#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>

Inheritance diagram for CSeqDBGiList:

Collaboration diagram for CSeqDBGiList:

Classes
struct	SGiOid
	Structure that holds GI,OID pairs. More...

struct	SPigOid

struct	SSiOid
	Structure that holds Seq-id,OID pairs. More...

struct	STaxIdsOids

struct	STiOid
	Structure that holds TI,OID pairs. More...

Public Types
enum	ESortOrder { eNone , eGi }
	Possible sorting states. 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
	CSeqDBGiList ()
	Constructor. More...

virtual	~CSeqDBGiList ()
	Destructor. More...

void	InsureOrder (ESortOrder order)
	Sort if necessary to insure order of elements. More...

bool	FindGi (TGi gi) const
	Test for existence of a GI. More...

bool	GiToOid (TGi gi, int &oid)
	Try to find a GI and return the associated OID. More...

bool	GiToOid (TGi gi, int &oid, int &index)
	Find a GI, returning the index and the associated OID. More...

bool	FindTi (TTi ti) const
	Test for existence of a TI. More...

bool	TiToOid (TTi ti, int &oid)
	Try to find a TI and return the associated OID. More...

bool	TiToOid (TTi ti, int &oid, int &index)
	Find a TI, returning the index and the associated OID. More...

bool	FindSi (const string &si) const

bool	SiToOid (const string &si, int &oid)

bool	SiToOid (const string &si, int &oid, int &index)

bool	FindPig (TPig pig) const

bool	PigToOid (TPig pig, int &oid)

bool	PigToOid (TPig pig, int &oid, int &index)

bool	FindId (const CSeq_id &id)
	Test for existence of a Seq-id by type. More...

const SGiOid &	GetGiOid (int index) const
	Access an element of the array. More...

const STiOid &	GetTiOid (int index) const
	Access an element of the array. More...

const SSiOid &	GetSiOid (int index) const
	Access an element of the array. More...

const SPigOid &	GetPigOid (int index) const

int	GetNumGis () const
	Get the number of GIs in the array. More...

int	GetNumTis () const
	Get the number of TIs in the array. More...

int	GetNumSis () const
	Get the number of Seq-ids in the array. More...

int	GetNumTaxIds () const

int	GetNumOidsForTaxIdList () const

int	GetNumPigs () const

Uint8	GetMaskOpts () const

bool	Empty () const
	Return false if there are elements present. More...

bool	NotEmpty () const
	Return true if there are elements present. More...

bool	HasIdFilters () const

void	SetGiTranslation (int index, int oid)
	Specify the correct OID for a GI. More...

void	SetTiTranslation (int index, int oid)
	Specify the correct OID for a TI. More...

void	SetSiTranslation (int index, int oid)
	Specify the correct OID for a Seq-id. More...

void	SetPigTranslation (int index, int oid)

int	Size () const

template<class T >
int	GetSize () const

template<class T >
T	GetKey (int index) const

template<class T >
bool	IsValueSet (int index) const

template<class T >
void	SetValue (int index, int oid)

void	GetGiList (vector< TGi > &gis) const
	Get the gi list. More...

void	GetTiList (vector< TTi > &tis) const
	Get the ti list. More...

void	GetSiList (vector< string > &sis) const
	TODO Get the seqid list? More...

void	GetPigList (vector< TPig > &pigs) const

set< TTaxId > &	GetTaxIdsList ()

const vector< blastdb::TOid > &	GetOidsForTaxIdsList ()

vector< blastdb::TOid > &	SetOidsForTaxIdsList ()

void	AddGi (TGi gi)
	Add a new GI to the list. More...

void	AddTi (TTi ti)
	Add a new TI to the list. More...

void	AddSi (const string &si)
	Add a new SeqId to the list. More...

void	AddTaxIds (const set< TTaxId > &tax_ids)

void	SetPigList (const vector< TPig > &list)

void	AddPig (TPig pig)

void	ReserveGis (size_t n)
	Reserve space for GIs. More...

void	ReserveTis (size_t n)
	Reserve space for TIs. More...

void	ReserveSis (size_t n)

void	ReservePigs (size_t n)

void	PreprocessIdsForISAMSiLookup ()
	Preprocess ids for ISAM string id lookup. More...

void	SetListInfo (const SBlastSeqIdListInfo &list_info)
	TODO Reserve space for seqids? More...

const SBlastSeqIdListInfo &	GetListInfo ()

void	SetSiList (const vector< string > &new_list)

void	SetMaskOpts (EOidMaskType mask_opts)

template<>
int	GetSize () const

template<>
TTi	GetKey (int index) const

template<>
bool	IsValueSet (int index) const

template<>
void	SetValue (int index, int oid)

template<>
int	GetSize () const

template<>
string	GetKey (int index) const

template<>
bool	IsValueSet (int index) const

template<>
void	SetValue (int index, int oid)

template<>
int	GetSize () const

template<>
TPig	GetKey (int index) const

template<>
bool	IsValueSet (int index) const

template<>
void	SetValue (int index, int oid)

