Search Toolkit Book for CWriteDB_Volume

#include "writedb_volume.hpp"
(Private to src/objtools/blast/seqdb_writer.)

Inheritance diagram for CWriteDB_Volume:

Collaboration diagram for CWriteDB_Volume:

Public Types
typedef CWriteDB::EIndexType	EIndexType
	Whether and what kind of indices to build. More...

typedef vector< CRef< CSeq_id > >	TIdList
	Type used for lists of identifiers. More...

typedef vector< CRef< CBlastDbBlob > >	TBlobList
	Type used for lists of identifiers. More...

typedef CWriteDB_Column::TColumnMeta	TColumnMeta
	Type used for database column meta-data. More...

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...

Public Member Functions
	CWriteDB_Volume (const string &dbname, bool protein, const string &title, const string &date, int index, Uint8 max_file_size, Uint8 max_letters, EIndexType indices, EBlastDbVersion dbver=eBDB_Version5, Uint8 oid_masks=EOidMaskType::fNone)
	Build a database volume. More...

	~CWriteDB_Volume ()
	Destructor. More...

bool	WriteSequence (const string &seq, const string &ambig, const string &binhdr, const TIdList &ids, int pig, int hash, const TBlobList &blobs, int maskcol_id=-1)
	Add a sequence to this volume. More...

void	RenameSingle ()
	Rename all volumes files to single-volume names. More...

void	RenameFileIndex (unsigned int num_digits)

void	Close ()
	Close the volume. More...

const string &	GetVolumeName () const
	Get the name of the volume. More...

const int &	GetOID () const
	Get the current OID of the volume. More...

void	ListFiles (vector< string > &files) const
	List all files associated with this volume. More...

int	CreateColumn (const string &title, const TColumnMeta &meta, Uint8 max_sz, bool mbo=true)
	Create a new database column. More...

void	AddColumnMetaData (int col_id, const string &key, const string &value)
	Add meta data to a column. More...

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

Private Member Functions
int	x_FindNuclLength (const string &seq)
	Compute base-length of compressed nucleotide sequence. More...

Private Attributes
string	m_DbName
	Base name of the database. More...

string	m_VolName
	Database name plus version (if used). More...

bool	m_Protein
	True for protein; false for nucleotide. More...

string	m_Title
	Database title (same for all volumes). More...

string	m_Date
	Construct time (same for all volumes). More...

int	m_Index
	Index of this volume (1 based). More...

EIndexType	m_Indices
	Indices are sparse, full, or disabled. More...

EBlastDbVersion	m_DbVersion
	Blast DB version. More...

Uint8	m_OidMasks
	Oid masks. More...

int	m_OID
	Next assigned OID. More...

bool	m_Open
	True if user can still append sequences. More...

CRef< CWriteDB_IndexFile >	m_Idx
	Index file (pin / nin). More...

CRef< CWriteDB_HeaderFile >	m_Hdr
	Header file (phr / nhr). More...

CRef< CWriteDB_SequenceFile >	m_Seq
	Sequence file (psq / nsq). More...

CRef< CWriteDB_Isam >	m_AccIsam
	Accession index (psi+psd / nsi+nsd). More...

CRef< CWriteDB_Isam >	m_GiIsam
	GI index (pni+pnd / nni+nnd). More...

CRef< CWriteDB_Isam >	m_PigIsam
	PIG index (ppi+ppd, protein only). More...

CRef< CWriteDB_Isam >	m_TraceIsam
	Trace ID index (pti+ptd or nti+ntd). More...

CRef< CWriteDB_Isam >	m_HashIsam
	Hash index (phi+phd or nhi+nhd). More...

CRef< CWriteDB_GiIndex >	m_GiIndex
	OID->GI lookup (pgx or ngx). More...

CRef< CWriteDB_OidList >	m_ExModelList

vector< CRef< CWriteDB_Column > >	m_Columns
	Database columns. More...

set< string >	m_IdSet
	Included Seq_ids. More...

Additional Inherited Members
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)

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

CWriteDB_Volume class.

This manufactures a blast database volume from sequences.

Definition at line 140 of file writedb_volume.hpp.

Member Typedef Documentation

◆ EIndexType

typedef CWriteDB::EIndexType CWriteDB_Volume::EIndexType

Whether and what kind of indices to build.

