NCBI C++ ToolKit
Classes | Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Types | Private Attributes | Friends | List of all members
CWGSDb_Impl Class Reference

Search Toolkit Book for CWGSDb_Impl

#include <sra/readers/sra/wgsread.hpp>

+ Inheritance diagram for CWGSDb_Impl:
+ Collaboration diagram for CWGSDb_Impl:

Classes

struct  SAmbiguityInfo
 
struct  SFeatTableCursor
 
struct  SGiIdxTableCursor
 
struct  SProt0TableCursor
 
struct  SProtAccInfo
 
struct  SProtIdxTableCursor
 
struct  SProtTableCursor
 
struct  SScfTableCursor
 
struct  SSeq0TableCursor
 
struct  SSeq4naTableCursor
 
struct  SSeqTableCursor
 

Public Types

enum  ERowType { eRowType_contig = 0 , eRowType_scaffold = 'S' , eRowType_protein = 'P' }
 
enum  EAllowRowType { fAllowRowType_contig = 1<<0 , fAllowRowType_scaffold = 1<<1 , fAllowRowType_protein = 1<<2 }
 
enum  EGnlIdFlags { fGnlId_NoWGSVersion = 1<<0 , fGnlId_NoWGSId = 1<<1 , fGnlId_Default = 0 }
 
typedef char TRowType
 
typedef list< CRef< CSeqdesc > > TMasterDescr
 
typedef CSimpleBufferT< char > TMasterDescrBytes
 
typedef COpenRange< TIntIdTGiRange
 
typedef vector< TGiRangeTGiRanges
 
typedef COpenRange< Uint4TIdRange
 
typedef map< SProtAccInfo, TIdRangeTProtAccRanges
 
- 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 Types inherited from SWGSDb_Defs
enum  EFlags {
  fIds_gi = 1<<0 , fIds_acc = 1<<1 , fIds_gnl = 1<<2 , fMaskIds = fIds_gi|fIds_acc|fIds_gnl ,
  fDefaultIds = fIds_gi|fIds_acc|fIds_gnl , fInst_ncbi4na = 0<<3 , fInst_delta = 1<<3 , fMaskInst = fInst_ncbi4na|fInst_delta ,
  fDefaultInst = fInst_delta , fSeqDescr = 1<<4 , fNucProtDescr = 1<<12 , fMasterDescr = 1<<5 ,
  fMasterDescrMark = 1<<13 , fSeqDescrObj = 1<<14 , fMaskDescr = fSeqDescr|fNucProtDescr|fMasterDescr , fDefaultDescr = fSeqDescr|fNucProtDescr|fMasterDescr ,
  fSeqAnnot = 1<<6 , fQualityGraph = 1<<7 , fMaskAnnot = fSeqAnnot|fQualityGraph , fDefaultAnnot = fSeqAnnot|fQualityGraph ,
  fSplitQualityGraph = 1<<8 , fSplitSeqData = 1<<9 , fSplitProducts = 1<<10 , fSplitFeatures = 1<<11 ,
  fSplitAll = fSplitQualityGraph | fSplitSeqData | fSplitProducts | fSplitFeatures , fSplitMask = fSplitQualityGraph | fSplitSeqData | fSplitProducts | fSplitFeatures , fDefaultSplit = fSplitAll , fDefaultFlags = fDefaultIds|fDefaultDescr|fDefaultAnnot|fDefaultInst|fDefaultSplit
}
 
enum  EFeatLocIdType : Int1 { eFeatLocIdUninitialized = -1 , eFeatLocIdGi = 0 , eFeatLocIdAccVer , eFeatLocIdAccNoVer }
 
typedef int TSplitVersion
 
typedef int TChunkId
 

Public Member Functions

 CWGSDb_Impl (CVDBMgr &mgr, CTempString path_or_acc, CTempString vol_path=CTempString())
 
virtual ~CWGSDb_Impl (void)
 
const stringGetIdPrefix (void) const
 
const stringGetIdPrefixWithVersion (void) const
 
const stringGetWGSPath (void) const
 
 DECLARE_SAFE_FLAGS_TYPE (EAllowRowType, TAllowRowType)
 
TVDBRowId ParseRow (CTempString acc, bool *is_scaffold) const
 
Uint4 GetIdRowDigits (void) const
 
bool IsTSA (void) const
 
 DECLARE_SAFE_FLAGS_TYPE (EGnlIdFlags, TGnlIdFlags)
 
CRef< CSeq_idGetGeneralSeq_id (CTempString prefix, CTempString tag) const
 
CRef< CSeq_idGetGeneralSeq_id (CTempString tag, TGnlIdFlags gnl_id_flags=fGnlId_Default) const
 
CRef< CSeq_idGetPatentSeq_id (int id) const
 
CRef< CSeq_idGetGeneralOrPatentSeq_id (CTempString str, TVDBRowId row, TGnlIdFlags gnl_id_flags=fGnlId_Default) const
 
CRef< CSeq_idGetAccSeq_id (CTempString acc, int version) const
 
CRef< CSeq_idGetAccSeq_id (ERowType type, TVDBRowId row_id, int version) const
 
CRef< CSeq_idGetMasterSeq_id (void) const
 
TGi GetMasterGi (void) const
 
CRef< CSeq_idGetContigSeq_id (TVDBRowId row_id) const
 
CRef< CSeq_idGetScaffoldSeq_id (TVDBRowId row_id) const
 
CRef< CSeq_idGetProteinSeq_id (TVDBRowId row_id) const
 
CSeq_inst::TMol GetContigMolType (void) const
 
CSeq_inst::TMol GetScaffoldMolType (void) const
 
CSeq_inst::TMol GetProteinMolType (void) const
 
CRef< CSeq_entryGetMasterSeq_entry (void) const
 
bool IsSetMasterDescr (void) const
 
const TMasterDescrGetMasterDescr (void) const
 
size_t GetMasterDescrBytes (TMasterDescrBytes &buffer)
 