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

Protected Attributes
ESortOrder	m_CurrentOrder
	Indicates the current sort order, if any, of this container. More...

vector< SGiOid >	m_GisOids
	Pairs of GIs and OIDs. More...

vector< STiOid >	m_TisOids
	Pairs of GIs and OIDs. More...

vector< SSiOid >	m_SisOids
	Pairs of Seq-ids and OIDs. More...

vector< SPigOid >	m_PigsOids

STaxIdsOids	m_TaxIdsOids

SBlastSeqIdListInfo	m_ListInfo

Uint8	m_MaskOpts

Private Member Functions
	CSeqDBGiList (const CSeqDBGiList &other)
	Prevent copy constructor. More...

CSeqDBGiList &	operator= (const CSeqDBGiList &other)
	Prevent assignment. 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

CSeqDBGiList.

This class defines an interface to a list of GI,OID pairs. It is used by the CSeqDB class for user specified GI lists. This class should not be instantiated directly, instead use a subclass of this class. Subclasses should provide a way to populate the m_GisOids vector.

Definition at line 172 of file seqdbcommon.hpp.

Member Enumeration Documentation

◆ ESortOrder

enum CSeqDBGiList::ESortOrder

Possible sorting states.

Enumerator

eNone

The array is unsorted or the sortedness is unknown.

eGi

The array is sorted by GI.

TODO should we define eTi and eSi?

Definition at line 250 of file seqdbcommon.hpp.

Constructor & Destructor Documentation

◆ CSeqDBGiList() [1/2]

CSeqDBGiList::CSeqDBGiList ( )

Constructor.

Definition at line 509 of file seqdbcommon.cpp.

◆ ~CSeqDBGiList()

virtual CSeqDBGiList::~CSeqDBGiList ( )

inlinevirtual

Destructor.

Definition at line 264 of file seqdbcommon.hpp.

◆ CSeqDBGiList() [2/2]

CSeqDBGiList::CSeqDBGiList ( const CSeqDBGiList & other )

private

Prevent copy constructor.

Member Function Documentation

◆ AddGi()

void CSeqDBGiList::AddGi ( TGi gi )

inline

Add a new GI to the list.

Definition at line 512 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by BOOST_AUTO_TEST_CASE(), CSeqDBIdSet::GetPositiveList(), and s_ImportDatabase().

◆ AddPig()

void CSeqDBGiList::AddPig ( TPig pig )

inline

Definition at line 543 of file seqdbcommon.hpp.

References m_PigsOids.

Referenced by BOOST_AUTO_TEST_CASE(), and CSeqDBGiListSet::x_ResolveNegativeList().

◆ AddSi()

void CSeqDBGiList::AddSi ( const string & si )

inline

Add a new SeqId to the list.

Definition at line 524 of file seqdbcommon.hpp.

References m_SisOids, and si.

Referenced by BOOST_AUTO_TEST_CASE().

◆ AddTaxIds()

void CSeqDBGiList::AddTaxIds ( const set< TTaxId > & tax_ids )

inline

Definition at line 529 of file seqdbcommon.hpp.

References set< Key, Compare >::begin(), set< Key, Compare >::end(), set< Key, Compare >::insert(), m_TaxIdsOids, and CSeqDBGiList::STaxIdsOids::tax_ids.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastFormatterApp::PrintFormattedOutput(), s_GetTaxIDList(), s_ImportDatabase(), and CBlastDBCmdApp::x_InitBlastDB_TaxIdList().

◆ AddTi()

void CSeqDBGiList::AddTi ( TTi ti )

inline

Add a new TI to the list.

Definition at line 518 of file seqdbcommon.hpp.

References m_TisOids.

Referenced by CSeqDBIdSet::GetPositiveList().

◆ Empty()

bool CSeqDBGiList::Empty ( void ) const

inline

Return false if there are elements present.

Definition at line 392 of file seqdbcommon.hpp.

References GetMaskOpts(), GetNumGis(), GetNumPigs(), GetNumSis(), GetNumTaxIds(), and GetNumTis().

Referenced by CSearchDatabase::GetGiListLimitation(), CSearchDatabase::GetNegativeGiListLimitation(), NotEmpty(), CSeqDBOIDList::x_ApplyUserGiList(), and CSearchDatabase::x_InitializeDb().

◆ FindGi()

bool CSeqDBGiList::FindGi ( TGi gi ) const

Test for existence of a GI.

Definition at line 654 of file seqdbcommon.cpp.

Referenced by BOOST_AUTO_TEST_CASE(), and FindId().

