Search Toolkit Book for CSeqDBAliasFile

#include "seqdbalias.hpp"
(Private to src/objtools/blast/seqdb_reader.)

Inheritance diagram for CSeqDBAliasFile:

Collaboration diagram for CSeqDBAliasFile:

Public Member Functions
	CSeqDBAliasFile (CSeqDBAtlas &atlas, const string &name_list, char prot_nucl, bool expand_links=true)
	Constructor. More...

const vector< string > &	GetVolumeNames () const
	Get the list of volume names. More...

void	FindVolumePaths (vector< string > &vols, vector< string > *alias, bool recursive) const
	Find the base names of volumes. More...

string	GetTitle (const CSeqDBVolSet &volset) const
	Get the title. More...

Int4	GetMinLength (const CSeqDBVolSet &volset) const
	Get the number of sequences available. More...

Int8	GetNumSeqs (const CSeqDBVolSet &volset) const
	Get the number of sequences available. More...

Int8	GetNumSeqsStats (const CSeqDBVolSet &volset) const
	Get the number of sequences available. More...

Int8	GetNumOIDs (const CSeqDBVolSet &volset) const
	Get the size of the OID range. More...

Uint8	GetTotalLength (const CSeqDBVolSet &volset) const
	Get the total length of the set of databases. More...

Uint8	GetTotalLengthStats (const CSeqDBVolSet &volset) const
	Get the total length of the set of databases. More...

Uint8	GetVolumeLength (const CSeqDBVolSet &volset) const
	Get the sum of the volume lengths. More...

int	GetMembBit (const CSeqDBVolSet &volset) const
	Get the membership bit. More...

bool	NeedTotalsScan (const CSeqDBVolSet &volset) const
	Check whether a db scan is need to compute correct totals. More...

bool	HasFilters ()
	Check if any volume filtering exists. More...

CRef< CSeqDB_FilterTree >	GetFilterTree ()
	Get filtering tree for all volumes. More...

void	GetAliasFileValues (TAliasFileValues &afv, const CSeqDBVolSet &volset)
	Get Name/Value Data From Alias Files. More...

bool	HasGiMask () const
	Is the top node alias file associated with Gi based masks? More...

void	GetMaskList (vector< string > &mask_list)
	Get Gi-based Mask Names From Alias Files. More...

void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Dump debug information for this object. More...

int	GetOidMaskType (const CSeqDBVolSet &volset) const
	Get the Oid Mask Type. 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...

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 Types
typedef TSeqDBAliasFileValues	TAliasFileValues
	Import type to allow shorter name. More...

Private Member Functions
void	x_ComputeMasks ()
	Compute filtering options for all volumes. More...

CSeqDBAliasFile &	operator= (const CSeqDBAliasFile &)
	Disable copy operator. More...

	CSeqDBAliasFile (const CSeqDBAliasFile &)
	Disable copy constructor. More...

Private Attributes
CSeqDBAliasSets	m_AliasSets
	Combined alias files. More...

CRef< CSeqDBAliasNode >	m_Node
	This is the alias node tree's "artificial" topmost node, which aggregates the user provided database names. More...

vector< string >	m_VolumeNames
	The cached output of the topmost node's FindVolumePaths(recursive). More...

vector< string >	m_AliasNames
	The cached output of the topmost node's FindVolumePaths(recursive). More...

bool	m_IsProtein
	True if this is a protein database. More...

Int4	m_MinLength
	Shortest sequence length. More...

Int8	m_NumSeqs
	Number of sequences. More...

int	m_NumSeqsStats
	Number of sequences for statistics purposes. More...

Int8	m_NumOIDs
	Number of OIDs. More...

Int8	m_TotalLength
	Total length. More...

Int8	m_TotalLengthStats
	Total length for statistics purposes. More...

Int8	m_VolumeLength
	Total length ignoring filtering. More...

int	m_MembBit
	Membership bit. More...

bool	m_HasTitle
	True if we have the database title. More...

string	m_Title
	Database title. More...

int	m_NeedTotalsScan
	1 if we need a totals scan, 0 if not, -1 if not known. More...