CRef< CSeq_entryGetMasterDescrEntry (void)
 
void AddMasterDescr (CSeq_descr &descr, const CBioseq *main_seq=0, TFlags flags=fDefaultFlags) const
 
void ResetMasterDescr (void)
 
void SetMasterDescr (const TMasterDescr &descr, int filter)
 
bool LoadMasterDescr (int filter)
 
void SetPatentId (CRef< CSeq_id > id)
 
bool HasPatentId () const
 
const CRef< CSeq_id > & GetPatentId (void) const
 
pair< TGi, TGiGetNucGiRange (void)
 
pair< TGi, TGiGetProtGiRange (void)
 
pair< TVDBRowId, boolGetGiRowId (TGi gi)
 
TVDBRowId GetNucGiRowId (TGi gi)
 
TVDBRowId GetProtGiRowId (TGi gi)
 
TVDBRowId GetContigNameRowId (const string &name)
 
TVDBRowId GetScaffoldNameRowId (const string &name)
 
TVDBRowId GetProteinNameRowId (const string &name)
 
TVDBRowId GetProductNameRowId (const string &name)
 
TVDBRowId GetProtAccRowId (const string &acc, int version=-1)
 
TGiRanges GetNucGiRanges (void)
 
TGiRanges GetProtGiRanges (void)
 
TProtAccRanges GetProtAccRanges (void)
 
EFeatLocIdType GetFeatLocIdType ()
 
EFeatLocIdType DetermineFeatLocIdType ()
 
bool HasStandardFeatLocIdType ()
 
NCBI_gb_state GetProjectGBState () const
 
const stringGetReplacedBy () const
 
bool IsReplaced () const
 
bool HasCommonTaxId (void) const
 
TTaxId GetCommonTaxId (void) const
 
bool CanHaveGis ()
 
TVDBRowCount GetTotalFeatureCount ()
 
bool HasFeatures ()
 
- 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
 
- Public Member Functions inherited from SWGSDb_Defs
 DECLARE_SAFE_FLAGS_TYPE (EFlags, TFlags)
 

Static Public Member Functions

static string NormalizePathOrAccession (CTempString path_or_acc, CTempString vol_path=CTempString())
 
static pair< TVDBRowId, ERowTypeParseRowType (CTempString acc, TAllowRowType allow)
 
static TVDBRowId ParseContigRow (CTempString acc)
 
static TVDBRowId ParseScaffoldRow (CTempString acc)
 
static TVDBRowId ParseProteinRow (CTempString acc)
 
- 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)
 

Protected Member Functions

const CVDBTableSeqTable (void)
 
const CVDBTableScfTable (void)
 
const CVDBTableProtTable (void)
 
const CVDBTableFeatTable (void)
 
const CVDBTableGiIdxTable (void)
 
const CVDBTableProtIdxTable (void)
 
const CVDBTableIndexProtAccIndex (void)
 
const CVDBTableIndexContigNameIndex (void)
 
const CVDBTableIndexScaffoldNameIndex (void)
 
const CVDBTableIndexProteinNameIndex (void)
 
const CVDBTableIndexProductNameIndex (void)
 
CRef< SSeq0TableCursorSeq0 (TVDBRowId row=0)
 
CRef< SSeqTableCursorSeq (TVDBRowId row=0)
 
CRef< SSeq4naTableCursorSeq4na (TVDBRowId row=0)
 
CRef< SScfTableCursorScf (TVDBRowId row=0)
 
CRef< SProt0TableCursorProt0 (TVDBRowId row=0)
 
CRef< SProtTableCursorProt (TVDBRowId row=0)
 
CRef< SFeatTableCursorFeat (TVDBRowId row=0)
 
CRef< SGiIdxTableCursorGiIdx (TVDBRowId row=0)
 
CRef< SProtIdxTableCursorProtIdx (TVDBRowId row=0)
 
void Put (CRef< SSeq0TableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SSeqTableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SSeq4naTableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SScfTableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SProt0TableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SProtTableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SFeatTableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SGiIdxTableCursor > &curs, TVDBRowId row=0)
 
void Put (CRef< SProtIdxTableCursor > &curs, TVDBRowId row=0)
 
CRef< SAmbiguityInfoGetAmbiguityInfo (TVDBRowId row)
 
void PutAmbiguityInfo (CRef< SAmbiguityInfo > &ambiguity)
 
CRef< CSeq_idGetGeneralOrPatentSeq_id (CTempString str, const SSeq0TableCursor &cur, TVDBRowId row) const
 
CRef< CSeq_idGetGeneralOrPatentSeq_id (CTempString str, const SScfTableCursor &cur, TVDBRowId row) const
 
CRef< CSeq_idGetGeneralOrPatentSeq_id (CTempString str, const SProt0TableCursor &cur, TVDBRowId row) const
 
void OpenTable (CVDBTable &table, atomic< bool > &table_is_opened, const char *table_name)
 
void OpenIndex (const CVDBTable &table, CVDBTableIndex &index, atomic< Int1 > &index_is_opened, const char *index_name, const char *backup_index_name=0)
 
void OpenScfTable (void)
 
void OpenProtTable (void)
 
void OpenFeatTable (void)
 
void OpenGiIdxTable (void)
 
void OpenProtIdxTable (void)
 
void OpenProtAccIndex (void)
 
void OpenContigNameIndex (void)
 
void OpenScaffoldNameIndex (void)
 
void OpenProteinNameIndex (void)
 
void OpenProductNameIndex (void)
 
TVDBRowId Lookup (const string &name, const CVDBTableIndex &index, bool upcase)
 
void x_InitIdParams (void)
 
void x_LoadMasterDescr (int filter)
 
void x_SortGiRanges (TGiRanges &ranges)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Types

typedef limited_resource_map< TVDBRowId, CRef< SAmbiguityInfo >, size_t > TAmbiguityCache
 

