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NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbimpl.hpp Source File

1 #ifndef OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP 2 #define OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP 48 #include <shared_mutex> 68 void

AddMapping(

int

vol_id,

int id

const string

& desc);

71 void

GetIdList(vector<int> & algorithms);

76 return

m_Empty && m_IdToDesc.empty();

80 bool

GetDesc(

int

algorithm_id,

string

& desc);

98 int

GetVolAlgo(

int

vol_idx,

int

algo_id);

101 int

RealToVol(

int

vol_idx,

int

algo_id);

104 int

GetAlgoId(

const string

id

);

179 bool

use_atlas_lock);

210 int

GetSeqLengthApprox(

int

oid)

const

;

230 char

GetSeqType()

const

;

247 void

GetTaxIDs(

int

oid,

267 void

GetTaxIDs(

int

oid,

268

vector<TTaxId> & taxids,

293 void

GetAllTaxIDs(

int

oid,

314

vector<TTaxId>& gi_to_taxid_set,

379 int

GetAmbigSeq(

int

oid,

386 int

GetAmbigPartialSeq(

int

oid,

406 void

RetSequence(

const char

buffer

);

421 void

RetAmbigSeq(

const char

buffer

)

const

;

432

list< CRef<CSeq_id> > GetSeqIDs(

int

oid);

443 TGi

GetSeqGI(

int

oid);

457 string

GetDate()

const

;

460 int

GetNumSeqs()

const

;

465 int

GetNumSeqsStats()

const

;

468 int

GetNumOIDs()

const

;

476 Uint8

GetTotalLength()

const

;

483 Uint8

GetExactTotalLength();

490 Uint8

GetTotalLengthStats()

const

;

499 Uint8

GetVolumeLength()

const

;

505 int

GetMaxLength()

const

;

511 int

GetMinLength()

const

;

522 bool

CheckOrFindOID(

int

& next_oid);

556

GetNextOIDChunk(

int

& begin_chunk,

559

vector<int> & oid_list,

563 void

ResetInternalChunkBookmark();

570 const string

& GetDBNameList()

const

;

583 return

m_UserGiList.GetPointerOrNull();

607 void

FlushSeqMemory();

610 bool

PigToOid(

int

pig,

int

& oid)

const

;

613 bool

OidToPig(

int

oid,

int

& pig)

const

;

616 bool

TiToOid(

Int8

ti,

int

& oid);

619 bool

GiToOid(

TGi

gi,

int

& oid)

const

;

623 bool

GiToOidwFilterCheck(

TGi

gi,

int

& oid);

626 bool

OidToGi(

int

oid,

TGi

& gi);

629 void

AccessionToOids(

const string

& acc,

632 void

AccessionsToOids(

const

vector<string>& accs, vector<blastdb::TOid>& oids);

635 void

SeqidToOids(

const CSeq_id

& seqid, vector<int> & oids,

bool

multi);

639 int

GetOidAtOffset(

int

first_seq,

Uint8

residue)

const

;

661

FindVolumePaths(

const string

dbname

663

vector<string> & paths,

664

vector<string> * alias_paths,

678 void

FindVolumePaths(vector<string> & paths,

bool

recursive)

const

;

680 void

FindVolumePaths(vector<string> & paths, vector<string> & alias,

bool

recursive)

const

;

694 void

SetIterationRange(

int

oid_begin,

int

oid_end);

719 void

GetAliasFileValues(TAliasFileValues & afv);

758 void

GetTotals(ESummaryType sumtype,

760 Uint8

* total_length,

797 void

GetRawSeqAndAmbig(

int

oid,

800 int

* ambig_length)

const

;

812 void

GetGiBounds(

TGi

* low_id,

TGi

* high_id,

int

count

);

824 void

GetPigBounds(

int

* low_id,

int

* high_id,

int

count

);

838 void

GetStringBounds(

string

* low_id,

string

* high_id,

int

count

);

