Search Toolkit Book for CBuildDatabase

Build BlastDB format databases from various data sources. More...

#include <objtools/blast/seqdb_writer/build_db.hpp>

Inheritance diagram for CBuildDatabase:

Collaboration diagram for CBuildDatabase:

Public Member Functions
	CBuildDatabase (const string &dbname, const string &title, bool is_protein, CWriteDB::TIndexType indexing, bool use_gi_mask, ostream *logfile, bool long_seqids=false, EBlastDbVersion dbver=eBDB_Version4, bool limit_defline=false, Uint8 oid_masks=EOidMaskType::fNone, bool scan_bioseq_4_cfastareader_usrobj=true)
	Constructor. More...

	CBuildDatabase (const string &dbname, const string &title, bool is_protein, bool sparse, bool parse_seqids, bool use_gi_mask, ostream *logfil, bool long_seqids=false, EBlastDbVersion dbver=eBDB_Version4, bool limit_defline=false, Uint8 oid_masks=EOidMaskType::fNone, bool scan_bioseq_4_cfastareader_usrobj=true)
	Constructor. More...

	~CBuildDatabase ()

void	SetTaxids (CTaxIdSet &taxids)
	Specify a mapping of sequence ids to taxonomic ids. More...

void	SetMaskLetters (const string &mask_letters)
	Specify letters to mask out of protein sequence data. More...

void	SetSourceDb (const string &src_db_name)
	Specify source database(s) via the database name(s). More...

void	SetSourceDb (CRef< CSeqDBExpert > src_db)
	Specify source database. More...

void	SetLinkouts (const TLinkoutMap &linkouts, bool keep_links)
	Specify a linkout bit lookup object. More...

void	SetMembBits (const TLinkoutMap &membbits, bool keep_mbits)
	Specify a membership bit lookup object. More...

void	SetLeafTaxIds (const TIdToLeafs &taxids, bool keep_taxids)
	Specify a leaf-taxids object. More...

bool	Build (const vector< string > &ids, CNcbiIstream *fasta_file)
	Build the database. More...

void	StartBuild ()
	Start building a new database. More...

bool	AddIds (const vector< string > &ids)
	Add the specified sequences from the source database. More...

bool	AddFasta (CNcbiIstream &fasta_file)
	Add sequences from a file containing FASTA data. More...

bool	AddSequences (IBioseqSource &src, bool add_pig=false)
	Add sequences from an IBioseqSource object. More...

bool	AddSequences (IRawSequenceSource &src)
	Add sequences from an IRawSequenceSource object. More...

bool	EndBuild (bool erase=false)
	Finish building a new database. More...

void	SetUseRemote (bool use_remote)
	Specify whether to use remote fetching for locally absent IDs. More...

void	SetVerbosity (bool v)
	Specify level of output verbosity. More...

void	SetSkipCopyingGis (bool v)

void	SetMaxFileSize (Uint8 max_file_size)
	Set the maximum size of database component files. More...

int	RegisterMaskingAlgorithm (EBlast_filter_program program, const string &options, const string &name="")
	Define a masking algorithm. More...

int	RegisterMaskingAlgorithm (const string &program, const string &description, const string &options)
	Define a masking algorithm. More...

void	SetMaskDataSource (IMaskDataSource &ranges)
	Specify an object mapping Seq-id to subject masking data. More...

string	GetOutputDbName () const

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Static Public Member Functions
static void	CreateDirectories (const string &dbname)
	Create Directory for blast db. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Private Member Functions
objects::CScope &	x_GetScope ()
	Get a scope for remote loading of objects. More...

void	x_DupLocal ()
	Duplicate IDs from local databases. More...

void	x_ResolveRemoteId (CRef< objects::CSeq_id > &seqid, TGi &gi)
	Resolve an ID remotely. More...

CRef< CInputGiList >	x_ResolveGis (const vector< string > &ids)
	Resolve various input IDs (as strings) to GIs. More...

void	x_EditHeaders (CRef< objects::CBlast_def_line_set > headers)
	Modify deflines with linkout and membership bits and taxids. More...

void	x_AddPig (CRef< objects::CBlast_def_line_set > headers)
	Add pig if id can be extracted from the deflines. More...

bool	x_EditAndAddBioseq (CConstRef< objects::CBioseq > bs, objects::CSeqVector *sv, bool add_pig=false)
	Modify a Bioseq as needed and add it to the database. More...

void	x_AddMasksForSeqId (const list< CRef< CSeq_id > > &ids)
	Add the masks for the Seq-id(s) (usually just one) to the database being created. More...

bool	x_AddRemoteSequences (CInputGiList &gi_list)
	Duplicate IDs from local databases. More...

bool	x_ReportUnresolvedIds (const CInputGiList &gi_list) const
	Write log messages for any unresolved IDs. More...

void	x_SetLinkAndMbit (CRef< objects::CBlast_def_line_set > headers)
	Store linkout (now deprecated) and membership bits in provided headers. More...

void	x_SetLeafTaxids (CRef< objects::CBlast_def_line_set > headers)
	Store leaf taxids in provided headers. More...

void	x_AddOneRemoteSequence (const objects::CSeq_id &seqid, bool &found, bool &error)
	Fetch a sequence from the remote service and add it to the db. More...

bool	x_ResolveFromSource (const string &acc, CRef< objects::CSeq_id > &id)
	Determine if this string ID can be found in the source database. More...

bool	x_EndBuild (bool erase, const CException *close_exception)

Private Attributes
bool	m_IsProtein
	True for a protein database, false for nucleotide. More...

bool	m_KeepLinks
	True to keep linkout bits from source dbs, false to discard. More...

TIdToBits	m_Id2Links
	Table of linkout bits to apply to sequences. More...

bool	m_KeepMbits
	True to keep membership bits from source dbs, false to discard. More...

TIdToBits	m_Id2Mbits
	Table of membership bits to apply to sequences. More...

bool	m_KeepLeafs
	True to keep leaf taxids from source dbs, false to discard. More...

TIdToLeafs	m_Id2Leafs
	Table of leaf taxids to apply to sequences. More...

CRef< objects::CObjectManager >	m_ObjMgr
	Object manager, used for remote fetching. More...