Private Attributes

CVDBMgr m_Mgr
 
string m_WGSPath
 
CVDB m_Db
 
CVDBTable m_SeqTable
 
string m_IdPrefixWithVersion
 
string m_IdPrefix
 
string m_IdPrefixDbWithVersion
 
string m_IdPrefixDb
 
int m_IdVersion
 
Uint4 m_IdRowDigits
 
CFastMutex m_TableMutex
 
atomic< boolm_ScfTableIsOpened
 
atomic< boolm_ProtTableIsOpened
 
atomic< boolm_FeatTableIsOpened
 
atomic< boolm_GiIdxTableIsOpened
 
atomic< boolm_ProtIdxTableIsOpened
 
atomic< Int1m_ProtAccIndexIsOpened
 
atomic< Int1m_ContigNameIndexIsOpened
 
atomic< Int1m_ScaffoldNameIndexIsOpened
 
atomic< Int1m_ProteinNameIndexIsOpened
 
atomic< Int1m_ProductNameIndexIsOpened
 
CVDBTable m_ScfTable
 
CVDBTable m_ProtTable
 
CVDBTable m_FeatTable
 
CVDBTable m_GiIdxTable
 
CVDBTable m_ProtIdxTable
 
CVDBObjectCache< SSeq0TableCursorm_Seq0
 
CVDBObjectCache< SSeqTableCursorm_Seq
 
CVDBObjectCache< SScfTableCursorm_Scf
 
CVDBObjectCache< SProt0TableCursorm_Prot0
 
CVDBObjectCache< SProtTableCursorm_Prot
 
CVDBObjectCache< SFeatTableCursorm_Feat
 
CVDBObjectCache< SGiIdxTableCursorm_GiIdx
 
CVDBObjectCache< SProtIdxTableCursorm_ProtIdx
 
CVDBTableIndex m_ProtAccIndex
 
CVDBTableIndex m_ContigNameIndex
 
CVDBTableIndex m_ScaffoldNameIndex
 
CVDBTableIndex m_ProteinNameIndex
 
CVDBTableIndex m_ProductNameIndex
 
CFastMutex m_AmbiguityCacheMutex
 
TAmbiguityCache m_AmbiguityCache
 
CSeq_inst::TMol m_ContigMolType
 
bool m_IsSetMasterDescr
 
bool m_HasNoDefaultGnlId
 
bool m_HasCommonTaxId
 
atomic< EFeatLocIdTypem_FeatLocIdType
 
CRef< CSeq_entrym_MasterEntry
 
TMasterDescr m_MasterDescr
 
CRef< CSeq_idm_PatentId
 
NCBI_gb_state m_ProjectGBState
 
CSeq_id::E_Choice m_SeqIdType
 
string m_ReplacedBy
 
TTaxId m_CommonTaxId
 

Friends

class CWGSSeqIterator
 
class CWGSScaffoldIterator
 
class CWGSGiIterator
 
class CWGSProteinIterator
 
class CWGSFeatureIterator
 

Additional Inherited Members

- 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...
 
- Static Public Attributes inherited from SWGSDb_Defs
static const TSplitVersion kDefaultSplitVersion = 0
 

Detailed Description

Definition at line 194 of file wgsread.hpp.

Member Typedef Documentation

◆ TAmbiguityCache

Definition at line 625 of file wgsread.hpp.

◆ TGiRange

Definition at line 353 of file wgsread.hpp.

◆ TGiRanges

Definition at line 354 of file wgsread.hpp.

◆ TIdRange

Definition at line 391 of file wgsread.hpp.

◆ TMasterDescr

Definition at line 298 of file wgsread.hpp.

◆ TMasterDescrBytes

Definition at line 307 of file wgsread.hpp.

◆ TProtAccRanges

Definition at line 392 of file wgsread.hpp.

◆ TRowType

typedef char CWGSDb_Impl::TRowType

Definition at line 224 of file wgsread.hpp.

Member Enumeration Documentation

◆ EAllowRowType

Enumerator
fAllowRowType_contig 
fAllowRowType_scaffold 
fAllowRowType_protein 

Definition at line 225 of file wgsread.hpp.

◆ EGnlIdFlags

Enumerator
fGnlId_NoWGSVersion 
fGnlId_NoWGSId 
fGnlId_Default 

Definition at line 266 of file wgsread.hpp.

◆ ERowType

Enumerator
eRowType_contig 
eRowType_scaffold 
eRowType_protein 

Definition at line 219 of file wgsread.hpp.

Constructor & Destructor Documentation

◆ CWGSDb_Impl()

CWGSDb_Impl::CWGSDb_Impl ( CVDBMgr mgr,
CTempString  path_or_acc,
CTempString  vol_path = CTempString() 
)

Definition at line 843 of file wgsread.cpp.

References m_Db, m_SeqTable, m_WGSPath, PROFILE, and x_InitIdParams().

◆ ~CWGSDb_Impl()

CWGSDb_Impl::~CWGSDb_Impl ( void  )
virtual

Definition at line 877 of file wgsread.cpp.

Member Function Documentation

◆ AddMasterDescr()

void CWGSDb_Impl::AddMasterDescr ( CSeq_descr descr,
const CBioseq main_seq = 0,
TFlags  flags = fDefaultFlags 
) const

◆ CanHaveGis()

bool CWGSDb_Impl::CanHaveGis ( )

Definition at line 3659 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, Put(), Seq(), and rapidjson::value.

Referenced by DetermineFeatLocIdType().

◆ ContigNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ContigNameIndex ( void  )
inlineprotected

Definition at line 490 of file wgsread.hpp.

References m_ContigNameIndex, m_ContigNameIndexIsOpened, and OpenContigNameIndex().

Referenced by GetContigNameRowId().

◆ DECLARE_SAFE_FLAGS_TYPE() [1/2]

CWGSDb_Impl::DECLARE_SAFE_FLAGS_TYPE ( EAllowRowType  ,
TAllowRowType   
)

◆ DECLARE_SAFE_FLAGS_TYPE() [2/2]

CWGSDb_Impl::DECLARE_SAFE_FLAGS_TYPE ( EGnlIdFlags  ,
TGnlIdFlags   
)

◆ DetermineFeatLocIdType()

CWGSDb_Impl::EFeatLocIdType CWGSDb_Impl::DetermineFeatLocIdType ( )

◆ Feat()

CRef< CWGSDb_Impl::SFeatTableCursor > CWGSDb_Impl::Feat ( TVDBRowId  row = 0)
inlineprotected

Definition at line 961 of file wgsread.cpp.

References FeatTable(), m_Feat, row, and table.

Referenced by DetermineFeatLocIdType(), GetTotalFeatureCount(), and CWGSFeatureIterator::x_Init().

◆ FeatTable()

const CVDBTable& CWGSDb_Impl::FeatTable ( void  )
inlineprotected

Definition at line 466 of file wgsread.hpp.