CRef< CSeqDB_FilterTree >	m_TopTree
	Filter tree representing all alias file filtering. More...

bool	m_HasFilters
	Are there filters for this database? More...

int	m_OidMaskType
	Oid Mask Type. More...

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 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

CSeqDBAliasFile class.

This class is an interface to the alias node tree. It provides functionality to classes like CSeqDBImpl (and others) that do not need to understand alias walkers, nodes, and tree traversal.

Definition at line 982 of file seqdbalias.hpp.

Member Typedef Documentation

◆ TAliasFileValues

typedef TSeqDBAliasFileValues CSeqDBAliasFile::TAliasFileValues

private

Import type to allow shorter name.

Definition at line 984 of file seqdbalias.hpp.

Constructor & Destructor Documentation

◆ CSeqDBAliasFile() [1/2]

CSeqDBAliasFile::CSeqDBAliasFile	(	CSeqDBAtlas &	atlas,
		const string &	name_list,
		char	prot_nucl,
		bool	expand_links = `true`
	)

Constructor.

This builds a tree of CSeqDBAliasNode objects from a space-seperated list of database names. Every database instance has at least one node, because the top most node is an "artificial" node, which serves only to aggregate the list of databases specified to the constructor. The tree is constructed in a depth first manner, and will be complete upon return from this constructor.

Parameters

atlas	The SeqDB memory management layer.
name_list	A space seperated list of database names.
prot_nucl	Indicates whether the database is protein or nucleotide.
expand_links	Indicates whether the soft links should be expanded

Definition at line 55 of file seqdbalias.cpp.

References CSeqDBAliasNode::FindVolumePaths(), m_AliasNames, m_AliasSets, m_Node, m_VolumeNames, and CRef< C, Locker >::Reset().

◆ CSeqDBAliasFile() [2/2]

CSeqDBAliasFile::CSeqDBAliasFile ( const CSeqDBAliasFile & )

private

Disable copy constructor.

Member Function Documentation

◆ DebugDump()

void CSeqDBAliasFile::DebugDump	(	CDebugDumpContext	ddc,
		unsigned int	depth
	)		const

virtual

Dump debug information for this object.

See also: CDebugDumpable

Reimplemented from CObject.

Definition at line 1916 of file seqdbalias.cpp.

References CObject::DebugDump(), depth, i, CDebugDumpContext::Log(), m_AliasNames, m_HasFilters, m_HasTitle, m_IsProtein, m_MembBit, m_MinLength, m_NeedTotalsScan, m_NumOIDs, m_NumSeqs, m_NumSeqsStats, m_Title, m_TotalLength, m_TotalLengthStats, m_VolumeLength, m_VolumeNames, CDebugDumpContext::SetFrame(), and NStr::SizetToString().

◆ FindVolumePaths()

void CSeqDBAliasFile::FindVolumePaths	(	vector< string > &	vols,
		vector< string > *	alias,
		bool	recursive
	)		const

inline

Find the base names of volumes.

This method populates the vector with volume names.

Parameters

vols	The vector to be populated with volume names
recursive	If true, vol will include all volume names within the alias node tree. Otherwise, only the top-node volume names are included

Definition at line 1032 of file seqdbalias.hpp.

Referenced by CSeqDBImpl::FindVolumePaths().

◆ GetAliasFileValues()

void CSeqDBAliasFile::GetAliasFileValues	(	TAliasFileValues &	afv,
		const CSeqDBVolSet &	volset
	)

Get Name/Value Data From Alias Files.

SeqDB treats each alias file as a map from a variable name to a value. This method will return a map from the basename of the filename of each alias file, to a mapping from variable name to value for each entry in that file. For example, the value of the "DBLIST" entry in the "wgs.nal" file would be values["wgs"]["DBLIST"]. The lines returned have been processed somewhat by SeqDB, including normalizing tabs to whitespace, trimming leading and trailing whitespace, and removal of comments and other non-value lines. Care should be taken when using the values returned by this method. SeqDB uses an internal "virtual" alias file entry to aggregate the values passed into SeqDB by the user. This mapping uses a filename of "-" and contains a single entry mapping "DBLIST" to SeqDB's database name input. This entry is the root of the alias file inclusion tree. Also note that alias files that appear in several places in the alias file inclusion tree only have one entry in the returned map (and are only parsed once by SeqDB).