CRef< objects::CScope >	m_Scope
	Sequence scope, used for remote fetching. More...

CRef< CTaxIdSet >	m_Taxids
	Set of TaxIDs configured to apply to sequences. More...

CRef< CWriteDB >	m_OutputDb
	Database being produced here. More...

CRef< CSeqDBExpert >	m_SourceDb
	Database for duplicating sequences locally (-sourcedb option.) More...

CRef< IMaskDataSource >	m_MaskData
	Subject masking data. More...

ostream &	m_LogFile
	Logfile. More...

bool	m_UseRemote
	Whether to use remote resolution and sequence fetching. More...

int	m_DeflineCount
	Define count. More...

int	m_OIDCount
	Number of OIDs stored in this database. More...

bool	m_Verbose
	If true, more detailed log messages will be produced. More...

bool	m_ParseIDs
	If true, string IDs found in FASTA input will be parsed as Seq-ids. More...

bool	m_LongIDs
	If true, use long sequence ids (database\|accession) More...

bool	m_FoundMatchingMasks
	If true, there were sequences whose IDs matched those in the provided masking locations (via SetMaskDataSource). More...

bool	m_SkipCopyingGis
	If set to true, when copying BLASTDBs, skip the GIs. More...

bool	m_SkipLargeGis
	If set to true, skip GIs with value > 0x7FFFFFFF. More...

string	m_OutputDbName

bool	m_ScanBioseq4CFastaReaderUsrObjct

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Build BlastDB format databases from various data sources.

This class provides an API for building BlastDB format databases. The WriteDB library is used internally to produce the actual database; the functionality provided by this class helps to bridge the gap between the WriteDB API and the needs of a command line database construction tool.

Definition at line 136 of file build_db.hpp.

Constructor & Destructor Documentation

◆ CBuildDatabase() [1/2]

CBuildDatabase::CBuildDatabase	(	const string &	dbname,
		const string &	title,
		bool	is_protein,
		CWriteDB::TIndexType	indexing,
		bool	use_gi_mask,
		ostream *	logfile,
		bool	long_seqids = `false`,
		EBlastDbVersion	dbver = `eBDB_Version4`,
		bool	limit_defline = `false`,
		Uint8	oid_masks = `EOidMaskType::fNone`,
		bool	scan_bioseq_4_cfastareader_usrobj = `true`
	)

Constructor.

Create a database with the specified name, type, and other characteristics. The database will use the specified dbname as the base name for database volumes. Note that the indexing argument will be combined with either eSparseIndex or eDefault, depending on the "sparse" flag.

Parameters

dbname	Name of the database to create. [in]
title	Title to use for newly created database. [in]
is_protein	Use true for protein, false for nucleotide. [in]
sparse	Specify true to use sparse Seq-id indexing. [in]
Logging	will be done to this stream. [in]
use_gi_mask	if true will generate GI-based mask files [in]
logfile	file to write the log to [in]
long_seqids	if true, requires long sequence ids (database\|accession) when parsing fasta sequences [in]
dbver	version of BLAST database to generate [in]
scan_bioseq_4_cfastareader_usrobj	[in] If true, scan the Bioseq objects for a CFastaReader-created User-object containing a defline

Definition at line 1073 of file build_db.cpp.

References CTime::AsString(), CDirEntry::CreateAbsolutePath(), CreateDirectories(), dbname(), DeleteBlastDb(), CTime::eCurrent, CWriteDB::eNucleotide, CWriteDB::eProtein, m_LogFile, m_LongIDs, m_OutputDb, m_OutputDbName, m_ParseIDs, ParseMoleculeTypeString(), CRef< C, Locker >::Reset(), and CWriteDB::SetMaxFileSize().

◆ CBuildDatabase() [2/2]

CBuildDatabase::CBuildDatabase	(	const string &	dbname,
		const string &	title,
		bool	is_protein,
		bool	sparse,
		bool	parse_seqids,
		bool	use_gi_mask,
		ostream *	logfil,
		bool	long_seqids = `false`,
		EBlastDbVersion	dbver = `eBDB_Version4`,
		bool	limit_defline = `false`,
		Uint8	oid_masks = `EOidMaskType::fNone`,
		bool	scan_bioseq_4_cfastareader_usrobj = `true`
	)

Constructor.

Create a database with the specified name, type, and other characteristics. The database will use the specified dbname as the base name for database volumes. Note that the indexing argument will be combined with either eSparseIndex or eDefault, depending on the "sparse" flag.

Parameters

dbname	Name of the database to create. [in]
title	Title to use for newly created database. [in]
is_protein	Use true for protein, false for nucleotide. [in]
sparse	Specify true to use sparse Seq-id indexing. [in]
parse_seqids	specify true to parse the sequence IDs [in]
use_gi_mask	if true will generate GI-based mask files [in]
indexing	index fields to add to database. [in]
long_seqids	if true, requires long sequence ids (database\|accession) when parsing fasta sequences [in]
scan_bioseq_4_cfastareader_usrobj	[in] If true, scan the Bioseq objects for a CFastaReader-created User-object containing a defline

Definition at line 1136 of file build_db.cpp.

References CTime::AsString(), CDirEntry::CreateAbsolutePath(), CreateDirectories(), dbname(), DeleteBlastDb(), CTime::eCurrent, CWriteDB::eDefault, CWriteDB::eNucleotide, CWriteDB::eProtein, CWriteDB::eSparseIndex, m_LogFile, m_OutputDb, m_OutputDbName, m_ParseIDs, ParseMoleculeTypeString(), CRef< C, Locker >::Reset(), and CWriteDB::SetMaxFileSize().

◆ ~CBuildDatabase()

CBuildDatabase::~CBuildDatabase ( )

Definition at line 1204 of file build_db.cpp.

References ERR_POST, Error(), CTaxIdSet::HasEverFixedId(), m_FoundMatchingMasks, m_MaskData, m_Taxids, and CRef< C, Locker >::NotEmpty().

Member Function Documentation

◆ AddFasta()

bool CBuildDatabase::AddFasta ( CNcbiIstream & fasta_file )

Add sequences from a file containing FASTA data.

The provided file is expected to contain FASTA data for one or more sequences. The data should be suitable input as required by CFastaReader.