References m_FeatTable, m_FeatTableIsOpened, and OpenFeatTable().

Referenced by Feat().

◆ GetAccSeq_id() [1/2]

CRef< CSeq_id > CWGSDb_Impl::GetAccSeq_id ( CTempString  acc,
int  version 
) const

◆ GetAccSeq_id() [2/2]

CRef< CSeq_id > CWGSDb_Impl::GetAccSeq_id ( ERowType  type,
TVDBRowId  row_id,
int  version 
) const

◆ GetAmbiguityInfo()

CRef< CWGSDb_Impl::SAmbiguityInfo > CWGSDb_Impl::GetAmbiguityInfo ( TVDBRowId  row)
protected

◆ GetCommonTaxId()

TTaxId CWGSDb_Impl::GetCommonTaxId ( void  ) const
inline

Definition at line 415 of file wgsread.hpp.

References m_CommonTaxId.

Referenced by CWGSSeqIterator::GetTaxId(), and CWGSProteinIterator::GetTaxId().

◆ GetContigMolType()

CSeq_inst::TMol CWGSDb_Impl::GetContigMolType ( void  ) const

Definition at line 2987 of file wgsread.cpp.

References m_ContigMolType.

Referenced by IsTSA().

◆ GetContigNameRowId()

TVDBRowId CWGSDb_Impl::GetContigNameRowId ( const string name)

◆ GetContigSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetContigSeq_id ( TVDBRowId  row_id) const

Definition at line 2969 of file wgsread.cpp.

References eRowType_contig, and GetAccSeq_id().

◆ GetFeatLocIdType()

CWGSDb_Impl::EFeatLocIdType CWGSDb_Impl::GetFeatLocIdType ( )

◆ GetGeneralOrPatentSeq_id() [1/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id ( CTempString  str,
const SProt0TableCursor cur,
TVDBRowId  row 
) const
protected

◆ GetGeneralOrPatentSeq_id() [2/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id ( CTempString  str,
const SScfTableCursor cur,
TVDBRowId  row 
) const
protected

Definition at line 2872 of file wgsread.cpp.

References GetGeneralSeq_id(), GetPatentSeq_id(), HasPatentId(), str(), and sx_GetStringId().

◆ GetGeneralOrPatentSeq_id() [3/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id ( CTempString  str,
const SSeq0TableCursor cur,
TVDBRowId  row 
) const
protected

Definition at line 2851 of file wgsread.cpp.

References GetGeneralSeq_id(), GetPatentSeq_id(), HasPatentId(), str(), and sx_GetStringId().

◆ GetGeneralOrPatentSeq_id() [4/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id ( CTempString  str,
TVDBRowId  row,
TGnlIdFlags  gnl_id_flags = fGnlId_Default 
) const

◆ GetGeneralSeq_id() [1/2]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralSeq_id ( CTempString  prefix,
CTempString  tag 
) const

◆ GetGeneralSeq_id() [2/2]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralSeq_id ( CTempString  tag,
TGnlIdFlags  gnl_id_flags = fGnlId_Default 
) const

◆ GetGiRowId()

pair< TVDBRowId, bool > CWGSDb_Impl::GetGiRowId ( TGi  gi)

Definition at line 3482 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, GI_TO, GiIdx(), Put(), and rapidjson::value.

Referenced by CWGSDb::GetGiRowId().

◆ GetIdPrefix()

const string& CWGSDb_Impl::GetIdPrefix ( void  ) const
inline

Definition at line 202 of file wgsread.hpp.

References m_IdPrefix.

◆ GetIdPrefixWithVersion()

const string& CWGSDb_Impl::GetIdPrefixWithVersion ( void  ) const
inline

Definition at line 205 of file wgsread.hpp.

References m_IdPrefixWithVersion.

◆ GetIdRowDigits()

Uint4 CWGSDb_Impl::GetIdRowDigits ( void  ) const
inline

Definition at line 260 of file wgsread.hpp.

References m_IdRowDigits.

◆ GetMasterDescr()

const TMasterDescr& CWGSDb_Impl::GetMasterDescr ( void  ) const
inline

Definition at line 303 of file wgsread.hpp.

References m_MasterDescr.

Referenced by AddMasterDescr(), and CWGSScaffoldIterator::HasSeq_descr().

◆ GetMasterDescrBytes()

size_t CWGSDb_Impl::GetMasterDescrBytes ( TMasterDescrBytes buffer)

◆ GetMasterDescrEntry()

CRef< CSeq_entry > CWGSDb_Impl::GetMasterDescrEntry ( void  )

◆ GetMasterGi()

TGi CWGSDb_Impl::GetMasterGi ( void  ) const

◆ GetMasterSeq_entry()

CRef< CSeq_entry > CWGSDb_Impl::GetMasterSeq_entry ( void  ) const

◆ GetMasterSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetMasterSeq_id ( void  ) const

Definition at line 2953 of file wgsread.cpp.

References m_IdPrefix, m_IdRowDigits, m_IdVersion, and sx_SetVersion().

Referenced by GetMasterSeq_entry().

◆ GetNucGiRange()

pair< TGi, TGi > CWGSDb_Impl::GetNucGiRange ( void  )

Definition at line 3310 of file wgsread.cpp.

References GiIdx(), Put(), and s_ToGi().

Referenced by CWGSDb::GetNucGiRange().

◆ GetNucGiRanges()

CWGSDb_Impl::TGiRanges CWGSDb_Impl::GetNucGiRanges ( void  )

Definition at line 3369 of file wgsread.cpp.

References GI_TO, i, Put(), s_ToGi(), Seq(), and x_SortGiRanges().

Referenced by CWGSDb::GetNucGiRanges().

◆ GetNucGiRowId()

TVDBRowId CWGSDb_Impl::GetNucGiRowId ( TGi  gi)

Definition at line 3507 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, GI_TO, GiIdx(), Put(), and rapidjson::value.

Referenced by CWGSDb::GetNucGiRowId().

◆ GetPatentId()

const CRef<CSeq_id>& CWGSDb_Impl::GetPatentId ( void  ) const
inline

Definition at line 324 of file wgsread.hpp.

References m_PatentId.