◆ FindId()

bool CSeqDBGiList::FindId ( const CSeq_id & id )

Test for existence of a Seq-id by type.

This method uses FindGi or FindTi if the input ID is a GI or TI. If not, or if not found, it falls back to a Seq-id lookup to find the ID. It returns true iff ID was found, otherwise it returns false. This method is used by SeqDB to filter Blast Defline lists.

Parameters

id	The identifier to find.

Returns: true iff the id is found in the list.

Definition at line 1633 of file seqdbcommon.cpp.

References FindGi(), FindSi(), FindTi(), GetBlastSeqIdString(), CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CObject_id_Base::IsId(), SeqDB_SimplifySeqid(), and NStr::StringToInt8().

Referenced by CSeqDBVol::x_ListIncludesId().

◆ FindPig()

bool CSeqDBGiList::FindPig ( TPig pig ) const

◆ FindSi()

bool CSeqDBGiList::FindSi ( const string & si ) const

Definition at line 733 of file seqdbcommon.cpp.

References si.

Referenced by FindId().

◆ FindTi()

bool CSeqDBGiList::FindTi ( TTi ti ) const

Test for existence of a TI.

Definition at line 694 of file seqdbcommon.cpp.

Referenced by FindId().

◆ GetGiList()

void CSeqDBGiList::GetGiList ( vector< TGi > & gis ) const

Get the gi list.

Definition at line 771 of file seqdbcommon.cpp.

References GetNumGis(), ITERATE, and m_GisOids.

Referenced by BOOST_AUTO_TEST_CASE(), CSearchDatabase::GetGiListLimitation(), CSearchDatabase::GetNegativeGiListLimitation(), CBlastKmerThread::Main(), CSearchDatabase::x_InitializeDb(), and CSeqDBImpl::x_InitIdSet().

◆ GetGiOid()

const SGiOid& CSeqDBGiList::GetGiOid ( int index ) const

inline

Access an element of the array.

Parameters

index The index of the element to access. [in]

Returns: A reference to the GI/OID pair.

Definition at line 328 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by CBuildDatabase::AddIds(), CIntersectionGiList::CIntersectionGiList(), CBuildDatabase::x_AddRemoteSequences(), CSeqDBOIDList::x_ApplyUserGiList(), CBlastDbBioseqSource::x_GetOidFromSeqID(), CSeqDBOIDList::x_IdsToBitSet(), CBuildDatabase::x_ReportUnresolvedIds(), and CSeqDBGiListSet::x_TranslateGisFromUserList().

◆ GetKey() [1/4]

template<class T >

T CSeqDBGiList::GetKey ( int index ) const

inline

Definition at line 466 of file seqdbcommon.hpp.

References GI_TO, m_GisOids, and T.

Referenced by BOOST_AUTO_TEST_CASE(), s_AdvanceGiList(), s_SetTranslation(), CBuildDatabase::x_AddRemoteSequences(), CBuildDatabase::x_ReportUnresolvedIds(), and CSeqDBIsam::x_TranslateGiList().

◆ GetKey() [2/4]

template<>

TTi CSeqDBGiList::GetKey ( int index ) const

inline

Definition at line 639 of file seqdbcommon.hpp.

References m_TisOids.

◆ GetKey() [3/4]

template<>

string CSeqDBGiList::GetKey ( int index ) const

inline

Definition at line 663 of file seqdbcommon.hpp.

References m_SisOids.

◆ GetKey() [4/4]

template<>

TPig CSeqDBGiList::GetKey ( int index ) const

inline

Definition at line 687 of file seqdbcommon.hpp.

References m_PigsOids.

◆ GetListInfo()

const SBlastSeqIdListInfo& CSeqDBGiList::GetListInfo ( )

inline

Definition at line 578 of file seqdbcommon.hpp.

References m_ListInfo.

Referenced by BOOST_AUTO_TEST_CASE(), s_ProcessPositiveSeqIDsForV5(), CSearchDatabase::x_InitializeDb(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ GetMaskOpts()

Uint8 CSeqDBGiList::GetMaskOpts ( ) const

inline

Definition at line 387 of file seqdbcommon.hpp.

References m_MaskOpts.

Referenced by CSeqDBVol::CSeqDBVol(), Empty(), and CSeqDBGiListSet::GetUserMaskOpts().

◆ GetNumGis()

int CSeqDBGiList::GetNumGis ( ) const

inline

Get the number of GIs in the array.

Definition at line 355 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by CBuildDatabase::AddIds(), BOOST_AUTO_TEST_CASE(), CBlastDbBioseqSource::CBlastDbBioseqSource(), CIntersectionGiList::CIntersectionGiList(), Empty(), GetGiList(), CSeqDBGiListSet::GetNodeIdList(), HasIdFilters(), CSeqDBVol::IdsToOids(), CBuildDatabase::x_AddRemoteSequences(), CSeqDBOIDList::x_ApplyUserGiList(), CSeqDBOIDList::x_IdsToBitSet(), CSearchDatabase::x_InitializeDb(), CSeqDBImpl::x_InitIdSet(), CBuildDatabase::x_ReportUnresolvedIds(), CSeqDBGiListSet::x_ResolvePositiveList(), and CSeqDBGiListSet::x_TranslateGisFromUserList().