Definition at line 143 of file writedb_volume.hpp.

◆ TBlobList

typedef vector< CRef<CBlastDbBlob> > CWriteDB_Volume::TBlobList

Type used for lists of identifiers.

Definition at line 149 of file writedb_volume.hpp.

◆ TColumnMeta

typedef CWriteDB_Column::TColumnMeta CWriteDB_Volume::TColumnMeta

Type used for database column meta-data.

Definition at line 250 of file writedb_volume.hpp.

◆ TIdList

typedef vector< CRef<CSeq_id> > CWriteDB_Volume::TIdList

Type used for lists of identifiers.

Definition at line 146 of file writedb_volume.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_Volume()

CWriteDB_Volume::CWriteDB_Volume	(	const string &	dbname,
		bool	protein,
		const string &	title,
		const string &	date,
		int	index,
		Uint8	max_file_size,
		Uint8	max_letters,
		EIndexType	indices,
		EBlastDbVersion	dbver = `eBDB_Version5`,
		Uint8	oid_masks = `EOidMaskType::fNone`
	)

Build a database volume.

Parameters

dbname	Base name of the database, such as 'nr'.
protein	True if the database is a protein database.
title	Title of the database.
date	Creation date of the database.
index	Volume index (for filename).
max_file_size	Maximum file size for this volume.
max_letters	Maximum number of letters for this volume.
indices	Type of indices to build.

Definition at line 44 of file writedb_volume.cpp.

References dbname(), eAcc, CWriteDB::eAddHash, CWriteDB::eAddTrace, eBDB_Version5, eGi, eHash, CWriteDB::eNoIndex, ePig, CWriteDB::eSparseIndex, eTrace, fExcludeModel, m_AccIsam, m_DbName, m_DbVersion, m_ExModelList, m_GiIndex, m_GiIsam, m_HashIsam, m_Hdr, m_Idx, m_Index, m_Indices, m_OidMasks, m_PigIsam, m_Protein, m_Seq, m_TraceIsam, m_VolName, CWriteDB_File::MakeShortName(), and CRef< C, Locker >::Reset().

◆ ~CWriteDB_Volume()

CWriteDB_Volume::~CWriteDB_Volume ( )

Destructor.

The Close() method will be called if it has not already been.

Definition at line 146 of file writedb_volume.cpp.

References Close(), and m_Open.

Member Function Documentation

◆ AddColumnMetaData()

void CWriteDB_Volume::AddColumnMetaData	(	int	col_id,
		const string &	key,
		const string &	value
	)

Add meta data to a column.

In addition to normal blob data, database columns can store a `dictionary' of user-defined metadata in key/value form. This method adds one such key/value pair to the column. Specifying a key a second time causes replacement of the previous value. Using this mechanism to store large amounts of data may have a negative impact on performance.

Parameters

col_id	Specifies the column to add this metadata to.
key	A unique key string.
value	A value string.

Definition at line 559 of file writedb_volume.cpp.

References ncbi::grid::netcache::search::fields::key, m_Columns, NCBI_THROW, and rapidjson::value.

Referenced by CWriteDB_Impl::AddColumnMetaData().

◆ Close()

void CWriteDB_Volume::Close ( void )

Close the volume.

This method finalizes and closes all files associated with this volume. (This is not a trivial operation, because ISAM indices and the index file (pin or nin) cannot be written until all of the data has been seen.)

Definition at line 334 of file writedb_volume.cpp.

References set< Key, Compare >::clear(), CWriteDB_File::Close(), CWriteDB_Isam::Close(), CWriteDB_OidList::Close(), CWriteDB::eNoIndex, GetOID(), m_AccIsam, m_Columns, m_ExModelList, m_GiIndex, m_GiIsam, m_HashIsam, m_Hdr, m_IdSet, m_Idx, m_Indices, m_Open, m_PigIsam, m_Protein, m_Seq, m_TraceIsam, NON_CONST_ITERATE, and CRef< C, Locker >::NotEmpty().

Referenced by CWriteDB_Impl::Close(), CWriteDB_Impl::x_Publish(), and ~CWriteDB_Volume().