Parameters

fasta_file A file containing FASTA data.

Returns: True if at least one sequence was added.

Definition at line 1398 of file build_db.cpp.

References AddSequences(), EndBuild(), m_IsProtein, m_LongIDs, m_ParseIDs, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), Build(), and CMakeBlastDBApp::x_AddFasta().

◆ AddIds()

bool CBuildDatabase::AddIds ( const vector< string > & ids )

Add the specified sequences from the source database.

The list of strings are interpreted as GIs if they're composed only of numeric digits, or as Seq-ids otherwise. The sequence IDs will be resolved, and a sequence corresponding to each ID will be added to the output database. If remote resolution is enabled, it will be used to find up-to-date versions for any ambiguously versioned IDs (i.e. unversioned IDs of versioned Seq-id types). Then local fetching will be used to process IDs using the source database if one was specified. If any sequences have not be found, and remote services are enabled, remote fetching will be used for IDs not resolved locally. If any IDs are not found at all, they will be reported as part of the logging output.

Parameters

ids	List of sequence IDs as strings.

Returns: true if all sequences were found locally or remotely.

Definition at line 1321 of file build_db.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), CSeqDB::GetDBNameList(), CSeqDBGiList::GetGiOid(), CSeqDBGiList::GetNumGis(), CSeqDBGiList::GetNumSis(), CSeqDB::GetSequenceType(), CSeqDBGiList::SGiOid::gi, i, m_LogFile, m_SourceDb, m_UseRemote, m_Verbose, CRef< C, Locker >::NotEmpty(), CSeqDBGiList::SGiOid::oid, x_AddRemoteSequences(), x_DupLocal(), x_ReportUnresolvedIds(), and x_ResolveGis().

Referenced by BOOST_AUTO_TEST_CASE(), and Build().

◆ AddSequences() [1/2]

bool CBuildDatabase::AddSequences	(	IBioseqSource &	src,
		bool	add_pig = `false`
	)

Add sequences from an IBioseqSource object.

The provided `src' object is queried using GetNext() to get a Bioseq object. The Bioseq is added to the output database (with appropriate modifications of taxid, membership bits, and linkout bits, as configured here). This process repeats until the GetNext() method returns NULL.

Parameters

src	An object providing one or more Bioseq objects.
add_pig	true if PIG should be added if available

Returns: True if at least one sequence was added.

Definition at line 794 of file build_db.cpp.

References CBioseq_Base::CanGetId(), debug_mode, CSeq_id_Base::e_Local, CStopWatch::Elapsed(), CStopWatch::eStart, CSeq_id::fAcc_nuc, CSeq_id::fAcc_prot, CBioseq_Base::GetId(), CBioseq::GetLength(), IBioseqSource::GetNext(), CConstRef< C, Locker >::GetNonNullPointer(), GI_CONST, info, CBioseq::IsAa(), label, m_IsProtein, m_LogFile, m_LongIDs, m_SkipLargeGis, m_Verbose, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), NULL, CBioseq_Base::SetId(), sw, t, and x_EditAndAddBioseq().

Referenced by AddFasta(), BOOST_AUTO_TEST_CASE(), s_TestReadPDBAsn1(), CMakeBlastDBApp::x_AddSeqEntries(), CMakeClusterDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), BlastdbCopyApplication::x_MakeDBwIDList(), and CMakeBlastDBApp::x_ProcessInputData().

◆ AddSequences() [2/2]

bool CBuildDatabase::AddSequences ( IRawSequenceSource & src )

Add sequences from an IRawSequenceSource object.

The provided `src' object is queried using GetNext() to get various "raw format" sequence data and metadata components. These pieces of data are added to the output database (with appropriate modifications of taxid, membership bits, and linkout bits, as configured here). This process repeats until the GetNext() method returns false.

Parameters

src	An object providing one or more "raw" sequences.

Returns: True if at least one sequence was added.

Definition at line 904 of file build_db.cpp.

References _ASSERT, CWriteDB::AddColumnMetaData(), CWriteDB::AddSequence(), CBlastDbBlob::Clear(), CWriteDB::CreateUserColumn(), CTempString::data(), done, CStopWatch::Elapsed(), CMaskedRangesVector::empty(), CTempString::empty(), CRef< C, Locker >::Empty(), map_checker< Container >::end(), CStopWatch::eStart, map_checker< Container >::find(), CWriteDB::FindColumn(), CBlast_def_line_set_Base::Get(), IRawSequenceSource::GetColumnId(), IRawSequenceSource::GetColumnMetaData(), IRawSequenceSource::GetColumnNames(), IRawSequenceSource::GetNext(), IMaskDataSource::GetRanges(), i, int, ITERATE, m_FoundMatchingMasks, m_IsProtein, m_LogFile, m_MaskData, m_OutputDb, NCBI_THROW, CWriteDB::SetBlobData(), CWriteDB::SetDeflines(), CWriteDB::SetMaskData(), ncbi::grid::netcache::search::fields::size, CTempString::size(), sw, t, CBlastDbBlob::WriteRaw(), x_AddPig(), and x_EditHeaders().

◆ Build()

bool CBuildDatabase::Build	(	const vector< string > &	ids,
		CNcbiIstream *	fasta_file
	)

Build the database.

This method builds a database from the given list of Sequence IDs and the provided file, which should contain FASTA format data. It is equivalent to calling StartBuild(), AddIds(), AddFasta(), and EndBuild() in that order (except that a little additional logging is done with summary information.).

Parameters

ids	List of identifiers to add to the database.
fasta_file	FASTA format data for

Definition at line 1289 of file build_db.cpp.

References AddFasta(), AddIds(), CStopWatch::Elapsed(), EndBuild(), CStopWatch::eStart, m_DeflineCount, m_LogFile, m_OIDCount, StartBuild(), sw, and t.

Referenced by BOOST_AUTO_TEST_CASE().

◆ CreateDirectories()

void CBuildDatabase::CreateDirectories ( const string & dbname )

static

Create Directory for blast db.

Parameters

dbname output blast db name (with path)

Definition at line 1051 of file build_db.cpp.

