NCBI C++ ToolKit
Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
CSeqDBAliasFile Class Reference

Search Toolkit Book for CSeqDBAliasFile

CSeqDBAliasFile class. More...

#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_FilterTreeGetFilterTree ()
 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...
 
CObjectoperator= (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...
 
CSeqDBAliasFileoperator= (const CSeqDBAliasFile &)
 Disable copy operator. More...
 
 CSeqDBAliasFile (const CSeqDBAliasFile &)
 Disable copy constructor. More...
 

Private Attributes

CSeqDBAliasSets m_AliasSets
 Combined alias files. More...
 
CRef< CSeqDBAliasNodem_Node
 This is the alias node tree's "artificial" topmost node, which aggregates the user provided database names. More...
 
vector< stringm_VolumeNames
 The cached output of the topmost node's FindVolumePaths(recursive). More...
 
vector< stringm_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_FilterTreem_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< Uint8TCounter
 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

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
atlasThe SeqDB memory management layer.
name_listA space seperated list of database names.
prot_nuclIndicates whether the database is protein or nucleotide.
expand_linksIndicates 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

◆ 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
volsThe vector to be populated with volume names
recursiveIf 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
afvThe alias file values will be returned here.
volsetThe 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_listThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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
volsetThe 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:
Modified on Tue May 21 10:58:39 2024 by modify_doxy.py rev. 669887