◆ GetNumOidsForTaxIdList()

int CSeqDBGiList::GetNumOidsForTaxIdList ( ) const

inline

Definition at line 377 of file seqdbcommon.hpp.

References m_TaxIdsOids, and CSeqDBGiList::STaxIdsOids::oids.

◆ GetNumPigs()

int CSeqDBGiList::GetNumPigs ( ) const

inline

Definition at line 382 of file seqdbcommon.hpp.

References m_PigsOids.

Referenced by Empty(), GetPigList(), CSeqDBVol::IdsToOids(), CSeqDBOIDList::x_ApplyUserGiList(), CSearchDatabase::x_InitializeDb(), CSeqDBGiListSet::x_ResolveNegativeList(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ GetNumSis()

int CSeqDBGiList::GetNumSis ( ) const

inline

Get the number of Seq-ids in the array.

Definition at line 367 of file seqdbcommon.hpp.

References m_SisOids.

Referenced by CBuildDatabase::AddIds(), CBlastDbBioseqSource::CBlastDbBioseqSource(), Empty(), CSeqDBGiListSet::GetNodeIdList(), GetSiList(), HasIdFilters(), CSeqDBVol::IdsToOids(), CSeqDBVol::OptimizeGiLists(), s_ProcessSeqIdFilters(), CBuildDatabase::x_AddRemoteSequences(), CSeqDBOIDList::x_ApplyUserGiList(), CSeqDBOIDList::x_IdsToBitSet(), CSearchDatabase::x_InitializeDb(), CBuildDatabase::x_ReportUnresolvedIds(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ GetNumTaxIds()

int CSeqDBGiList::GetNumTaxIds ( ) const

inline

Definition at line 372 of file seqdbcommon.hpp.

References m_TaxIdsOids, set< Key, Compare >::size(), and CSeqDBGiList::STaxIdsOids::tax_ids.

Referenced by Empty(), CSeqDBGiListSet::GetNodeIdList(), s_ProcessTaxIdFilters(), CSeqDBVol::x_GetFilteredHeader(), CSearchDatabase::x_InitializeDb(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ GetNumTis()

int CSeqDBGiList::GetNumTis ( ) const

inline

Get the number of TIs in the array.

Definition at line 361 of file seqdbcommon.hpp.

References m_TisOids.

Referenced by Empty(), CSeqDBGiListSet::GetNodeIdList(), GetTiList(), HasIdFilters(), CSeqDBVol::IdsToOids(), CSeqDBVol::OptimizeGiLists(), CSeqDBOIDList::x_ApplyUserGiList(), CSeqDBOIDList::x_IdsToBitSet(), CSeqDBImpl::x_InitIdSet(), CSeqDBGiListSet::x_ResolvePositiveList(), and CSeqDBGiListSet::x_TranslateTisFromUserList().

◆ GetOidsForTaxIdsList()

const vector<blastdb::TOid>& CSeqDBGiList::GetOidsForTaxIdsList ( )

inline

Definition at line 500 of file seqdbcommon.hpp.

References m_TaxIdsOids, and CSeqDBGiList::STaxIdsOids::oids.

Referenced by CSeqDBOIDList::x_ApplyUserGiList().

◆ GetPigList()

void CSeqDBGiList::GetPigList ( vector< TPig > & pigs ) const

Definition at line 782 of file seqdbcommon.cpp.

References GetNumPigs(), ITERATE, and m_PigsOids.

Referenced by BOOST_AUTO_TEST_CASE(), and CSearchDatabase::x_InitializeDb().

◆ GetPigOid()

const SPigOid& CSeqDBGiList::GetPigOid ( int index ) const

inline

Definition at line 349 of file seqdbcommon.hpp.

References m_PigsOids.

Referenced by CSeqDBOIDList::x_ApplyUserGiList(), and CSeqDBGiListSet::x_ResolveNegativeList().

◆ GetSiList()

void CSeqDBGiList::GetSiList ( vector< string > & sis ) const

TODO Get the seqid list?

Definition at line 805 of file seqdbcommon.cpp.

References GetNumSis(), ITERATE, and m_SisOids.

Referenced by BOOST_AUTO_TEST_CASE(), s_ProcessPositiveSeqIDsForV5(), s_ProcessSeqIdFilters(), CSearchDatabase::x_InitializeDb(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ GetSiOid()

const SSiOid& CSeqDBGiList::GetSiOid ( int index ) const

inline

Access an element of the array.