◆ GetPatentSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetPatentSeq_id ( int  id) const

◆ GetProductNameRowId()

TVDBRowId CWGSDb_Impl::GetProductNameRowId ( const string name)

Definition at line 3600 of file wgsread.cpp.

References Lookup(), m_ProductNameIndexIsOpened, and ProductNameIndex().

Referenced by CWGSDb::GetProductNameRowId().

◆ GetProjectGBState()

NCBI_gb_state CWGSDb_Impl::GetProjectGBState ( ) const
inline

Definition at line 401 of file wgsread.hpp.

References m_ProjectGBState.

Referenced by HasStandardFeatLocIdType().

◆ GetProtAccRanges()

CWGSDb_Impl::TProtAccRanges CWGSDb_Impl::GetProtAccRanges ( void  )

◆ GetProtAccRowId()

TVDBRowId CWGSDb_Impl::GetProtAccRowId ( const string acc,
int  version = -1 
)

◆ GetProteinMolType()

CSeq_inst::TMol CWGSDb_Impl::GetProteinMolType ( void  ) const

Definition at line 2999 of file wgsread.cpp.

References CSeq_inst_Base::eMol_aa.

◆ GetProteinNameRowId()

TVDBRowId CWGSDb_Impl::GetProteinNameRowId ( const string name)

Definition at line 3593 of file wgsread.cpp.

References Lookup(), m_ProteinNameIndexIsOpened, and ProteinNameIndex().

Referenced by CWGSDb::GetProteinNameRowId().

◆ GetProteinSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetProteinSeq_id ( TVDBRowId  row_id) const

Definition at line 2981 of file wgsread.cpp.

References eRowType_protein, and GetAccSeq_id().

Referenced by CWGSProteinIterator::GetAccSeq_id().

◆ GetProtGiRange()

pair< TGi, TGi > CWGSDb_Impl::GetProtGiRange ( void  )

Definition at line 3330 of file wgsread.cpp.

References GiIdx(), Put(), and s_ToGi().

Referenced by CWGSDb::GetProtGiRange().

◆ GetProtGiRanges()

CWGSDb_Impl::TGiRanges CWGSDb_Impl::GetProtGiRanges ( void  )

Definition at line 3401 of file wgsread.cpp.

Referenced by CWGSDb::GetProtGiRanges().

◆ GetProtGiRowId()

TVDBRowId CWGSDb_Impl::GetProtGiRowId ( TGi  gi)

Definition at line 3525 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, GI_TO, GiIdx(), Put(), and rapidjson::value.

Referenced by CWGSDb::GetProtGiRowId().

◆ GetReplacedBy()

const string& CWGSDb_Impl::GetReplacedBy ( ) const
inline

Definition at line 404 of file wgsread.hpp.

References m_ReplacedBy.

◆ GetScaffoldMolType()

CSeq_inst::TMol CWGSDb_Impl::GetScaffoldMolType ( void  ) const

Definition at line 2993 of file wgsread.cpp.

References CSeq_inst_Base::eMol_dna.

◆ GetScaffoldNameRowId()

TVDBRowId CWGSDb_Impl::GetScaffoldNameRowId ( const string name)

Definition at line 3586 of file wgsread.cpp.

References Lookup(), m_ScaffoldNameIndexIsOpened, and ScaffoldNameIndex().

Referenced by CWGSDb::GetScaffoldNameRowId().

◆ GetScaffoldSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetScaffoldSeq_id ( TVDBRowId  row_id) const

Definition at line 2975 of file wgsread.cpp.

References eRowType_scaffold, and GetAccSeq_id().

Referenced by CWGSScaffoldIterator::GetAccSeq_id().

◆ GetTotalFeatureCount()

TVDBRowCount CWGSDb_Impl::GetTotalFeatureCount ( )

Definition at line 3677 of file wgsread.cpp.

References Feat(), and Put().

Referenced by HasFeatures().

◆ GetWGSPath()

const string& CWGSDb_Impl::GetWGSPath ( void  ) const
inline

Definition at line 208 of file wgsread.hpp.

References m_WGSPath.

Referenced by GetAmbiguityInfo(), CWGSDb::GetWGSPath(), HasStandardFeatLocIdType(), and PutAmbiguityInfo().

◆ GiIdx()

CRef< CWGSDb_Impl::SGiIdxTableCursor > CWGSDb_Impl::GiIdx ( TVDBRowId  row = 0)
inlineprotected

◆ GiIdxTable()

const CVDBTable& CWGSDb_Impl::GiIdxTable ( void  )
inlineprotected

Definition at line 472 of file wgsread.hpp.

References m_GiIdxTable, m_GiIdxTableIsOpened, and OpenGiIdxTable().

Referenced by GiIdx().

◆ HasCommonTaxId()

bool CWGSDb_Impl::HasCommonTaxId ( void  ) const
inline

Definition at line 411 of file wgsread.hpp.

References m_HasCommonTaxId.

Referenced by CWGSSeqIterator::HasTaxId().

◆ HasFeatures()

bool CWGSDb_Impl::HasFeatures ( )

Definition at line 3688 of file wgsread.cpp.

References GetTotalFeatureCount().

◆ HasPatentId()

bool CWGSDb_Impl::HasPatentId ( ) const
inline

Definition at line 320 of file wgsread.hpp.

References m_PatentId.

Referenced by GetGeneralOrPatentSeq_id().

◆ HasStandardFeatLocIdType()

bool CWGSDb_Impl::HasStandardFeatLocIdType ( )

◆ IsReplaced()

bool CWGSDb_Impl::IsReplaced ( void  ) const
inline

Definition at line 407 of file wgsread.hpp.

References m_ReplacedBy.

Referenced by HasStandardFeatLocIdType().

◆ IsSetMasterDescr()

bool CWGSDb_Impl::IsSetMasterDescr ( void  ) const
inline

Definition at line 300 of file wgsread.hpp.

References m_IsSetMasterDescr.

Referenced by LoadMasterDescr().

◆ IsTSA()

bool CWGSDb_Impl::IsTSA ( void  ) const

Definition at line 2771 of file wgsread.cpp.

References CSeq_inst_Base::eMol_rna, and GetContigMolType().

Referenced by x_InitIdParams().