◆ CreateColumn()

int CWriteDB_Volume::CreateColumn	(	const string &	title,
		const TColumnMeta &	meta,
		Uint8	max_sz,
		bool	mbo = `true`
	)

Create a new database column.

Parameters

title	The title of the new column.
meta	Metadata to store in the new column.
max_sz	max file size.

Returns: The numeric column ID.

Definition at line 505 of file writedb_volume.cpp.

References m_Columns, m_DbName, m_Index, m_OID, m_Protein, and NCBI_THROW.

Referenced by CWriteDB_Impl::CreateColumn(), and CWriteDB_Impl::x_Publish().

◆ GetOID()

const int& CWriteDB_Volume::GetOID ( ) const

inline

Get the current OID of the volume.

The current OID is needed for generating BL_ORD_ID.

Returns: the OID

Definition at line 238 of file writedb_volume.hpp.

References m_OID.

Referenced by CWriteDB_Impl::Close(), Close(), and CWriteDB_Impl::x_CookHeader().

◆ GetVolumeName()

const string& CWriteDB_Volume::GetVolumeName ( ) const

inline

Get the name of the volume.

The volume name includes the path and version (if a version is used) but does not include the extension. It is the name that would be provided to SeqDB to open this volume. This method should be called after RenameSingle() if that method is going to be called.

Returns: The volume name.

Definition at line 228 of file writedb_volume.hpp.

References m_VolName.

Referenced by CWriteDB_Impl::Close(), and CWriteDB_Impl::x_MakeAlias().

◆ ListFiles()

void CWriteDB_Volume::ListFiles ( vector< string > & files ) const

List all files associated with this volume.

Parameters

files The filenames will be appended to this vector.

Definition at line 461 of file writedb_volume.cpp.

References CWriteDB_File::GetFilename(), ITERATE, CWriteDB_Isam::ListFiles(), m_AccIsam, m_Columns, m_ExModelList, m_GiIndex, m_GiIsam, m_HashIsam, m_Hdr, m_Idx, m_PigIsam, m_Seq, m_TraceIsam, and CRef< C, Locker >::NotEmpty().

◆ RenameFileIndex()

void CWriteDB_Volume::RenameFileIndex ( unsigned int num_digits )

Definition at line 417 of file writedb_volume.cpp.

References _ASSERT, CWriteDB::eNoIndex, CWriteDB_File::GetFilename(), log10(), m_AccIsam, m_Columns, m_ExModelList, m_GiIndex, m_GiIsam, m_HashIsam, m_Hdr, m_Idx, m_Index, m_Indices, m_Open, m_PigIsam, m_Protein, m_Seq, m_TraceIsam, m_VolName, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), CWriteDB_File::RenameFileIndex(), CWriteDB_Isam::RenameFileIndex(), and t.

Referenced by CWriteDB_Impl::Close().

◆ RenameSingle()

void CWriteDB_Volume::RenameSingle ( )

Rename all volumes files to single-volume names.

When volume component files are generated by WriteDB, the volume names include a volume index. This method renames the generated files for this volume to names that do not include the volume index. This method should not be called until the volume is Close()s.

Definition at line 376 of file writedb_volume.cpp.

References _ASSERT, CWriteDB::eNoIndex, m_AccIsam, m_Columns, m_DbName, m_ExModelList, m_GiIndex, m_GiIsam, m_HashIsam, m_Hdr, m_Idx, m_Indices, m_Open, m_PigIsam, m_Protein, m_Seq, m_TraceIsam, m_VolName, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), CWriteDB_File::RenameSingle(), and CWriteDB_Isam::RenameSingle().

Referenced by CWriteDB_Impl::Close().

◆ WriteSequence()

bool CWriteDB_Volume::WriteSequence	(	const string &	seq,
		const string &	ambig,
		const string &	binhdr,
		const TIdList &	ids,
		int	pig,
		int	hash,
		const TBlobList &	blobs,
		int	maskcol_id = `-1`
	)

Add a sequence to this volume.

The provided data represents all information for one non-redundant sequence that will be added to this volume.

Parameters

seq	Sequence data in format ncbi2na or ncbistdaa.
ambig	Ambiguities (for protein this should be empty).
binhdr	Binary headers (blast deflines in binary ASN.1).
ids	List of identifiers for ISAM construction.
pig	PIG protein identifier (zero if not available.)
hash	Sequence Hash (zero if not available.)