Parameters

index The index of the element to access. [in]

Returns: A reference to the Seq-id/OID pair.

Definition at line 344 of file seqdbcommon.hpp.

References m_SisOids.

Referenced by CBuildDatabase::x_AddRemoteSequences(), CSeqDBOIDList::x_ApplyUserGiList(), CBlastDbBioseqSource::x_GetOidFromSeqID(), CSeqDBOIDList::x_IdsToBitSet(), and CBuildDatabase::x_ReportUnresolvedIds().

◆ GetSize() [1/4]

template<class T >

int CSeqDBGiList::GetSize ( void ) const

inline

Definition at line 460 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by CSeqDBIsam::x_TranslateGiList().

◆ GetSize() [2/4]

template<>

int CSeqDBGiList::GetSize ( void ) const

inline

Definition at line 633 of file seqdbcommon.hpp.

References m_TisOids.

◆ GetSize() [3/4]

template<>

int CSeqDBGiList::GetSize ( void ) const

inline

Definition at line 657 of file seqdbcommon.hpp.

References m_SisOids.

◆ GetSize() [4/4]

template<>

int CSeqDBGiList::GetSize ( void ) const

inline

Definition at line 681 of file seqdbcommon.hpp.

References m_PigsOids.

◆ GetTaxIdsList()

set<TTaxId>& CSeqDBGiList::GetTaxIdsList ( )

inline

Definition at line 495 of file seqdbcommon.hpp.

References m_TaxIdsOids, and CSeqDBGiList::STaxIdsOids::tax_ids.

Referenced by s_ProcessTaxIdFilters(), CSeqDBVol::x_GetFilteredHeader(), CSearchDatabase::x_InitializeDb(), CExportStrategy::x_Process_SearchDb(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ GetTiList()

void CSeqDBGiList::GetTiList ( vector< TTi > & tis ) const

Get the ti list.

Definition at line 793 of file seqdbcommon.cpp.

References GetNumTis(), ITERATE, and m_TisOids.

Referenced by CSeqDBImpl::x_InitIdSet().

◆ GetTiOid()

const STiOid& CSeqDBGiList::GetTiOid ( int index ) const

inline

Access an element of the array.

Parameters

index The index of the element to access. [in]

Returns: A reference to the TI/OID pair.

Definition at line 336 of file seqdbcommon.hpp.

References m_TisOids.

Referenced by CSeqDBOIDList::x_ApplyUserGiList(), CSeqDBOIDList::x_IdsToBitSet(), and CSeqDBGiListSet::x_TranslateTisFromUserList().

◆ GiToOid() [1/2]

bool CSeqDBGiList::GiToOid	(	TGi	gi,
		int &	oid
	)

Try to find a GI and return the associated OID.

Parameters

gi	The gi for which to search. [in]
oid	The resulting oid if found. [out]

Returns: True if the GI was found.

Definition at line 661 of file seqdbcommon.cpp.

◆ GiToOid() [2/2]

bool CSeqDBGiList::GiToOid	(	TGi	gi,
		int &	oid,
		int &	index
	)

Find a GI, returning the index and the associated OID.

Parameters

gi	The gi for which to search. [in]
oid	The resulting oid if found. [out]
index	The index of this GI (if found). [out]

Returns: True if the GI was found.

Definition at line 668 of file seqdbcommon.cpp.

References b, eGi, InsureOrder(), and m_GisOids.

◆ HasIdFilters()

bool CSeqDBGiList::HasIdFilters ( ) const

inline

Definition at line 403 of file seqdbcommon.hpp.

References GetNumGis(), GetNumSis(), and GetNumTis().

Referenced by CSeqDBVol::x_FilterHasId().

◆ InsureOrder()

void CSeqDBGiList::InsureOrder ( ESortOrder order )

Sort if necessary to insure order of elements.

Definition at line 616 of file seqdbcommon.cpp.

References eGi, eNone, m_CurrentOrder, m_GisOids, m_PigsOids, m_SisOids, m_TisOids, mtx, and NCBI_THROW.

Referenced by CIntersectionGiList::CIntersectionGiList(), GiToOid(), SiToOid(), TiToOid(), CSeqDBIsam::x_TranslateGiList(), CSeqDBGiListSet::x_TranslateGisFromUserList(), and CSeqDBGiListSet::x_TranslateTisFromUserList().

◆ IsValueSet() [1/4]

template<class T >

bool CSeqDBGiList::IsValueSet ( int index ) const

inline

Definition at line 472 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by s_AdvanceGiList().

◆ IsValueSet() [2/4]

template<>

bool CSeqDBGiList::IsValueSet ( int index ) const

inline

Definition at line 645 of file seqdbcommon.hpp.

References m_TisOids.