◆ LoadMasterDescr()

bool CWGSDb_Impl::LoadMasterDescr ( int  filter)

Definition at line 3012 of file wgsread.cpp.

References IsSetMasterDescr(), NCBI_PARAM_TYPE, and x_LoadMasterDescr().

Referenced by CWGSDb::LoadMasterDescr().

◆ Lookup()

TVDBRowId CWGSDb_Impl::Lookup ( const string name,
const CVDBTableIndex index,
bool  upcase 
)
inlineprotected

◆ NormalizePathOrAccession()

string CWGSDb_Impl::NormalizePathOrAccession ( CTempString  path_or_acc,
CTempString  vol_path = CTempString() 
)
static

◆ OpenContigNameIndex()

void CWGSDb_Impl::OpenContigNameIndex ( void  )
protected

Definition at line 2449 of file wgsread.cpp.

References m_ContigNameIndex, m_ContigNameIndexIsOpened, OpenIndex(), and SeqTable().

Referenced by ContigNameIndex().

◆ OpenFeatTable()

void CWGSDb_Impl::OpenFeatTable ( void  )
protected

Definition at line 2431 of file wgsread.cpp.

References m_FeatTable, m_FeatTableIsOpened, and OpenTable().

Referenced by FeatTable().

◆ OpenGiIdxTable()

void CWGSDb_Impl::OpenGiIdxTable ( void  )
protected

Definition at line 2437 of file wgsread.cpp.

References m_GiIdxTable, m_GiIdxTableIsOpened, and OpenTable().

Referenced by GiIdxTable().

◆ OpenIndex()

void CWGSDb_Impl::OpenIndex ( const CVDBTable table,
CVDBTableIndex index,
atomic< Int1 > &  index_is_opened,
const char *  index_name,
const char *  backup_index_name = 0 
)
inlineprotected

◆ OpenProductNameIndex()

void CWGSDb_Impl::OpenProductNameIndex ( void  )
protected

Definition at line 2470 of file wgsread.cpp.

References m_ProductNameIndex, m_ProductNameIndexIsOpened, OpenIndex(), and ProtTable().

Referenced by ProductNameIndex().

◆ OpenProtAccIndex()

void CWGSDb_Impl::OpenProtAccIndex ( void  )
protected

Definition at line 2477 of file wgsread.cpp.

References m_ProtAccIndex, m_ProtAccIndexIsOpened, OpenIndex(), and ProtTable().

Referenced by ProtAccIndex().

◆ OpenProteinNameIndex()

void CWGSDb_Impl::OpenProteinNameIndex ( void  )
protected

Definition at line 2463 of file wgsread.cpp.

References m_ProteinNameIndex, m_ProteinNameIndexIsOpened, OpenIndex(), and ProtTable().

Referenced by ProteinNameIndex().

◆ OpenProtIdxTable()

void CWGSDb_Impl::OpenProtIdxTable ( void  )
protected

Definition at line 2443 of file wgsread.cpp.

References m_ProtIdxTable, m_ProtIdxTableIsOpened, and OpenTable().

Referenced by ProtIdxTable().

◆ OpenProtTable()

void CWGSDb_Impl::OpenProtTable ( void  )
protected

Definition at line 2425 of file wgsread.cpp.

References m_ProtTable, m_ProtTableIsOpened, and OpenTable().

Referenced by ProtTable().

◆ OpenScaffoldNameIndex()

void CWGSDb_Impl::OpenScaffoldNameIndex ( void  )
protected

Definition at line 2456 of file wgsread.cpp.

References m_ScaffoldNameIndex, m_ScaffoldNameIndexIsOpened, OpenIndex(), and ScfTable().

Referenced by ScaffoldNameIndex().

◆ OpenScfTable()

void CWGSDb_Impl::OpenScfTable ( void  )
protected

Definition at line 2419 of file wgsread.cpp.

References m_ScfTable, m_ScfTableIsOpened, and OpenTable().

Referenced by ScfTable().

◆ OpenTable()

void CWGSDb_Impl::OpenTable ( CVDBTable table,
atomic< bool > &  table_is_opened,
const char *  table_name 
)
inlineprotected

◆ ParseContigRow()

static TVDBRowId CWGSDb_Impl::ParseContigRow ( CTempString  acc)
inlinestatic

Definition at line 245 of file wgsread.hpp.

References fAllowRowType_contig, and ParseRowType().

Referenced by CWGSDb::ParseContigRow().

◆ ParseProteinRow()

static TVDBRowId CWGSDb_Impl::ParseProteinRow ( CTempString  acc)
inlinestatic

Definition at line 257 of file wgsread.hpp.

References fAllowRowType_protein, and ParseRowType().

Referenced by CWGSDb::ParseProteinRow().

◆ ParseRow()

TVDBRowId CWGSDb_Impl::ParseRow ( CTempString  acc,
bool is_scaffold 
) const

◆ ParseRowType()

pair< TVDBRowId, CWGSDb_Impl::ERowType > CWGSDb_Impl::ParseRowType ( CTempString  acc,
TAllowRowType  allow 
)
static

◆ ParseScaffoldRow()

static TVDBRowId CWGSDb_Impl::ParseScaffoldRow ( CTempString  acc)
inlinestatic

Definition at line 251 of file wgsread.hpp.

References fAllowRowType_scaffold, and ParseRowType().

Referenced by CWGSDb::ParseScaffoldRow().

◆ ProductNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ProductNameIndex ( void  )
inlineprotected

Definition at line 508 of file wgsread.hpp.

References m_ProductNameIndex, m_ProductNameIndexIsOpened, and OpenProductNameIndex().

Referenced by GetProductNameRowId().

◆ Prot()

CRef< CWGSDb_Impl::SProtTableCursor > CWGSDb_Impl::Prot ( TVDBRowId  row = 0)
inlineprotected

Definition at line 947 of file wgsread.cpp.

References m_Prot, ProtTable(), row, and table.

Referenced by CWGSProteinIterator::x_Cur().

◆ Prot0()

CRef< CWGSDb_Impl::SProt0TableCursor > CWGSDb_Impl::Prot0 ( TVDBRowId  row = 0)
inlineprotected

Definition at line 933 of file wgsread.cpp.

References m_Prot0, ProtTable(), row, and table.