Parameters

afv	The alias file values will be returned here.
volset	The set of database volumes

Definition at line 1758 of file seqdbalias.cpp.

References CSeqDBAliasNode::CompleteAliasFileValues(), map_checker< Container >::end(), map_checker< Container >::find(), CSeqDBAliasNode::GetAliasFileValues(), CSeqDBVolSet::GetNumVols(), CSeqDBVol::GetTitle(), CSeqDBVolSet::GetVol(), CSeqDBVol::GetVolName(), i, ncbi::grid::netcache::search::fields::key, m_IsProtein, and m_Node.

Referenced by CSeqDBImpl::GetAliasFileValues().

◆ GetFilterTree()

CRef< CSeqDB_FilterTree > CSeqDBAliasFile::GetFilterTree ( )

Get filtering tree for all volumes.

This method applies the filtering options found in the alias node tree to all associated volumes (iterating over the tree recursively). The virtual OID lists are not built as a result of this process, but the data necessary for virtual OID construction is copied to the volume objects.

Returns: A filter tree for all volumes.

Definition at line 1903 of file seqdbalias.cpp.

References CSeqDBAliasNode::BuildFilterTree(), CRef< C, Locker >::Empty(), m_Node, m_TopTree, CRef< C, Locker >::Reset(), and x_ComputeMasks().

Referenced by CSeqDBImpl::x_GetOidList().

◆ GetMaskList()

void CSeqDBAliasFile::GetMaskList ( vector< string > & mask_list )

inline

Get Gi-based Mask Names From Alias Files.

This will return the MASKLIST field of the top alias node.

Parameters

mask_list The mask names will be returned here.

Definition at line 1250 of file seqdbalias.hpp.

Referenced by CSeqDBImpl::CSeqDBImpl().

◆ GetMembBit()

int CSeqDBAliasFile::GetMembBit ( const CSeqDBVolSet & volset ) const

Get the membership bit.

This iterates the alias node tree to find the membership bit, if there is one. If more than one alias node provides a membership bit, only one will be used. This value can only be found in alias files (volumes do not have a single internal membership bit).

Parameters

volset The set of database volumes

Returns: The membership bit, or zero if none was found.

Definition at line 1788 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetMembBit(), m_MembBit, and m_Node.

◆ GetMinLength()

Int4 CSeqDBAliasFile::GetMinLength ( const CSeqDBVolSet & volset ) const

Get the number of sequences available.

This iterates this node and possibly subnodes of it to compute the shortest sequence length.

Parameters

volset The set of database volumes

Returns: The shortest sequence length

Definition at line 1807 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetMinLength(), m_MinLength, and m_Node.

Referenced by CSeqDBImpl::x_GetMinLength().

◆ GetNumOIDs()

Int8 CSeqDBAliasFile::GetNumOIDs ( const CSeqDBVolSet & volset ) const

Get the size of the OID range.

This iterates the alias node tree to compute the number of sequences in all volumes as encountered in traversal. Alias files cannot override this value. Filtering does not affect this value.

Parameters

volset The set of database volumes

Returns: The number of OIDs found during traversal

Definition at line 1833 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetNumOIDs(), m_Node, and m_NumOIDs.

Referenced by CSeqDBImpl::x_GetNumOIDs().

◆ GetNumSeqs()

Int8 CSeqDBAliasFile::GetNumSeqs ( const CSeqDBVolSet & volset ) const

Get the number of sequences available.

This iterates the alias node tree to compute the number of sequences available here. Alias files may override this value (stopping traversal at that depth). It is normally used to provide information on how many OIDs exist after filtering has been applied.