◆ IsValueSet() [3/4]

template<>

bool CSeqDBGiList::IsValueSet ( int index ) const

inline

Definition at line 669 of file seqdbcommon.hpp.

References m_SisOids.

◆ IsValueSet() [4/4]

template<>

bool CSeqDBGiList::IsValueSet ( int index ) const

inline

Definition at line 693 of file seqdbcommon.hpp.

References m_PigsOids.

◆ NotEmpty()

bool CSeqDBGiList::NotEmpty ( void ) const

inline

Return true if there are elements present.

Definition at line 398 of file seqdbcommon.hpp.

References Empty().

Referenced by CBlastDbSet::CreateLocalDbAdapter(), CBlastKmerThread::Main(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ operator=()

CSeqDBGiList& CSeqDBGiList::operator= ( const CSeqDBGiList & other )

private

Prevent assignment.

◆ PigToOid() [1/2]

bool CSeqDBGiList::PigToOid	(	TPig	pig,
		int &	oid
	)

◆ PigToOid() [2/2]

bool CSeqDBGiList::PigToOid	(	TPig	pig,
		int &	oid,
		int &	index
	)

◆ PreprocessIdsForISAMSiLookup()

void CSeqDBGiList::PreprocessIdsForISAMSiLookup ( )

Preprocess ids for ISAM string id lookup.

Definition at line 608 of file seqdbcommon.cpp.

References m_SisOids, NON_CONST_ITERATE, SeqDB_SimplifyAccession(), and NStr::ToLower().

Referenced by CSeqDBGiListSet::GetNodeIdList(), and CSeqDBGiListSet::x_ResolvePositiveList().

◆ ReserveGis()

void CSeqDBGiList::ReserveGis ( size_t n )

inline

Reserve space for GIs.

Definition at line 549 of file seqdbcommon.hpp.

References m_GisOids, and n.

Referenced by CSeqDBIdSet::GetPositiveList().

◆ ReservePigs()

void CSeqDBGiList::ReservePigs ( size_t n )

inline

Definition at line 565 of file seqdbcommon.hpp.

References m_PigsOids, and n.

Referenced by CSeqDBGiListSet::x_ResolveNegativeList().

◆ ReserveSis()

void CSeqDBGiList::ReserveSis ( size_t n )

inline

Definition at line 560 of file seqdbcommon.hpp.

References m_SisOids, and n.

Referenced by BOOST_AUTO_TEST_CASE().

◆ ReserveTis()

void CSeqDBGiList::ReserveTis ( size_t n )

inline

Reserve space for TIs.

Definition at line 555 of file seqdbcommon.hpp.

References m_TisOids, and n.

Referenced by CSeqDBIdSet::GetPositiveList().

◆ SetGiTranslation()

void CSeqDBGiList::SetGiTranslation	(	int	index,
		int	oid
	)

inline

Specify the correct OID for a GI.

When SeqDB translates a GI into an OID, this method is called to store the oid in the array.

Parameters

index	The location in the array of the GI, OID pair.
oid	The oid to store in that element.

Definition at line 416 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by CSeqDBGiListSet::x_TranslateGisFromUserList().

◆ SetListInfo()

void CSeqDBGiList::SetListInfo ( const SBlastSeqIdListInfo & list_info )

inline

TODO Reserve space for seqids?

Definition at line 574 of file seqdbcommon.hpp.

References m_ListInfo.

Referenced by BOOST_AUTO_TEST_CASE(), and s_ProcessPositiveSeqIDsForV5().

◆ SetMaskOpts()

void CSeqDBGiList::SetMaskOpts ( EOidMaskType mask_opts )

inline

Definition at line 591 of file seqdbcommon.hpp.

References m_MaskOpts.

◆ SetOidsForTaxIdsList()

vector<blastdb::TOid>& CSeqDBGiList::SetOidsForTaxIdsList ( )

inline

Definition at line 505 of file seqdbcommon.hpp.

References m_TaxIdsOids, and CSeqDBGiList::STaxIdsOids::oids.

Referenced by CSeqDBGiListSet::x_ResolvePositiveList().

◆ SetPigList()

void CSeqDBGiList::SetPigList ( const vector< TPig > & list )

inline

Definition at line 535 of file seqdbcommon.hpp.

References ITERATE, and m_PigsOids.

◆ SetPigTranslation()

void CSeqDBGiList::SetPigTranslation	(	int	index,
		int	oid
	)

inline

Definition at line 449 of file seqdbcommon.hpp.

References m_PigsOids.

◆ SetSiList()

void CSeqDBGiList::SetSiList ( const vector< string > & new_list )

inline

Definition at line 583 of file seqdbcommon.hpp.

References ITERATE, and m_SisOids.

Referenced by s_ProcessPositiveSeqIDsForV5().