Referenced by GetProtAccRanges(), GetProtAccRowId(), and CWGSProteinIterator::x_Init().

◆ ProtAccIndex()

const CVDBTableIndex& CWGSDb_Impl::ProtAccIndex ( void  )
inlineprotected

Definition at line 484 of file wgsread.hpp.

References m_ProtAccIndex, m_ProtAccIndexIsOpened, and OpenProtAccIndex().

◆ ProteinNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ProteinNameIndex ( void  )
inlineprotected

Definition at line 502 of file wgsread.hpp.

References m_ProteinNameIndex, m_ProteinNameIndexIsOpened, and OpenProteinNameIndex().

Referenced by GetProteinNameRowId().

◆ ProtIdx()

CRef< CWGSDb_Impl::SProtIdxTableCursor > CWGSDb_Impl::ProtIdx ( TVDBRowId  row = 0)
inlineprotected

Definition at line 989 of file wgsread.cpp.

References m_ProtIdx, ProtIdxTable(), row, and table.

Referenced by GetProtAccRowId().

◆ ProtIdxTable()

const CVDBTable& CWGSDb_Impl::ProtIdxTable ( void  )
inlineprotected

Definition at line 478 of file wgsread.hpp.

References m_ProtIdxTable, m_ProtIdxTableIsOpened, and OpenProtIdxTable().

Referenced by ProtIdx().

◆ ProtTable()

const CVDBTable& CWGSDb_Impl::ProtTable ( void  )
inlineprotected

◆ Put() [1/9]

void CWGSDb_Impl::Put ( CRef< SFeatTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1045 of file wgsread.cpp.

References m_Feat, and row.

◆ Put() [2/9]

void CWGSDb_Impl::Put ( CRef< SGiIdxTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1052 of file wgsread.cpp.

References m_GiIdx, and row.

◆ Put() [3/9]

void CWGSDb_Impl::Put ( CRef< SProt0TableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1031 of file wgsread.cpp.

References m_Prot0, and row.

◆ Put() [4/9]

void CWGSDb_Impl::Put ( CRef< SProtIdxTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1059 of file wgsread.cpp.

References m_ProtIdx, and row.

◆ Put() [5/9]

void CWGSDb_Impl::Put ( CRef< SProtTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1038 of file wgsread.cpp.

References m_Prot, and row.

◆ Put() [6/9]

void CWGSDb_Impl::Put ( CRef< SScfTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1024 of file wgsread.cpp.

References m_Scf, and row.

◆ Put() [7/9]

void CWGSDb_Impl::Put ( CRef< SSeq0TableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

◆ Put() [8/9]

void CWGSDb_Impl::Put ( CRef< SSeq4naTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1017 of file wgsread.cpp.

◆ Put() [9/9]

void CWGSDb_Impl::Put ( CRef< SSeqTableCursor > &  curs,
TVDBRowId  row = 0 
)
inlineprotected

Definition at line 1010 of file wgsread.cpp.

References m_Seq, and row.

◆ PutAmbiguityInfo()

void CWGSDb_Impl::PutAmbiguityInfo ( CRef< SAmbiguityInfo > &  ambiguity)
protected

◆ ResetMasterDescr()

void CWGSDb_Impl::ResetMasterDescr ( void  )

Definition at line 3005 of file wgsread.cpp.

References m_IsSetMasterDescr, and m_MasterDescr.

◆ ScaffoldNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ScaffoldNameIndex ( void  )
inlineprotected

◆ Scf()

CRef< CWGSDb_Impl::SScfTableCursor > CWGSDb_Impl::Scf ( TVDBRowId  row = 0)
inlineprotected

Definition at line 919 of file wgsread.cpp.

References m_Scf, row, ScfTable(), and table.

Referenced by CWGSScaffoldIterator::x_Init().

◆ ScfTable()

const CVDBTable& CWGSDb_Impl::ScfTable ( void  )
inlineprotected

Definition at line 454 of file wgsread.hpp.

References m_ScfTable, m_ScfTableIsOpened, and OpenScfTable().

Referenced by OpenScaffoldNameIndex(), and Scf().

◆ Seq()

CRef< CWGSDb_Impl::SSeqTableCursor > CWGSDb_Impl::Seq ( TVDBRowId  row = 0)
inlineprotected

◆ Seq0()

CRef< CWGSDb_Impl::SSeq0TableCursor > CWGSDb_Impl::Seq0 ( TVDBRowId  row = 0)
inlineprotected

Definition at line 883 of file wgsread.cpp.

References m_Seq0, row, and SeqTable().

Referenced by CWGSSeqIterator::x_Init(), and x_InitIdParams().

◆ Seq4na()

CRef< CWGSDb_Impl::SSeq4naTableCursor > CWGSDb_Impl::Seq4na ( TVDBRowId  row = 0)
inlineprotected

◆ SeqTable()

const CVDBTable& CWGSDb_Impl::SeqTable ( void  )
inlineprotected

Definition at line 451 of file wgsread.hpp.

References m_SeqTable.

Referenced by GetMasterDescrBytes(), OpenContigNameIndex(), Seq(), Seq0(), Seq4na(), and x_InitIdParams().

◆ SetMasterDescr()

void CWGSDb_Impl::SetMasterDescr ( const TMasterDescr descr,
int  filter 
)

◆ SetPatentId()

void CWGSDb_Impl::SetPatentId ( CRef< CSeq_id id)

Definition at line 3258 of file wgsread.cpp.

References m_PatentId.

Referenced by GetMasterDescrEntry().

◆ x_InitIdParams()

void CWGSDb_Impl::x_InitIdParams ( void  )
protected

◆ x_LoadMasterDescr()

void CWGSDb_Impl::x_LoadMasterDescr ( int  filter)
protected

Definition at line 3097 of file wgsread.cpp.

References GetMasterDescrEntry(), and SetMasterDescr().

Referenced by LoadMasterDescr().

◆ x_SortGiRanges()

void CWGSDb_Impl::x_SortGiRanges ( TGiRanges ranges)
protected

Definition at line 3350 of file wgsread.cpp.

References i, and ct::sort().

Referenced by GetNucGiRanges().

Friends And Related Function Documentation

◆ CWGSFeatureIterator

friend class CWGSFeatureIterator
friend

Definition at line 430 of file wgsread.hpp.