Definition at line 153 of file writedb_volume.cpp.

References _ASSERT, CWriteDB_GiIndex::AddGi(), CWriteDB_Isam::AddHash(), CWriteDB_Isam::AddIds(), CWriteDB_OidList::AddOid(), CWriteDB_Isam::AddPig(), CWriteDB_HeaderFile::AddSequence(), CWriteDB_SequenceFile::AddSequence(), CWriteDB_IndexFile::AddSequence(), ambig(), CWriteDB_IndexFile::CanFit(), CWriteDB_Isam::CanFit(), CWriteDB_HeaderFile::CanFit(), CWriteDB_SequenceFile::CanFit(), CSeq_id::eDefault, CRef< C, Locker >::Empty(), CWriteDB::eNoIndex, CSeq_id::fAcc_predicted, CSeq_id::fLabel_Default, CSeq_id::fLabel_UpperCase, CSeq_id_Base::GetGi(), set< Key, Compare >::insert(), int, INVALID_GI, CSeq_id_Base::IsGi(), ITERATE, kEmptyStr, m_AccIsam, m_Columns, m_ExModelList, m_GiIndex, m_GiIsam, m_HashIsam, m_Hdr, m_IdSet, m_Idx, m_Indices, m_OID, m_Open, m_PigIsam, m_Protein, m_Seq, m_TraceIsam, msg(), NCBI_THROW, CRef< C, Locker >::NotEmpty(), set< Key, Compare >::size(), and x_FindNuclLength().

Referenced by CWriteDB_Impl::x_Publish().

◆ x_FindNuclLength()

int CWriteDB_Volume::x_FindNuclLength ( const string & seq )

private

Compute base-length of compressed nucleotide sequence.

Nucleotide sequences stored on disk are packed 4 bases to a byte, except for the last byte. That byte has 0-3 bases of real sequence data plus a 'remainder' value (from 0-3) that indicates how many of the bases of the last byte are sequence data. This method finds the exact length in bases for a nucleotide sequence packed in this way.

Parameters

seq	Ncbi2na sequence with length remainder encoding.

Returns: Length in bases of actual sequence data in this sequence.

Definition at line 326 of file writedb_volume.cpp.

References _ASSERT, m_Protein, and WriteDB_FindSequenceLength().

Referenced by WriteSequence().

Member Data Documentation

◆ m_AccIsam

CRef<CWriteDB_Isam> CWriteDB_Volume::m_AccIsam

private

Accession index (psi+psd / nsi+nsd).

Definition at line 304 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_Columns

vector< CRef<CWriteDB_Column> > CWriteDB_Volume::m_Columns

private

Database columns.

Definition at line 315 of file writedb_volume.hpp.

Referenced by AddColumnMetaData(), Close(), CreateColumn(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_Date

string CWriteDB_Volume::m_Date

private

Construct time (same for all volumes).

Definition at line 287 of file writedb_volume.hpp.

◆ m_DbName

string CWriteDB_Volume::m_DbName

private

Base name of the database.

Definition at line 283 of file writedb_volume.hpp.

Referenced by CreateColumn(), CWriteDB_Volume(), and RenameSingle().

◆ m_DbVersion

EBlastDbVersion CWriteDB_Volume::m_DbVersion

private

Blast DB version.

Definition at line 290 of file writedb_volume.hpp.

Referenced by CWriteDB_Volume().

◆ m_ExModelList

CRef<CWriteDB_OidList> CWriteDB_Volume::m_ExModelList

private

Definition at line 310 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_GiIndex

CRef<CWriteDB_GiIndex> CWriteDB_Volume::m_GiIndex

private

OID->GI lookup (pgx or ngx).

Definition at line 309 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_GiIsam

CRef<CWriteDB_Isam> CWriteDB_Volume::m_GiIsam

private

GI index (pni+pnd / nni+nnd).

Definition at line 305 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_HashIsam

CRef<CWriteDB_Isam> CWriteDB_Volume::m_HashIsam

private

Hash index (phi+phd or nhi+nhd).

Definition at line 308 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_Hdr

CRef<CWriteDB_HeaderFile> CWriteDB_Volume::m_Hdr

private

Header file (phr / nhr).