References CDirEntry::CheckAccess(), CDir::CreatePath(), dbname(), CDirEntry::eIfEmptyPath_Empty, CDir::Exists(), CDirEntry::fWrite, CDirEntry::GetDir(), CDirEntry::GetName(), and NCBI_THROW.

Referenced by CBuildDatabase(), CBlastdbConvertApp::Run(), and CMakeProfileDBApp::x_Run().

◆ EndBuild()

bool CBuildDatabase::EndBuild ( bool erase = false )

Finish building a new database.

This method closes the newly constructed database, flushing any unflushed volumes, creating an alias file to tie the volumes together, and so on.

Parameters

erase Will erase all files created if true.

Definition at line 1423 of file build_db.cpp.

References CWriteDB::Close(), eUnknown, m_OutputDb, NCBI_EXCEPTION_VAR, NULL, CException::what(), and x_EndBuild().

Referenced by AddFasta(), BOOST_AUTO_TEST_CASE(), Build(), s_TestReadPDBAsn1(), CMakeBlastDBApp::x_BuildDatabase(), CMakeClusterDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ GetOutputDbName()

string CBuildDatabase::GetOutputDbName ( ) const

inline

Definition at line 465 of file build_db.hpp.

References m_OutputDbName.

Referenced by CMakeBlastDBApp::x_BuildDatabase(), and CMakeClusterDBApp::x_BuildDatabase().

◆ RegisterMaskingAlgorithm() [1/2]

int CBuildDatabase::RegisterMaskingAlgorithm	(	const string &	program,
		const string &	description,
		const string &	options
	)

Define a masking algorithm.

The returned integer ID will be defined as corresponding to the provided program enumeration (e.g. DUST, SEG, etc) and options string, for subject masking. Each program enumeration (such as DUST) may be used several times with different options strings, however, the combination of program and options should be unique for each algorithm ID. The options string is a free-form string (at least from this class's point of view).

Parameters

program	A string to identify the filtering algorithm [in]
description	A free-form string describing the data [in]
options	A free-form string describing the options used [in]

Definition at line 1597 of file build_db.cpp.

References m_OutputDb, and CWriteDB::RegisterMaskAlgorithm().

◆ RegisterMaskingAlgorithm() [2/2]

int CBuildDatabase::RegisterMaskingAlgorithm	(	EBlast_filter_program	program,
		const string &	options,
		const string &	name = `""`
	)

Define a masking algorithm.

The returned integer ID will be defined as corresponding to the provided program enumeration (e.g. DUST, SEG, etc) and options string, for subject masking. Each program enumeration (such as DUST) may be used several times with different options strings, however, the combination of program and options should be unique for each algorithm ID. The options string is a free-form string (at least from this class's point of view).

Parameters

program	One of the predefined masking types (dust etc). [in]
options	A free-form string describing this type of data. The empty string should be used to indicate default parameters. [in]
name	Name of the GI-base mask file [in]

Definition at line 1584 of file build_db.cpp.

References m_OutputDb, and CWriteDB::RegisterMaskAlgorithm().

Referenced by CClusterDBSource::CClusterDBSource(), CRawSeqDBSource::CRawSeqDBSource(), and CMakeBlastDBApp::x_ProcessMaskData().

◆ SetLeafTaxIds()

void CBuildDatabase::SetLeafTaxIds	(	const TIdToLeafs &	taxids,
		bool	keep_taxids
	)

Specify a leaf-taxids object.

Definition at line 1278 of file build_db.cpp.

References m_Id2Leafs, m_KeepLeafs, and m_LogFile.

Referenced by CMakeClusterDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), BlastdbCopyApplication::x_MakeDBwIDList(), and CMakeBlastDBApp::x_ProcessInputData().

◆ SetLinkouts()

void CBuildDatabase::SetLinkouts	(	const TLinkoutMap &	linkouts,
		bool	keep_links
	)

Specify a linkout bit lookup object.

The provided mapping will be used to look up linkout bits for sequences added to the database.

Parameters

src_db The source database. [in]

Definition at line 1262 of file build_db.cpp.

References m_Id2Links, m_KeepLinks, m_LogFile, and MapToLMBits().

◆ SetMaskDataSource()

void CBuildDatabase::SetMaskDataSource ( IMaskDataSource & ranges )

Specify an object mapping Seq-id to subject masking data.

Masking data is provided to CBuildDatabase by implementing an interface that can produce masking data given the Seq-ids for the sequence that is to be masked. This object could wrap a simple lookup table, an algorithm that produces the data on the fly, or a wrapper around an existing database that fetches the masking data from that database.

Parameters

ranges An object mapping Seq-ids to their masking data.

Definition at line 1609 of file build_db.cpp.

References m_MaskData, and CRef< C, Locker >::Reset().

Referenced by CMakeBlastDBApp::x_ProcessMaskData().

◆ SetMaskLetters()

void CBuildDatabase::SetMaskLetters ( const string & mask_letters )

Specify letters to mask out of protein sequence data.

Protein sequences sometimes contain rare (or recently defined) letters that cause trouble for some algorithms. This method specifies a list of protein letters that might be found in the input sequences, but which should be replaced by "X" before adding those sequences to the database.

Parameters

taxids An object providing defline-to-TaxID lookups. [in]

Definition at line 1221 of file build_db.cpp.

References m_OutputDb, and CWriteDB::SetMaskedLetters().

◆ SetMaxFileSize()

void CBuildDatabase::SetMaxFileSize ( Uint8 max_file_size )

Set the maximum size of database component files.

This will specify the maximum size of file that will be made as a component of a database volume manufactured by the WriteDB library. The default value is 10^9 (one billion bytes.)

Parameters

max_file_size Maximum file size in bytes.

Definition at line 1578 of file build_db.cpp.

References m_OutputDb, and CWriteDB::SetMaxFileSize().

Referenced by CMakeBlastDBApp::x_BuildDatabase(), CMakeClusterDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ SetMembBits()

void CBuildDatabase::SetMembBits	(	const TLinkoutMap &	membbits,
		bool	keep_mbits
	)

Specify a membership bit lookup object.

The provided mapping will be used to look up membership bit data for sequences added to the database.

Parameters

src_db The source database. [in]

Definition at line 1270 of file build_db.cpp.