Parameters

volset The set of database volumes

Returns: The number of included sequences

Definition at line 1815 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetNumSeqs(), m_Node, and m_NumSeqs.

Referenced by CSeqDBImpl::x_GetNumSeqs().

◆ GetNumSeqsStats()

Int8 CSeqDBAliasFile::GetNumSeqsStats ( const CSeqDBVolSet & volset ) const

Get the number of sequences available.

This iterates the alias node tree to compute the number of sequences available here. Alias files may override this value (stopping traversal at that depth). It is normally used to provide information on how many OIDs exist after filtering has been applied. This is like GetNumSeqs, but uses STATS_NSEQ.

Parameters

volset The set of database volumes

Returns: The number of included sequences

Definition at line 1824 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetNumSeqsStats(), int, m_Node, and m_NumSeqsStats.

Referenced by CSeqDBImpl::x_GetNumSeqsStats().

◆ GetOidMaskType()

int CSeqDBAliasFile::GetOidMaskType ( const CSeqDBVolSet & volset ) const

Get the Oid Mask Type.

This iterates the alias node tree to find the oid mask type, if there is one.

Parameters

volset The set of database volumes

Returns: Oid mask type, or zero if none was found.

Definition at line 1895 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetOidMaskType(), m_Node, and m_OidMaskType.

◆ GetTitle()

string CSeqDBAliasFile::GetTitle ( const CSeqDBVolSet & volset ) const

Get the title.

This iterates the alias node tree to build and return a title string. Alias files may override this value (stopping traversal at that depth).

Parameters

volset The set of database volumes

Returns: A string describing the database

Definition at line 1799 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetTitle(), m_HasTitle, m_Node, and m_Title.

Referenced by CSeqDBImpl::GetTitle().

◆ GetTotalLength()

Uint8 CSeqDBAliasFile::GetTotalLength ( const CSeqDBVolSet & volset ) const

Get the total length of the set of databases.

This iterates the alias node tree to compute the total length of all sequences in all volumes included in the database. This may count volumes several times (depending on alias tree structure). Alias files can override this value (stopping traversal at that depth). It is normally used to describe the amount of sequence data remaining after filtering has been applied.

Parameters

volset The set of database volumes

Returns: The total length of all included sequences

Definition at line 1842 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetTotalLength(), m_Node, and m_TotalLength.

Referenced by CSeqDBImpl::x_GetTotalLength().

◆ GetTotalLengthStats()

Uint8 CSeqDBAliasFile::GetTotalLengthStats ( const CSeqDBVolSet & volset ) const

Get the total length of the set of databases.

This iterates the alias node tree to compute the total length of all sequences in all volumes included in the database. This may count volumes several times (depending on alias tree structure). Alias files can override this value (stopping traversal at that depth). It is normally used to describe the amount of sequence data remaining after filtering has been applied. This is like GetTotalLength but uses STATS_TOTLEN.

Parameters

volset The set of database volumes

Returns: The total length of all included sequences

Definition at line 1851 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetTotalLengthStats(), m_Node, and m_TotalLengthStats.

Referenced by CSeqDBImpl::x_GetTotalLengthStats().

◆ GetVolumeLength()

Uint8 CSeqDBAliasFile::GetVolumeLength ( const CSeqDBVolSet & volset ) const

Get the sum of the volume lengths.

This iterates the alias node tree to compute the total length of all sequences in all volumes as encountered in traversal. This may count volumes several times (depending on alias tree structure). Alias files cannot override this value.

Parameters

volset The set of database volumes

Returns: The sum of all volumes lengths as traversed

Definition at line 1860 of file seqdbalias.cpp.

References CSeqDBAliasNode::GetVolumeLength(), m_Node, and m_VolumeLength.

◆ GetVolumeNames()

const vector<string>& CSeqDBAliasFile::GetVolumeNames ( ) const

inline

Get the list of volume names.

This method returns a reference to the vector of volume names. The vector will contain all volume names mentioned in any of the DBLIST lines in the hierarchy of the alias node tree. The volume names do not include an extension (such as .pin or .nin).