Definition at line 301 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_IdSet

set<string> CWriteDB_Volume::m_IdSet

private

Included Seq_ids.

Definition at line 319 of file writedb_volume.hpp.

Referenced by Close(), and WriteSequence().

◆ m_Idx

CRef<CWriteDB_IndexFile> CWriteDB_Volume::m_Idx

private

Index file (pin / nin).

Definition at line 300 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_Index

int CWriteDB_Volume::m_Index

private

Index of this volume (1 based).

Definition at line 288 of file writedb_volume.hpp.

Referenced by CreateColumn(), CWriteDB_Volume(), and RenameFileIndex().

◆ m_Indices

EIndexType CWriteDB_Volume::m_Indices

private

Indices are sparse, full, or disabled.

Definition at line 289 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_OID

int CWriteDB_Volume::m_OID

private

Next assigned OID.

Definition at line 295 of file writedb_volume.hpp.

Referenced by CreateColumn(), GetOID(), and WriteSequence().

◆ m_OidMasks

Uint8 CWriteDB_Volume::m_OidMasks

private

Oid masks.

Definition at line 291 of file writedb_volume.hpp.

Referenced by CWriteDB_Volume().

◆ m_Open

bool CWriteDB_Volume::m_Open

private

True if user can still append sequences.

Definition at line 296 of file writedb_volume.hpp.

Referenced by Close(), RenameFileIndex(), RenameSingle(), WriteSequence(), and ~CWriteDB_Volume().

◆ m_PigIsam

CRef<CWriteDB_Isam> CWriteDB_Volume::m_PigIsam

private

PIG index (ppi+ppd, protein only).

Definition at line 306 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_Protein

bool CWriteDB_Volume::m_Protein

private

True for protein; false for nucleotide.

Definition at line 285 of file writedb_volume.hpp.

Referenced by Close(), CreateColumn(), CWriteDB_Volume(), RenameFileIndex(), RenameSingle(), WriteSequence(), and x_FindNuclLength().

◆ m_Seq

CRef<CWriteDB_SequenceFile> CWriteDB_Volume::m_Seq

private

Sequence file (psq / nsq).

Definition at line 302 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_Title

string CWriteDB_Volume::m_Title

private

Database title (same for all volumes).

Definition at line 286 of file writedb_volume.hpp.

◆ m_TraceIsam

CRef<CWriteDB_Isam> CWriteDB_Volume::m_TraceIsam

private

Trace ID index (pti+ptd or nti+ntd).

Definition at line 307 of file writedb_volume.hpp.

Referenced by Close(), CWriteDB_Volume(), ListFiles(), RenameFileIndex(), RenameSingle(), and WriteSequence().

◆ m_VolName

string CWriteDB_Volume::m_VolName

private

Database name plus version (if used).

Definition at line 284 of file writedb_volume.hpp.

Referenced by CWriteDB_Volume(), GetVolumeName(), RenameFileIndex(), and RenameSingle().

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

src/objtools/blast/seqdb_writer/writedb_volume.hpp
src/objtools/blast/seqdb_writer/writedb_volume.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EIndexType

◆ TBlobList

◆ TColumnMeta

◆ TIdList

Constructor & Destructor Documentation

◆ CWriteDB_Volume()

◆ ~CWriteDB_Volume()

Member Function Documentation

◆ AddColumnMetaData()

◆ Close()

◆ CreateColumn()

◆ GetOID()

◆ GetVolumeName()

◆ ListFiles()

◆ RenameFileIndex()

◆ RenameSingle()

◆ WriteSequence()

◆ x_FindNuclLength()

Member Data Documentation

◆ m_AccIsam

◆ m_Columns

◆ m_Date

◆ m_DbName

◆ m_DbVersion

◆ m_ExModelList

◆ m_GiIndex

◆ m_GiIsam

◆ m_HashIsam

◆ m_Hdr

◆ m_IdSet

◆ m_Idx

◆ m_Index

◆ m_Indices

◆ m_OID

◆ m_OidMasks

◆ m_Open

◆ m_PigIsam

◆ m_Protein

◆ m_Seq

◆ m_Title

◆ m_TraceIsam

◆ m_VolName