References m_Id2Mbits, m_KeepMbits, m_LogFile, and MapToLMBits().

Referenced by CMakeBlastDBApp::x_BuildDatabase(), BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ SetSkipCopyingGis()

void CBuildDatabase::SetSkipCopyingGis ( bool v )

inline

Definition at line 397 of file build_db.hpp.

References m_SkipCopyingGis.

Referenced by BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ SetSourceDb() [1/2]

void CBuildDatabase::SetSourceDb ( const string & src_db_name )

Specify source database(s) via the database name(s).

The provided name will be used to find a source database (or several) to look up sequence information for the list of sequences specified by AddIds().

Parameters

src_db_name Database name of the source database. [in]

Definition at line 1250 of file build_db.cpp.

References _ASSERT, CSeqDB::eNucleotide, CSeqDB::eProtein, and m_IsProtein.

Referenced by BOOST_AUTO_TEST_CASE(), BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ SetSourceDb() [2/2]

void CBuildDatabase::SetSourceDb ( CRef< CSeqDBExpert > src_db )

Specify source database.

The provided source database will be used to look up sequence information for the list of sequences specified by AddIds().

Parameters

src_db The source database. [in]

Definition at line 1242 of file build_db.cpp.

References CSeqDB::GetDate(), CSeqDB::GetDBNameList(), CSeqDB::GetTitle(), m_LogFile, and m_SourceDb.

◆ SetTaxids()

void CBuildDatabase::SetTaxids ( CTaxIdSet & taxids )

Specify a mapping of sequence ids to taxonomic ids.

When adding sequences CBuildDatabase will use the object provided here to find TaxIDs for sequences it adds to the newly created database.

Parameters

taxids An object providing defline-to-TaxID lookups. [in]

Definition at line 1216 of file build_db.cpp.

References m_Taxids, and CRef< C, Locker >::Reset().

Referenced by BOOST_AUTO_TEST_CASE(), and CMakeBlastDBApp::x_BuildDatabase().

◆ SetUseRemote()

void CBuildDatabase::SetUseRemote ( bool use_remote )

inline

Specify whether to use remote fetching for locally absent IDs.

If identifiers in the list provided to Build or to AddIds is not found in the source database (if any), remote sequence fetching APIs can be used to fetch those sequences. Normally this happens in two cases. First, sequences listed in the list of IDs are sometimes too new to be found in the source database. Secondly, sequences may be found in the source database, but newer versions might be available in the remote database.

If the use_remote flag is set to true, this class finds the latest version number for unversioned IDs (but only of types that can have versions in the first place), and will attempt to remotely fetch any sequences for which the source database does not have the latest version. If the flag is specified as false, no remote lookups will be done, and sequences found in ids but not found in the source database will not be added to the output database.

Note: This does not affect the AddSequences, AddRawSequences, or AddFasta methods; in those cases, all provided sequences are added in the form they are provided in.

The default value for this flag is "true".

Parameters

use_remote Specify true for remote checking & fetching.

Definition at line 385 of file build_db.hpp.

References m_UseRemote.

Referenced by BOOST_AUTO_TEST_CASE(), BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ SetVerbosity()

void CBuildDatabase::SetVerbosity ( bool v )

inline

Specify level of output verbosity.

Parameters

v	Specify true if output should be more detailed.

Definition at line 392 of file build_db.hpp.

References m_Verbose.

Referenced by CMakeBlastDBApp::x_BuildDatabase(), and CMakeClusterDBApp::x_BuildDatabase().

◆ StartBuild()

void CBuildDatabase::StartBuild ( )

Start building a new database.

This method sets up a new database to begin receiving sequences. It should be called before AddIds, AddFasta, AddSequences, or AddRawSequences is called.

Definition at line 1317 of file build_db.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), Build(), s_TestReadPDBAsn1(), BlastdbCopyApplication::x_CopyDB(), and BlastdbCopyApplication::x_MakeDBwIDList().

◆ x_AddMasksForSeqId()

void CBuildDatabase::x_AddMasksForSeqId ( const list< CRef< CSeq_id > > & ids )

private

Add the masks for the Seq-id(s) (usually just one) to the database being created.

Parameters

ids	Seq-id(s) of the sequence to which masks should be added [in]

Definition at line 447 of file build_db.cpp.

References CMaskedRangesVector::empty(), CRef< C, Locker >::Empty(), IMaskDataSource::GetRanges(), ITERATE, m_FoundMatchingMasks, m_MaskData, m_OutputDb, and CWriteDB::SetMaskData().

Referenced by x_EditAndAddBioseq().

◆ x_AddOneRemoteSequence()

void CBuildDatabase::x_AddOneRemoteSequence	(	const objects::CSeq_id &	seqid,
		bool &	found,
		bool &	error
	)

private

Fetch a sequence from the remote service and add it to the db.

The provided Seq-id will be used to fetch a Bioseq remotely, and this Bioseq will be added to this database. If

Parameters

seqid	Identifies the sequence to fetch. [in]
found	Will be set to true if a sequence was found. [out]
error	Will be set to true if an error occurred. [out]

Definition at line 507 of file build_db.cpp.

References debug_mode, CBioseq_Handle::fState_not_found, CBioseq_Handle::GetCompleteBioseq(), CBioseq_Handle::GetState(), m_LogFile, MSerial_AsnText, CException::what(), x_EditAndAddBioseq(), and x_GetScope().

Referenced by x_AddRemoteSequences().

◆ x_AddPig()

void CBuildDatabase::x_AddPig ( CRef< objects::CBlast_def_line_set > headers )

private

Add pig if id can be extracted from the deflines.

Parameters

headers Headers to extract the id if available.

Definition at line 418 of file build_db.cpp.

References CBlast_def_line_Base::GetOther_info(), CBlast_def_line_Base::IsSetOther_info(), m_OutputDb, and CWriteDB::SetPig().

Referenced by AddSequences(), and x_EditAndAddBioseq().

◆ x_AddRemoteSequences()

bool CBuildDatabase::x_AddRemoteSequences ( CInputGiList & gi_list )

private

Duplicate IDs from local databases.