873 void

SetOffsetRanges(

int

oid,

879 void

FlushOffsetRangeCache();

888 unsigned

GetSequenceHash(

int

oid);

896 void

HashToOids(

unsigned hash

, vector<int> & oids);

898 #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ 899 (!defined(NCBI_COMPILER_MIPSPRO)) ) 908 void

ListColumns(vector<string> & titles);

919 int

GetColumnId(

const string

& title);

949

GetColumnMetaData(

int

column_id,

950 const string

& volname);

972 void

GetColumnBlob(

int

col_id,

int

oid,

bool

keep,

CBlastDbBlob

& blob);

988 void

GetAvailableMaskAlgorithms(vector<int> & algorithms);

991 int

GetMaskAlgorithmId(

const string

&algo_name);

995 string

GetAvailableMaskAlgorithmDescriptions();

1012 void

GetMaskAlgorithmDetails(

int

algorithm_id,

1014 string

& program_name,

1015 string

& algo_opts);

1030 void

GetMaskData(

int

oid,

1057 void

SetNumberOfThreads(

int

num_threads,

bool

force_mt =

false

);

1060 void

SetVolsMemBit(

int

mbit);

1062 void

SetVolsOidMaskType(

int

oid_mask_type);

1074 void

TaxIdsToOids(

set<TTaxId>

& tax_ids, vector<blastdb::TOid>& rv);

1080 void

GetTaxIdsForOids(

const

vector<blastdb::TOid> & oids,

set<TTaxId>

& tax_ids);

1082 int

GetNumOfVols()

const

;

1084 void

GetLMDBFileNames(vector<string> & lmdb_list)

const

;

1086 void

GetTaxIdsForSeqId(

const CSeq_id

& seq_id, vector<TTaxId> & taxids);

1117 int

x_GetNumSeqs()

const

;

1120 int

x_GetNumSeqsStats()

const

;

1123 int

x_GetNumOIDs()

const

;

1158 int

x_GetMaxLength()

const

;

1161 int

x_GetMinLength()

const

;

1229 void

x_ScanTotals(

bool approx

1236 #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ 1237 (!defined(NCBI_COMPILER_MIPSPRO)) ) 1242 int

x_GetColumnId(

const string

& title,

1273 int

x_GetSeqLength(

int

oid)

const

;

1283 int

x_SetCacheID(

int

threadID);

1367 #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ 1368 (!defined(NCBI_COMPILER_MIPSPRO)) ) 1382

kColumnNotFound = -2

1436 template

typename

T >

void

x_CheckOid(

& list,

CSeqDBLockHold

& locked);

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

`Blob' Class for SeqDB (and WriteDB).

CObjectIStreamAsnBinary â.

Guard object for the SeqDBAtlas singleton.

SeqDB ID list for performing boolean set operations.

int m_NumSeqsStats

Number of sequences in the overall database.

CSeqDBAliasFile m_Aliases

Alias node hierarchy management object.

CRef< CSeqDBGiList > m_UserGiList

The User GI list for the entire CSeqDB object.

CSeqDBAtlasHolder m_AtlasHolder

Memory management layer guard (RIIA) object.

int m_NumThreads

number of thread clients

std::shared_mutex m_CacheIDMutex

mapping thread ID to storage ID

CSeqDBIdSet m_IdSet

The positive or negative ID list for the entire CSeqDB object.

string m_Date

Cached most recent date string for GetDate().

CRef< CSeqDBOIDList > m_OIDList

The list of included OIDs (construction is deferred).

int m_MaskDataColumn

Column ID for mask data column.

CFastMutex m_OIDLock

Mutex which synchronizes access to the OID list.

Uint8 m_TotalLength

Total length of database (in bases).

bool m_UseGiMask

Which type of masks are we using?

CSeqDBAtlas & m_Atlas

Reference to memory management layer.