Returns: Reference to the internal vector of volume names.

Definition at line 1019 of file seqdbalias.hpp.

◆ HasFilters()

bool CSeqDBAliasFile::HasFilters ( )

inline

Check if any volume filtering exists.

This method computes and caches the sequence filtering for this node and any subnodes, and returns true if any filtering exists. Subsequent calls will just return the cached value.

Returns: True if any filtering exists.

Definition at line 1188 of file seqdbalias.hpp.

Referenced by CSeqDBImpl::CSeqDBImpl().

◆ HasGiMask()

bool CSeqDBAliasFile::HasGiMask ( ) const

inline

Is the top node alias file associated with Gi based masks?

This will return true if the MASKLIST field of the top alias node is set.

Returns: TRUE if MASKLIST field is present

Definition at line 1239 of file seqdbalias.hpp.

◆ NeedTotalsScan()

bool CSeqDBAliasFile::NeedTotalsScan ( const CSeqDBVolSet & volset ) const

Check whether a db scan is need to compute correct totals.

This traverses this node and its subnodes to determine whether accurate estimation of the total number of sequences and bases requires a linear time scan of the index files.

Parameters

volset The set of database volumes.

Returns: True if the database scan is required.

Definition at line 1869 of file seqdbalias.cpp.

References m_NeedTotalsScan, m_Node, and CSeqDBAliasNode::NeedTotalsScan().

Referenced by CSeqDBImpl::CSeqDBImpl().

◆ operator=()

CSeqDBAliasFile& CSeqDBAliasFile::operator= ( const CSeqDBAliasFile & )

private

Disable copy operator.

◆ x_ComputeMasks()

void CSeqDBAliasFile::x_ComputeMasks ( )

inlineprivate

Compute filtering options for all volumes.

This method applies the filtering options found in the alias node tree to all associated volumes (iterating over the tree recursively). The virtual OID lists are not built as a result of this process, but the data necessary for virtual OID construction is copied to the volume objects.

Definition at line 1278 of file seqdbalias.hpp.

Referenced by GetFilterTree().

Member Data Documentation

◆ m_AliasNames

vector<string> CSeqDBAliasFile::m_AliasNames

private

The cached output of the topmost node's FindVolumePaths(recursive).

Definition at line 1294 of file seqdbalias.hpp.

Referenced by CSeqDBAliasFile(), and DebugDump().

◆ m_AliasSets

CSeqDBAliasSets CSeqDBAliasFile::m_AliasSets

private

Combined alias files.

Definition at line 1284 of file seqdbalias.hpp.

Referenced by CSeqDBAliasFile().

◆ m_HasFilters

bool CSeqDBAliasFile::m_HasFilters

private

Are there filters for this database?

Definition at line 1336 of file seqdbalias.hpp.

Referenced by DebugDump().

◆ m_HasTitle

bool CSeqDBAliasFile::m_HasTitle

mutableprivate

True if we have the database title.

Definition at line 1324 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetTitle().

◆ m_IsProtein

bool CSeqDBAliasFile::m_IsProtein

private

True if this is a protein database.

Definition at line 1297 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetAliasFileValues().

◆ m_MembBit

int CSeqDBAliasFile::m_MembBit

mutableprivate

Membership bit.

Definition at line 1321 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetMembBit().

◆ m_MinLength

Int4 CSeqDBAliasFile::m_MinLength

mutableprivate

Shortest sequence length.

Definition at line 1300 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetMinLength().

◆ m_NeedTotalsScan

int CSeqDBAliasFile::m_NeedTotalsScan

mutableprivate

1 if we need a totals scan, 0 if not, -1 if not known.

Definition at line 1330 of file seqdbalias.hpp.

Referenced by DebugDump(), and NeedTotalsScan().

◆ m_Node

CRef<CSeqDBAliasNode> CSeqDBAliasFile::m_Node

private

This is the alias node tree's "artificial" topmost node, which aggregates the user provided database names.

Definition at line 1288 of file seqdbalias.hpp.