This method iterates over the list of IDs; any IDs that were not found in the source database are added by fetching the sequence from remote services. (Whether an ID was found locally can be determined by whether the OID found in the GI list is valid.)

Parameters

gi_list A list of GIs and Seq-ids.

Returns: True if all IDs could be added.

Definition at line 555 of file build_db.cpp.

References CStopWatch::Elapsed(), CStopWatch::eStart, CSeqDBGiList::GetGiOid(), CSeqDBGiList::GetKey(), CSeqDBGiList::GetNumGis(), CSeqDBGiList::GetNumSis(), CSeqDBGiList::GetSiOid(), i, m_LogFile, m_Verbose, CSeqDBGiList::SGiOid::oid, CSeqDBGiList::SSiOid::oid, sw, t, and x_AddOneRemoteSequence().

Referenced by AddIds().

◆ x_DupLocal()

void CBuildDatabase::x_DupLocal ( )

private

Duplicate IDs from local databases.

This method iterates over the list of IDs, copying sequences found in the source databases to the output database.

Definition at line 235 of file build_db.cpp.

References CWriteDB::AddSequence(), ambig(), buffer, CSeqDB::CheckOrFindOID(), CStopWatch::Elapsed(), CStopWatch::eStart, CTaxIdSet::FixTaxId(), CBlast_def_line_set_Base::Get(), CSeqDB::GetHdr(), CSeqDBExpert::GetRawSeqAndAmbig(), m_DeflineCount, m_LogFile, m_OIDCount, m_OutputDb, m_SourceDb, m_Taxids, CWriteDB::SetDeflines(), sw, t, and x_SetLinkAndMbit().

Referenced by AddIds().

◆ x_EditAndAddBioseq()

bool CBuildDatabase::x_EditAndAddBioseq	(	CConstRef< objects::CBioseq >	bs,
		objects::CSeqVector *	sv,
		bool	add_pig = `false`
	)

private

Modify a Bioseq as needed and add it to the database.

The provided Bioseq is added to the database. Modifications are made to the data as needed (but the input object is not affected). In particular, the taxid is set (0 is used if no taxid is known), and linkout and membership bits are set.

Parameters

bs	Bioseq to add to the database.
bs	Sequence data to add to the database.
add_pig	true if PIG should be added if available

Returns: ture if bioseq has been added, otherwise false

Definition at line 469 of file build_db.cpp.

References CWriteDB::AddSequence(), CWriteDB::ExtractBioseqDeflines(), CBlast_def_line_set_Base::Get(), m_DeflineCount, m_LongIDs, m_OIDCount, m_OutputDb, m_ParseIDs, m_ScanBioseq4CFastaReaderUsrObjct, s_FixBioseqDeltas(), CWriteDB::SetDeflines(), x_AddMasksForSeqId(), x_AddPig(), and x_EditHeaders().

Referenced by AddSequences(), and x_AddOneRemoteSequence().

◆ x_EditHeaders()

void CBuildDatabase::x_EditHeaders ( CRef< objects::CBlast_def_line_set > headers )

private

Modify deflines with linkout and membership bits and taxids.

The provided deflines are modified: the taxid is set (0 is used if no taxid is known), and linkout and membership bits are set. The input object is modified.

Parameters

headers Headers to modify.

Definition at line 428 of file build_db.cpp.

References CTaxIdSet::FixTaxId(), m_SkipCopyingGis, m_Taxids, and x_SetLinkAndMbit().

Referenced by AddSequences(), and x_EditAndAddBioseq().

◆ x_EndBuild()

bool CBuildDatabase::x_EndBuild	(	bool	erase,
		const CException *	close_exception
	)

private

Definition at line 1439 of file build_db.cpp.

References _ASSERT, _TRACE, CException::GetMsg(), ITERATE, CWriteDB::ListFiles(), CWriteDB::ListVolumes(), m_LogFile, m_OutputDb, NCBI_RETHROW, and CDirEntry::Remove().

Referenced by EndBuild().

◆ x_GetScope()

CScope & CBuildDatabase::x_GetScope ( )

private

Get a scope for remote loading of objects.

Definition at line 1226 of file build_db.cpp.

References CRef< C, Locker >::Empty(), CObjectManager::GetInstance(), m_ObjMgr, m_Scope, and CRef< C, Locker >::Reset().

Referenced by x_AddOneRemoteSequence(), and x_ResolveRemoteId().

◆ x_ReportUnresolvedIds()

bool CBuildDatabase::x_ReportUnresolvedIds ( const CInputGiList & gi_list ) const

private

Write log messages for any unresolved IDs.

Parameters

gi_list List of GIs and Seq-ids.

Returns: True if all sequences were resolved.

Definition at line 626 of file build_db.cpp.

References CSeqDBGiList::GetGiOid(), CSeqDBGiList::GetKey(), CSeqDBGiList::GetNumGis(), CSeqDBGiList::GetNumSis(), CSeqDBGiList::GetSiOid(), i, m_LogFile, m_Verbose, CSeqDBGiList::SGiOid::oid, and CSeqDBGiList::SSiOid::oid.

Referenced by AddIds().

◆ x_ResolveFromSource()

bool CBuildDatabase::x_ResolveFromSource	(	const string &	acc,
		CRef< objects::CSeq_id > &	id
	)

private

Determine if this string ID can be found in the source database.

The provided string will be looked up as an accession in the source database. If a corresponding sequence is found, it will be returned in the `id' field. The resolution is only considered a match if the provided string is a substring of the FASTA representation of the provided Seq-id, and if that substring seems to represent whole components (so that it's surrounded by delimeters such as `|' and `.' rather than by alphanumeric characters, which may be part of another ID).

Parameters

acc	The accession or ID to look up. [in]
id	The returned Seq-id if one is found. [out]

Returns: true if the resolution was successful.

Definition at line 185 of file build_db.cpp.

References CSeqDB::AccessionToOids(), CSeq_id::AsFastaString(), done, CRef< C, Locker >::Empty(), CSeqDB::GetSeqIDs(), ITERATE, m_SourceDb, and S.

Referenced by x_ResolveGis().

◆ x_ResolveGis()

CRef< CInputGiList > CBuildDatabase::x_ResolveGis ( const vector< string > & ids )

private

Resolve various input IDs (as strings) to GIs.

