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CSeqDBGiList Class Reference

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CSeqDBGiList. More...

#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< Uint8TCounter
 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 SGiOidGetGiOid (int index) const
 Access an element of the array. More...
 
const STiOidGetTiOid (int index) const
 Access an element of the array. More...
 
const SSiOidGetSiOid (int index) const
 Access an element of the array. More...
 
const SPigOidGetPigOid (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 SBlastSeqIdListInfoGetListInfo ()
 
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...
 
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...
 
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< SGiOidm_GisOids
 Pairs of GIs and OIDs. More...
 
vector< STiOidm_TisOids
 Pairs of GIs and OIDs. More...
 
vector< SSiOidm_SisOids
 Pairs of Seq-ids and OIDs. More...
 
vector< SPigOidm_PigsOids
 
STaxIdsOids m_TaxIdsOids
 
SBlastSeqIdListInfo m_ListInfo
 
Uint8 m_MaskOpts
 

Private Member Functions

 CSeqDBGiList (const CSeqDBGiList &other)
 Prevent copy constructor. More...
 
CSeqDBGiListoperator= (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

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

◆ 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

◆ 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
idThe 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

◆ GetGiOid()

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

◆ GetKey() [1/4]

template<class T >
T CSeqDBGiList::GetKey ( int  index) const
inline

◆ 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

◆ 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

◆ 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

◆ GetNumSis()

int CSeqDBGiList::GetNumSis ( ) const
inline

◆ GetNumTaxIds()

int CSeqDBGiList::GetNumTaxIds ( ) const
inline

◆ GetNumTis()

int CSeqDBGiList::GetNumTis ( ) const
inline

◆ 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

◆ GetSiList()

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

◆ GetSiOid()

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

Access an element of the array.

Parameters
indexThe 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

◆ 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
indexThe 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
giThe gi for which to search. [in]
oidThe 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
giThe gi for which to search. [in]
oidThe resulting oid if found. [out]
indexThe 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)

◆ 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
indexThe location in the array of the GI, OID pair.
oidThe 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

◆ 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
indexThe location in the array of Seq-id, OID pairs.
oidThe 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
indexThe location in the array of the TI, OID pair.
oidThe 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
tiThe ti for which to search. [in]
oidThe 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
tiThe ti for which to search. [in]
oidThe resulting oid if found. [out]
indexThe 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

◆ m_GisOids

vector<SGiOid> CSeqDBGiList::m_GisOids
protected

◆ 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

◆ m_SisOids

vector<SSiOid> CSeqDBGiList::m_SisOids
protected

◆ m_TaxIdsOids

STaxIdsOids CSeqDBGiList::m_TaxIdsOids
protected

◆ m_TisOids

vector<STiOid> CSeqDBGiList::m_TisOids
protected

The documentation for this class was generated from the following files:
Modified on Wed May 29 18:42:34 2024 by modify_doxy.py rev. 669887