◆ SetSiTranslation()

void CSeqDBGiList::SetSiTranslation	(	int	index,
		int	oid
	)

inline

Specify the correct OID for a Seq-id.

When SeqDB translates a Seq-id into an OID, this method is called to store the oid in the array.

Parameters

index	The location in the array of Seq-id, OID pairs.
oid	The oid to store in that element.

Definition at line 444 of file seqdbcommon.hpp.

References m_SisOids.

Referenced by CSeqDBGiListSet::x_ResolvePositiveList().

◆ SetTiTranslation()

void CSeqDBGiList::SetTiTranslation	(	int	index,
		int	oid
	)

inline

Specify the correct OID for a TI.

When SeqDB translates a TI into an OID, this method is called to store the oid in the array.

Parameters

index	The location in the array of the TI, OID pair.
oid	The oid to store in that element.

Definition at line 430 of file seqdbcommon.hpp.

References m_TisOids.

Referenced by CSeqDBGiListSet::x_TranslateTisFromUserList().

◆ SetValue() [1/4]

template<class T >

void CSeqDBGiList::SetValue	(	int	index,
		int	oid
	)

inline

Definition at line 478 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by s_SetTranslation().

◆ SetValue() [2/4]

template<>

void CSeqDBGiList::SetValue	(	int	index,
		int	oid
	)

inline

Definition at line 651 of file seqdbcommon.hpp.

References m_TisOids.

◆ SetValue() [3/4]

template<>

void CSeqDBGiList::SetValue	(	int	index,
		int	oid
	)

inline

Definition at line 675 of file seqdbcommon.hpp.

References m_SisOids.

◆ SetValue() [4/4]

template<>

void CSeqDBGiList::SetValue	(	int	index,
		int	oid
	)

inline

Definition at line 699 of file seqdbcommon.hpp.

References m_PigsOids.

◆ SiToOid() [1/2]

bool CSeqDBGiList::SiToOid	(	const string &	si,
		int &	oid
	)

Definition at line 739 of file seqdbcommon.cpp.

References si.

◆ SiToOid() [2/2]

bool CSeqDBGiList::SiToOid	(	const string &	si,
		int &	oid,
		int &	index
	)

Definition at line 745 of file seqdbcommon.cpp.

References b, eGi, InsureOrder(), m_SisOids, and si.

◆ Size()

int CSeqDBGiList::Size ( void ) const

inline

Definition at line 454 of file seqdbcommon.hpp.

References m_GisOids.

Referenced by CBlastKmer::x_SearchMultipleQueries().

◆ TiToOid() [1/2]

bool CSeqDBGiList::TiToOid	(	TTi	ti,
		int &	oid
	)

Try to find a TI and return the associated OID.

Parameters

ti	The ti for which to search. [in]
oid	The resulting oid if found. [out]

Returns: True if the TI was found.

Definition at line 701 of file seqdbcommon.cpp.

◆ TiToOid() [2/2]

bool CSeqDBGiList::TiToOid	(	TTi	ti,
		int &	oid,
		int &	index
	)

Find a TI, returning the index and the associated OID.

Parameters

ti	The ti for which to search. [in]
oid	The resulting oid if found. [out]
index	The index of this TI (if found). [out]

Returns: True if the TI was found.

Definition at line 708 of file seqdbcommon.cpp.

References b, eGi, InsureOrder(), and m_TisOids.

Member Data Documentation

◆ m_CurrentOrder

ESortOrder CSeqDBGiList::m_CurrentOrder

protected

Indicates the current sort order, if any, of this container.

Definition at line 597 of file seqdbcommon.hpp.

Referenced by CInputGiList::AppendGi(), CInputGiList::AppendSi(), CInputGiList::CInputGiList(), CIntersectionGiList::CIntersectionGiList(), CSeqDBFileGiList::CSeqDBFileGiList(), CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), and InsureOrder().

◆ m_GisOids

vector<SGiOid> CSeqDBGiList::m_GisOids

protected

Pairs of GIs and OIDs.

Definition at line 600 of file seqdbcommon.hpp.

Referenced by AddGi(), CInputGiList::AppendGi(), CInputGiList::CInputGiList(), CIntersectionGiList::CIntersectionGiList(), CSeqDBFileGiList::CSeqDBFileGiList(), CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), CSeqIdList::CSeqIdList(), CSimpleGiList::CSimpleGiList(), GetGiList(), GetGiOid(), GetKey(), GetNumGis(), GetSize(), GiToOid(), InsureOrder(), IsValueSet(), ReserveGis(), SetGiTranslation(), SetValue(), and Size().

◆ m_ListInfo

SBlastSeqIdListInfo CSeqDBGiList::m_ListInfo

protected

Definition at line 612 of file seqdbcommon.hpp.

Referenced by CSeqDBFileGiList::CSeqDBFileGiList(), GetListInfo(), and SetListInfo().