The input IDs are examined, the type of each is determined as a GIs or some other kind of Seq-id, and each ID is resolved to a GI where possible. The list of GIs and other Seq-ids found is returned in a GI list.

Parameters

ids	List of strings representing IDs to resolve.

Returns: GI list produced from the input ids.

Definition at line 116 of file build_db.cpp.

References CInputGiList::AppendGi(), CInputGiList::AppendSi(), CheckAccession(), debug_mode, ITERATE, m_LogFile, m_SourceDb, m_UseRemote, CRef< C, Locker >::NotEmpty(), x_ResolveFromSource(), x_ResolveRemoteId(), and ZERO_GI.

Referenced by AddIds().

◆ x_ResolveRemoteId()

void CBuildDatabase::x_ResolveRemoteId	(	CRef< objects::CSeq_id > &	seqid,
		TGi &	gi
	)

private

Resolve an ID remotely.

This method looks up the given ID via remote services in order to find an ID for the most up-to-date version of the sequence. The remote service will return a list of Seq-ids; if at least one of these is a GI, that will be returned in `gi'. If no GI is found, but at least one of the returned IDs is of the same type as the input Seq-id, the version number of the input Seq-id will be updated.

Parameters

seqid	Sequence identifier to look up remotely. [in\|out]
gi	Genomic ID if one is found, otherwise 0. [out]

Definition at line 65 of file build_db.cpp.

References debug_mode, CSeq_id::GetTextseq_Id(), CSeq_id_Base::IsGi(), CTextseq_id_Base::IsSetVersion(), ITERATE, m_LogFile, NULL, CRef< C, Locker >::Reset(), CSeq_id_Base::Which(), x_GetScope(), and ZERO_GI.

Referenced by x_ResolveGis().

◆ x_SetLeafTaxids()

void CBuildDatabase::x_SetLeafTaxids ( CRef< objects::CBlast_def_line_set > headers )

private

Store leaf taxids in provided headers.

Parameters

headers These deflines will be modified. [in|out]

◆ x_SetLinkAndMbit()

void CBuildDatabase::x_SetLinkAndMbit ( CRef< objects::CBlast_def_line_set > headers )

private

Store linkout (now deprecated) and membership bits in provided headers.

Each Seq-id found in each defline in the provided headers will be looked up in the set of linkout and membership bits provided for building this database, and the appropriate bits will be set for each defline.

Parameters

headers These deflines will be modified. [in|out]

Definition at line 1563 of file build_db.cpp.

References GetDeflineKeys(), m_Id2Leafs, m_Id2Mbits, m_KeepLeafs, m_KeepMbits, NON_CONST_ITERATE, s_SetDeflineBits(), and s_SetDeflineLeafs().

Referenced by x_DupLocal(), and x_EditHeaders().

Member Data Documentation

◆ m_DeflineCount

int CBuildDatabase::m_DeflineCount

private

Define count.

Definition at line 644 of file build_db.hpp.

Referenced by Build(), x_DupLocal(), and x_EditAndAddBioseq().

◆ m_FoundMatchingMasks

bool CBuildDatabase::m_FoundMatchingMasks

private

If true, there were sequences whose IDs matched those in the provided masking locations (via SetMaskDataSource).

Used to display a warning in case this didn't happen

Definition at line 661 of file build_db.hpp.

Referenced by AddSequences(), x_AddMasksForSeqId(), and ~CBuildDatabase().

◆ m_Id2Leafs

TIdToLeafs CBuildDatabase::m_Id2Leafs

private

Table of leaf taxids to apply to sequences.

Definition at line 617 of file build_db.hpp.

Referenced by SetLeafTaxIds(), and x_SetLinkAndMbit().

◆ m_Id2Links

TIdToBits CBuildDatabase::m_Id2Links

private

Table of linkout bits to apply to sequences.

DEPRECATED

Definition at line 605 of file build_db.hpp.

Referenced by SetLinkouts().

◆ m_Id2Mbits

TIdToBits CBuildDatabase::m_Id2Mbits

private

Table of membership bits to apply to sequences.

Definition at line 611 of file build_db.hpp.

Referenced by SetMembBits(), and x_SetLinkAndMbit().

◆ m_IsProtein

bool CBuildDatabase::m_IsProtein

private

True for a protein database, false for nucleotide.

Definition at line 597 of file build_db.hpp.

Referenced by AddFasta(), AddSequences(), and SetSourceDb().

◆ m_KeepLeafs

bool CBuildDatabase::m_KeepLeafs

private

True to keep leaf taxids from source dbs, false to discard.

Definition at line 614 of file build_db.hpp.

Referenced by SetLeafTaxIds(), and x_SetLinkAndMbit().

◆ m_KeepLinks

bool CBuildDatabase::m_KeepLinks

private

True to keep linkout bits from source dbs, false to discard.

DEPRECATED

Definition at line 601 of file build_db.hpp.

Referenced by SetLinkouts().

◆ m_KeepMbits

bool CBuildDatabase::m_KeepMbits

private

True to keep membership bits from source dbs, false to discard.

Definition at line 608 of file build_db.hpp.

Referenced by SetMembBits(), and x_SetLinkAndMbit().

◆ m_LogFile

ostream& CBuildDatabase::m_LogFile

private

Logfile.

Definition at line 638 of file build_db.hpp.

Referenced by AddIds(), AddSequences(), Build(), CBuildDatabase(), SetLeafTaxIds(), SetLinkouts(), SetMembBits(), SetSourceDb(), x_AddOneRemoteSequence(), x_AddRemoteSequences(), x_DupLocal(), x_EndBuild(), x_ReportUnresolvedIds(), x_ResolveGis(), and x_ResolveRemoteId().

◆ m_LongIDs

bool CBuildDatabase::m_LongIDs

private

If true, use long sequence ids (database|accession)

Definition at line 656 of file build_db.hpp.

Referenced by AddFasta(), AddSequences(), CBuildDatabase(), and x_EditAndAddBioseq().

◆ m_MaskData

CRef<IMaskDataSource> CBuildDatabase::m_MaskData

private

Subject masking data.

Definition at line 635 of file build_db.hpp.

