceNames(const TStrVec &names)

This is only used for debugging output.

static void NullSetUsingThreads(bool)

No-op callback for setting concurrency state.

TResultsHolder results_holder_

reference counted seed set holders

static void NullRunSearch(BLAST_SequenceBlk *, LookupTableOptions *, BlastInitialWordOptions *)

No-op callback to run indexed search.

CIndexedDb_Old(const string &indexname)

Object constructor.

vector< string > index_names_

List of index volume names.

static unsigned long s_MB_IdbGetResults(Int4 oid_i, Int4 chunk_i, BlastInitHitList *init_hitlist)

Get the seed search results for a give subject id and chunk number.

TVolList volumes_

index volume descriptors

static void IndexedDbSetQueryInfo(LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)

Set information about unmasked query segments.

virtual int MinIndexWordSize()

Get the minimum acceptable word size to use with indexed search.

virtual void DoPreSearch(BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)=0

Run preliminary indexed search functionality.

static int s_MB_IdbCheckOid(Int4 oid, Int4 *last_vol_oid)

CFastMutex mtx_

mutex used for thread sync

static DbIndexSetQueryInfoFnType SetQueryInfoFn

Global pointer to the appropriate callback to set query info, based on whether or not index search is...

static int s_GetMinimumSupportedWordSizeByIndex(const string &fname)

CIndexedDb_New(const string &indexname, bool &partial)

Object constructor.

TResultSet results_

Set of result sets, one per loaded index.

static void EnumerateDbVolumes(const TStrVec &db_names, TStrVec &db_vols)

Generate a list of leaf database volumes from a list of database names.

CConstRef< CDbIndex::CSearchResults > TVolResults

This type captures the seeds found by search of an index volume.

std::string DbIndexInit(const string &indexname, bool old_style, bool &partial, const int word_size)

TVolResults res

Seed set or null.

static void NullSetNumThreads(size_t)

No-op callback for setting the number of threads.

static void IndexedDbSetNumThreads(size_t n_threads)

Set the number of concurrent search threads in the index structure.

static void IndexedDbRunSearch(BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Run indexed search.

virtual unsigned long GetResults(CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const

Return results corresponding to a given subject sequence and chunk.

static void s_MB_IdxEndSearchIndication(Int4 last_vol_id)

DbIndexSetUsingThreadsFnType GetDbIndexSetUsingThreadsFn()

Return the appropriate callback to set the concurrency state in the index structure.

TSeqMap seqmap_

For each element of indices_ with index i seqmap_[i] contains one plus the last oid of that database ...

BLAST_SequenceBlk * queries_

query data (from BLAST)

void SetMultipleThreads(bool multiple_threads)

Set the concurrency status.

DbIndexRunSearchFnType GetDbIndexRunSearchFn()

Return the appropriate callback to run indexed seed search.

std::string s_CheckMinWordSize(int word_size)

DbIndexSetNumThreadsFnType GetDbIndexSetNumThreadsFn()

Return the appropriate callback to set the number of threads in the index structure.

static DbIndexRunSearchFnType RunSearchFn

Global pointer to the appropriate callback to run indexed search, based on whether or not index searc...

std::vector< SVolResults > TResultsHolder

List of reference counted result holders.

std::vector< SVolumeDescriptor > TVolList

List of leaf index volumes.

void SetNumThreads(size_t n_threads)

Set the number of threads used for concurrent search.

TSeqMap::size_type LocateIndex(CDbIndex::TSeqNum oid) const

Find an index corresponding to the given subject id.

CRef< CBlastSeqLocWrap > locs_wrap_

Current set of unmasked query locations.

vector< CDbIndex::TSeqNum > TSeqMap

Type used to map loaded indices to subject ids.

TVolList::const_iterator FindVolume(SIZE_TYPE oid) const

Find a volume containing the given subject ordinal id.

CRef< CDbIndex > index_

Currently loaded index.

virtual int CheckOid(Int4 oid, Int4 *)

Check whether any results were reported for a given subject sequence.

static CRef< CIndexedDb > Index_Set_Instance

Shared representation of currently loaded index volumes.

void SetUpDbIndexCallbacks(void)

SIZE_TYPE start_oid

OId of the first sequence of the volume.

static void NullSetQueryInfo(LookupTableWrap *, CRef< CBlastSeqLocWrap >)

No-op callback for setting query info.

void AddIndexInfo(const std::string &vol_name, bool &idx_not_resolved)

virtual int MinIndexWordSize()

size_t n_threads_

number of search threads running

SIZE_TYPE GetNextUnusedOID(void) const

Auxiliary function thet returns the oid value that is one more than the largest oid used so far.

void PreSearch(BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Invoke the seed search procedure on each of the loaded indices.

SIZE_TYPE n_oids

Number of sequences in the volume.

virtual unsigned long GetResults(CDbIndex::TSeqNum oid, CDbIndex::TSeqNum chunk, BlastInitHitList *init_hitlist) const =0

Return results corresponding to a given subject sequence and chunk.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

void * GetPtr(void) const

Get pointer to beginning of data.

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

Declarations for functions that extract hits from indexed blast databases (specialized for megablast)

#define LAST_VOL_IDX_NULL

#define LAST_VOL_IDX_INIT

constexpr auto sort(_Init &&init)

Magic spell ;-) needed for some weird compilers... very empiric.

#define ASSERT

macro for assert.

Multi-threading – classes, functions, and features.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Defines BLAST database access classes.

Defines exception class and several constants for SeqDB.

bool SeqDB_CompareVolume(const string &volpath1, const string &volpath2)

Compares two volume file names and determine the volume order.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Structure to hold a sequence.

Structure to hold all initial HSPs for a given subject sequence.

Options needed for initial word finding and processing.

Int4 window_size

Maximal allowed distance between 2 hits in case 2 hits are required to trigger the extension.

Used to hold a set of positions, mostly used for filtering.

Simple record type used to specify index search parameters.

unsigned long two_hits

Window for two-hit method (see megablast docs).

unsigned long word_size

Target seed length.

Reference count for the volume results.

Information about one leaf index volume.

Options needed to construct a lookup table Also needed: query sequence and query length.

Int4 word_size

Determines the size of the lookup table.

Wrapper structure for different types of BLAST lookup tables.

void * end_search_indication

function used to report that a thread is done iterating over the database in preliminary search

void * check_index_oid

function used to check if seeds for a given oid are present

void * read_indexed_db

function used to retrieve hits from an indexed database

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