Referenced by CSeqDBAliasFile(), GetAliasFileValues(), GetFilterTree(), GetMembBit(), GetMinLength(), GetNumOIDs(), GetNumSeqs(), GetNumSeqsStats(), GetOidMaskType(), GetTitle(), GetTotalLength(), GetTotalLengthStats(), GetVolumeLength(), and NeedTotalsScan().

◆ m_NumOIDs

Int8 CSeqDBAliasFile::m_NumOIDs

mutableprivate

Number of OIDs.

Definition at line 1309 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetNumOIDs().

◆ m_NumSeqs

Int8 CSeqDBAliasFile::m_NumSeqs

mutableprivate

Number of sequences.

Definition at line 1303 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetNumSeqs().

◆ m_NumSeqsStats

int CSeqDBAliasFile::m_NumSeqsStats

mutableprivate

Number of sequences for statistics purposes.

Definition at line 1306 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetNumSeqsStats().

◆ m_OidMaskType

int CSeqDBAliasFile::m_OidMaskType

mutableprivate

Oid Mask Type.

Definition at line 1339 of file seqdbalias.hpp.

Referenced by GetOidMaskType().

◆ m_Title

string CSeqDBAliasFile::m_Title

mutableprivate

Database title.

Definition at line 1327 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetTitle().

◆ m_TopTree

CRef<CSeqDB_FilterTree> CSeqDBAliasFile::m_TopTree

private

Filter tree representing all alias file filtering.

Definition at line 1333 of file seqdbalias.hpp.

Referenced by GetFilterTree().

◆ m_TotalLength

Int8 CSeqDBAliasFile::m_TotalLength

mutableprivate

Total length.

Definition at line 1312 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetTotalLength().

◆ m_TotalLengthStats

Int8 CSeqDBAliasFile::m_TotalLengthStats

mutableprivate

Total length for statistics purposes.

Definition at line 1315 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetTotalLengthStats().

◆ m_VolumeLength

Int8 CSeqDBAliasFile::m_VolumeLength

mutableprivate

Total length ignoring filtering.

Definition at line 1318 of file seqdbalias.hpp.

Referenced by DebugDump(), and GetVolumeLength().

◆ m_VolumeNames

vector<string> CSeqDBAliasFile::m_VolumeNames

private

The cached output of the topmost node's FindVolumePaths(recursive).

Definition at line 1291 of file seqdbalias.hpp.

Referenced by CSeqDBAliasFile(), and DebugDump().

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

src/objtools/blast/seqdb_reader/seqdbalias.hpp
src/objtools/blast/seqdb_reader/seqdbalias.cpp

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAliasFileValues

Constructor & Destructor Documentation

◆ CSeqDBAliasFile() [1/2]

◆ CSeqDBAliasFile() [2/2]

Member Function Documentation

◆ DebugDump()

◆ FindVolumePaths()

◆ GetAliasFileValues()

◆ GetFilterTree()

◆ GetMaskList()

◆ GetMembBit()

◆ GetMinLength()

◆ GetNumOIDs()

◆ GetNumSeqs()

◆ GetNumSeqsStats()

◆ GetOidMaskType()

◆ GetTitle()

◆ GetTotalLength()

◆ GetTotalLengthStats()

◆ GetVolumeLength()

◆ GetVolumeNames()

◆ HasFilters()

◆ HasGiMask()

◆ NeedTotalsScan()

◆ operator=()

◆ x_ComputeMasks()

Member Data Documentation

◆ m_AliasNames

◆ m_AliasSets

◆ m_HasFilters

◆ m_HasTitle

◆ m_IsProtein

◆ m_MembBit

◆ m_MinLength

◆ m_NeedTotalsScan

◆ m_Node

◆ m_NumOIDs

◆ m_NumSeqs

◆ m_NumSeqsStats

◆ m_OidMaskType

◆ m_Title

◆ m_TopTree

◆ m_TotalLength

◆ m_TotalLengthStats

◆ m_VolumeLength

◆ m_VolumeNames