◆ m_MaskOpts

Uint8 CSeqDBGiList::m_MaskOpts

protected

Definition at line 614 of file seqdbcommon.hpp.

Referenced by GetMaskOpts(), and SetMaskOpts().

◆ m_PigsOids

vector<SPigOid> CSeqDBGiList::m_PigsOids

protected

Definition at line 608 of file seqdbcommon.hpp.

Referenced by AddPig(), CSeqDBFileGiList::CSeqDBFileGiList(), CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), GetKey(), GetNumPigs(), GetPigList(), GetPigOid(), GetSize(), InsureOrder(), IsValueSet(), ReservePigs(), SetPigList(), SetPigTranslation(), and SetValue().

◆ m_SisOids

vector<SSiOid> CSeqDBGiList::m_SisOids

protected

Pairs of Seq-ids and OIDs.

Definition at line 606 of file seqdbcommon.hpp.

Referenced by AddSi(), CSeqIdList::Append(), CInputGiList::AppendSi(), CSeqDBFileGiList::CSeqDBFileGiList(), CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), CSeqIdList::CSeqIdList(), GetKey(), GetNumSis(), GetSiList(), GetSiOid(), GetSize(), InsureOrder(), IsValueSet(), PreprocessIdsForISAMSiLookup(), ReserveSis(), SetSiList(), SetSiTranslation(), SetValue(), and SiToOid().

◆ m_TaxIdsOids

STaxIdsOids CSeqDBGiList::m_TaxIdsOids

protected

Definition at line 610 of file seqdbcommon.hpp.

Referenced by AddTaxIds(), CSeqDBFileGiList::CSeqDBFileGiList(), GetNumOidsForTaxIdList(), GetNumTaxIds(), GetOidsForTaxIdsList(), GetTaxIdsList(), and SetOidsForTaxIdsList().

◆ m_TisOids

vector<STiOid> CSeqDBGiList::m_TisOids

protected

Pairs of GIs and OIDs.

Definition at line 603 of file seqdbcommon.hpp.

Referenced by AddTi(), CSeqDBFileGiList::CSeqDBFileGiList(), CSeqDBNodeFileIdList::CSeqDBNodeFileIdList(), GetKey(), GetNumTis(), GetSize(), GetTiList(), GetTiOid(), InsureOrder(), IsValueSet(), ReserveTis(), SetTiTranslation(), SetValue(), and TiToOid().

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

include/objtools/blast/seqdb_reader/seqdbcommon.hpp
src/objtools/blast/seqdb_reader/seqdbcommon.cpp

Classes

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ESortOrder

Constructor & Destructor Documentation

◆ CSeqDBGiList() [1/2]

◆ ~CSeqDBGiList()

◆ CSeqDBGiList() [2/2]

Member Function Documentation

◆ AddGi()

◆ AddPig()

◆ AddSi()

◆ AddTaxIds()

◆ AddTi()

◆ Empty()

◆ FindGi()

◆ FindId()

◆ FindPig()

◆ FindSi()

◆ FindTi()

◆ GetGiList()

◆ GetGiOid()

◆ GetKey() [1/4]

◆ GetKey() [2/4]

◆ GetKey() [3/4]

◆ GetKey() [4/4]

◆ GetListInfo()

◆ GetMaskOpts()

◆ GetNumGis()

◆ GetNumOidsForTaxIdList()

◆ GetNumPigs()

◆ GetNumSis()

◆ GetNumTaxIds()

◆ GetNumTis()

◆ GetOidsForTaxIdsList()

◆ GetPigList()

◆ GetPigOid()

◆ GetSiList()

◆ GetSiOid()

◆ GetSize() [1/4]

◆ GetSize() [2/4]

◆ GetSize() [3/4]

◆ GetSize() [4/4]

◆ GetTaxIdsList()

◆ GetTiList()

◆ GetTiOid()

◆ GiToOid() [1/2]

◆ GiToOid() [2/2]

◆ HasIdFilters()

◆ InsureOrder()

◆ IsValueSet() [1/4]

◆ IsValueSet() [2/4]

◆ IsValueSet() [3/4]

◆ IsValueSet() [4/4]

◆ NotEmpty()

◆ operator=()

◆ PigToOid() [1/2]

◆ PigToOid() [2/2]

◆ PreprocessIdsForISAMSiLookup()

◆ ReserveGis()

◆ ReservePigs()

◆ ReserveSis()

◆ ReserveTis()

◆ SetGiTranslation()

◆ SetListInfo()

◆ SetMaskOpts()

◆ SetOidsForTaxIdsList()

◆ SetPigList()

◆ SetPigTranslation()

◆ SetSiList()

◆ SetSiTranslation()

◆ SetTiTranslation()

◆ SetValue() [1/4]

◆ SetValue() [2/4]

◆ SetValue() [3/4]