Referenced by AddSequences(), SetMaskDataSource(), x_AddMasksForSeqId(), and ~CBuildDatabase().

◆ m_ObjMgr

CRef<objects::CObjectManager> CBuildDatabase::m_ObjMgr

private

Object manager, used for remote fetching.

Definition at line 620 of file build_db.hpp.

Referenced by x_GetScope().

◆ m_OIDCount

int CBuildDatabase::m_OIDCount

private

Number of OIDs stored in this database.

Definition at line 647 of file build_db.hpp.

Referenced by Build(), x_DupLocal(), and x_EditAndAddBioseq().

◆ m_OutputDb

CRef<CWriteDB> CBuildDatabase::m_OutputDb

private

Database being produced here.

Definition at line 629 of file build_db.hpp.

Referenced by AddSequences(), CBuildDatabase(), EndBuild(), RegisterMaskingAlgorithm(), SetMaskLetters(), SetMaxFileSize(), x_AddMasksForSeqId(), x_AddPig(), x_DupLocal(), x_EditAndAddBioseq(), and x_EndBuild().

◆ m_OutputDbName

string CBuildDatabase::m_OutputDbName

private

Definition at line 669 of file build_db.hpp.

Referenced by CBuildDatabase(), and GetOutputDbName().

◆ m_ParseIDs

bool CBuildDatabase::m_ParseIDs

private

If true, string IDs found in FASTA input will be parsed as Seq-ids.

Definition at line 653 of file build_db.hpp.

Referenced by AddFasta(), CBuildDatabase(), and x_EditAndAddBioseq().

◆ m_ScanBioseq4CFastaReaderUsrObjct

bool CBuildDatabase::m_ScanBioseq4CFastaReaderUsrObjct

private

Definition at line 671 of file build_db.hpp.

Referenced by x_EditAndAddBioseq().

◆ m_Scope

CRef<objects::CScope> CBuildDatabase::m_Scope

private

Sequence scope, used for remote fetching.

Definition at line 623 of file build_db.hpp.

Referenced by x_GetScope().

◆ m_SkipCopyingGis

bool CBuildDatabase::m_SkipCopyingGis

private

If set to true, when copying BLASTDBs, skip the GIs.

Definition at line 664 of file build_db.hpp.

Referenced by SetSkipCopyingGis(), and x_EditHeaders().

◆ m_SkipLargeGis

bool CBuildDatabase::m_SkipLargeGis

private

If set to true, skip GIs with value > 0x7FFFFFFF.

Definition at line 667 of file build_db.hpp.

Referenced by AddSequences().

◆ m_SourceDb

CRef<CSeqDBExpert> CBuildDatabase::m_SourceDb

private

Database for duplicating sequences locally (-sourcedb option.)

Definition at line 632 of file build_db.hpp.

Referenced by AddIds(), SetSourceDb(), x_DupLocal(), x_ResolveFromSource(), and x_ResolveGis().

◆ m_Taxids

CRef<CTaxIdSet> CBuildDatabase::m_Taxids

private

Set of TaxIDs configured to apply to sequences.

Definition at line 626 of file build_db.hpp.

Referenced by SetTaxids(), x_DupLocal(), x_EditHeaders(), and ~CBuildDatabase().

◆ m_UseRemote

bool CBuildDatabase::m_UseRemote

private

Whether to use remote resolution and sequence fetching.

Definition at line 641 of file build_db.hpp.

Referenced by AddIds(), SetUseRemote(), and x_ResolveGis().

◆ m_Verbose

bool CBuildDatabase::m_Verbose

private

If true, more detailed log messages will be produced.

Definition at line 650 of file build_db.hpp.

Referenced by AddIds(), AddSequences(), SetVerbosity(), x_AddRemoteSequences(), and x_ReportUnresolvedIds().

The documentation for this class was generated from the following files:

include/objtools/blast/seqdb_writer/build_db.hpp
src/objtools/blast/seqdb_writer/build_db.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBuildDatabase() [1/2]

◆ CBuildDatabase() [2/2]

◆ ~CBuildDatabase()

Member Function Documentation

◆ AddFasta()

◆ AddIds()

◆ AddSequences() [1/2]

◆ AddSequences() [2/2]

◆ Build()

◆ CreateDirectories()

◆ EndBuild()

◆ GetOutputDbName()

◆ RegisterMaskingAlgorithm() [1/2]

◆ RegisterMaskingAlgorithm() [2/2]

◆ SetLeafTaxIds()

◆ SetLinkouts()

◆ SetMaskDataSource()

◆ SetMaskLetters()

◆ SetMaxFileSize()

◆ SetMembBits()

◆ SetSkipCopyingGis()

◆ SetSourceDb() [1/2]

◆ SetSourceDb() [2/2]

◆ SetTaxids()

◆ SetUseRemote()

◆ SetVerbosity()

◆ StartBuild()

◆ x_AddMasksForSeqId()

◆ x_AddOneRemoteSequence()

◆ x_AddPig()

◆ x_AddRemoteSequences()

◆ x_DupLocal()

◆ x_EditAndAddBioseq()

◆ x_EditHeaders()

◆ x_EndBuild()

◆ x_GetScope()

◆ x_ReportUnresolvedIds()

◆ x_ResolveFromSource()

◆ x_ResolveGis()

◆ x_ResolveRemoteId()

◆ x_SetLeafTaxids()

◆ x_SetLinkAndMbit()

Member Data Documentation

◆ m_DeflineCount

◆ m_FoundMatchingMasks

◆ m_Id2Leafs

◆ m_Id2Links

◆ m_Id2Mbits

◆ m_IsProtein

◆ m_KeepLeafs

◆ m_KeepLinks

◆ m_KeepMbits

◆ m_LogFile

◆ m_LongIDs

◆ m_MaskData

◆ m_ObjMgr

◆ m_OIDCount

◆ m_OutputDb

◆ m_OutputDbName

◆ m_ParseIDs

◆ m_ScanBioseq4CFastaReaderUsrObjct

◆ m_Scope

◆ m_SkipCopyingGis

◆ m_SkipLargeGis

◆ m_SourceDb

◆ m_Taxids

◆ m_UseRemote

◆ m_Verbose