CRef< CSeqDBNegativeList > m_NegativeList

The Negative ID list for the entire CSeqDB object.

int m_RestrictEnd

Ending OID as provided to the constructor.

void SetCacheID()

Assign Cache ID to Thread For multi-threaded mode split by database, each thread needs to call this A...

CObjectIStreamAsnBinary * reusable_inpstr

char m_SeqType

Type of sequences used by this instance.

Uint8 m_TotalLengthStats

Total length of database (in bases).

std::atomic< bool > m_OidListSetup

True if OID list setup is done (or was not required).

set< pair< int, int > > TRangeList

List of sequence offset ranges.

string GetColumnValue(int column_id, const string &key)

Get all metadata for the specified column.

CRef< CSeqDBGiMask > m_GiMask

Gi-based mask.

map< string, int > m_ColumnTitleMap

Map string column titles to global column IDs.

int m_NextChunkOID

"Bookmark" for multithreaded chunk-type OID iteration.

EColumnStatus

Status of a database column title.

TSeqDBAliasFileValues TAliasFileValues

Import type to allow shorter name.

int m_MaxLength

Longest database sequence.

int m_RestrictBegin

Starting OID as provided to the constructor.

std::atomic< int > m_NextCacheID

Uint8 m_VolumeLength

Total length of all database volumes combined (in bases).

CSeqDB::ESummaryType ESummaryType

Defines types of database summary information.

CSeqDB_IdRemapper m_AlgorithmIds

Algorithm ID mapping.

const CSeqDBGiList * GetGiList() const

Get GI list attached to this database.

int m_MinLength

Shortest database sequence.

Uint8 m_ExactTotalLength

Total length of database (in bases).

string m_DBNames

The list of database names provided to the constructor.

vector< SSeqResBuffer * > m_CachedSeqs

Cached sequences.

vector< CRef< CSeqDB_ColumnEntry > > m_ColumnInfo

Map assigned global column IDs to column information.

std::map< int, int > m_CacheID

CSeqDBVolSet m_VolSet

Set of volumes used by this database instance.

int m_NumOIDs

Size of databases OID range.

bool m_NeedTotalsScan

True if this configuration cannot deduce totals without a scan.

int m_NumSeqs

Number of sequences in the overall database.

Map user algorithm IDs to volume algorithm IDs.

int m_CacheRealAlgo

Cached list of real algorithms for BuildVolAlgos.

map< int, string > m_IdToDesc

Map of real IDs to descriptions.

map< string, int > m_DescToId

Map of descriptions to real IDs.

int m_CacheVolAlgo

Cached list of volume algorithms for BuildVolAlgos.

void SetNotEmpty()

Is this object populated?

map< int, map< int, int > > m_RealIdToVolumeId

Map of volume# to map of real id to volume-based id.

bool m_Empty

Is this object initialized?

int m_CacheVolIndex

Cached volume index for BuildVolAlgos.

bool Empty()

Is this object populated?

int m_NextId

Next unassigned synthetic ID.

EOidListType

Indicates how block of OIDs was returned.

ESummaryType

Types of summary information available.

static unsigned char depth[2 *(256+1+29)+1]

int GetSeqLength(const CBioseq &bioseq)

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

strategy

Block allocation strategies.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

CBioseq_Info & GetBioseq(CTSE_Info &tse, const CBioObjectId &id)

const struct ncbi::grid::netcache::search::fields::KEY key

bool approx(T x_, T y_, T eps_)

Defines database alias file access classes.

#define CLASS_MARKER_FIELD(a)

Defines database column access classes.

ESeqDBAllocType

Certain methods have an "Alloc" version.

EBlastDbVersion

BLAST database version.

Defines gi-based mask data files.

The SeqDB oid filtering layer.

Manages a set of database volumes.

Structure to buffer multiple TSeqRes.

vector< SSeqRes > results

Structure to keep sequence retrieval results.

List of sequence offset ranges.

OID-Range type to simplify interfaces.

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