◆ CWGSGiIterator

friend class CWGSGiIterator
friend

Definition at line 428 of file wgsread.hpp.

◆ CWGSProteinIterator

friend class CWGSProteinIterator
friend

Definition at line 429 of file wgsread.hpp.

◆ CWGSScaffoldIterator

friend class CWGSScaffoldIterator
friend

Definition at line 427 of file wgsread.hpp.

◆ CWGSSeqIterator

friend class CWGSSeqIterator
friend

Definition at line 426 of file wgsread.hpp.

Member Data Documentation

◆ m_AmbiguityCache

TAmbiguityCache CWGSDb_Impl::m_AmbiguityCache
private

Definition at line 626 of file wgsread.hpp.

Referenced by GetAmbiguityInfo(), and PutAmbiguityInfo().

◆ m_AmbiguityCacheMutex

CFastMutex CWGSDb_Impl::m_AmbiguityCacheMutex
private

Definition at line 624 of file wgsread.hpp.

Referenced by GetAmbiguityInfo(), and PutAmbiguityInfo().

◆ m_CommonTaxId

TTaxId CWGSDb_Impl::m_CommonTaxId
private

Definition at line 639 of file wgsread.hpp.

Referenced by GetCommonTaxId(), and x_InitIdParams().

◆ m_ContigMolType

CSeq_inst::TMol CWGSDb_Impl::m_ContigMolType
private

Definition at line 628 of file wgsread.hpp.

Referenced by GetContigMolType(), and x_InitIdParams().

◆ m_ContigNameIndex

CVDBTableIndex CWGSDb_Impl::m_ContigNameIndex
private

Definition at line 619 of file wgsread.hpp.

Referenced by ContigNameIndex(), and OpenContigNameIndex().

◆ m_ContigNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ContigNameIndexIsOpened
private

Definition at line 600 of file wgsread.hpp.

Referenced by ContigNameIndex(), GetContigNameRowId(), and OpenContigNameIndex().

◆ m_Db

CVDB CWGSDb_Impl::m_Db
private

Definition at line 584 of file wgsread.hpp.

Referenced by CWGSDb_Impl(), OpenTable(), and CWGSSeqIterator::Reset().

◆ m_Feat

CVDBObjectCache<SFeatTableCursor> CWGSDb_Impl::m_Feat
private

Definition at line 615 of file wgsread.hpp.

Referenced by Feat(), and Put().

◆ m_FeatLocIdType

atomic<EFeatLocIdType> CWGSDb_Impl::m_FeatLocIdType
private

Definition at line 632 of file wgsread.hpp.

Referenced by GetFeatLocIdType().

◆ m_FeatTable

CVDBTable CWGSDb_Impl::m_FeatTable
private

Definition at line 606 of file wgsread.hpp.

Referenced by FeatTable(), and OpenFeatTable().

◆ m_FeatTableIsOpened

atomic<bool> CWGSDb_Impl::m_FeatTableIsOpened
private

Definition at line 596 of file wgsread.hpp.

Referenced by FeatTable(), and OpenFeatTable().

◆ m_GiIdx

CVDBObjectCache<SGiIdxTableCursor> CWGSDb_Impl::m_GiIdx
private

Definition at line 616 of file wgsread.hpp.

Referenced by GiIdx(), and Put().

◆ m_GiIdxTable

CVDBTable CWGSDb_Impl::m_GiIdxTable
private

Definition at line 607 of file wgsread.hpp.

Referenced by GiIdxTable(), and OpenGiIdxTable().

◆ m_GiIdxTableIsOpened

atomic<bool> CWGSDb_Impl::m_GiIdxTableIsOpened
private

Definition at line 597 of file wgsread.hpp.

Referenced by GiIdxTable(), and OpenGiIdxTable().

◆ m_HasCommonTaxId

bool CWGSDb_Impl::m_HasCommonTaxId
private

Definition at line 631 of file wgsread.hpp.

Referenced by HasCommonTaxId(), and x_InitIdParams().

◆ m_HasNoDefaultGnlId

bool CWGSDb_Impl::m_HasNoDefaultGnlId
private

Definition at line 630 of file wgsread.hpp.

Referenced by GetGeneralSeq_id(), and x_InitIdParams().

◆ m_IdPrefix

string CWGSDb_Impl::m_IdPrefix
private

Definition at line 587 of file wgsread.hpp.

Referenced by GetIdPrefix(), GetMasterSeq_id(), and x_InitIdParams().

◆ m_IdPrefixDb

string CWGSDb_Impl::m_IdPrefixDb
private

Definition at line 589 of file wgsread.hpp.

Referenced by GetGeneralSeq_id(), and x_InitIdParams().

◆ m_IdPrefixDbWithVersion

string CWGSDb_Impl::m_IdPrefixDbWithVersion
private

Definition at line 588 of file wgsread.hpp.

Referenced by GetGeneralSeq_id(), and x_InitIdParams().

◆ m_IdPrefixWithVersion

string CWGSDb_Impl::m_IdPrefixWithVersion
private

Definition at line 586 of file wgsread.hpp.

Referenced by GetAccSeq_id(), GetIdPrefixWithVersion(), and x_InitIdParams().

◆ m_IdRowDigits

Uint4 CWGSDb_Impl::m_IdRowDigits
private

Definition at line 591 of file wgsread.hpp.

Referenced by GetAccSeq_id(), GetIdRowDigits(), GetMasterSeq_id(), and x_InitIdParams().

◆ m_IdVersion

int CWGSDb_Impl::m_IdVersion
private

Definition at line 590 of file wgsread.hpp.

Referenced by GetMasterSeq_id(), and x_InitIdParams().

◆ m_IsSetMasterDescr

bool CWGSDb_Impl::m_IsSetMasterDescr
private

Definition at line 629 of file wgsread.hpp.

Referenced by IsSetMasterDescr(), ResetMasterDescr(), and SetMasterDescr().

◆ m_MasterDescr

TMasterDescr CWGSDb_Impl::m_MasterDescr
private

Definition at line 634 of file wgsread.hpp.

Referenced by GetMasterDescr(), GetMasterSeq_entry(), ResetMasterDescr(), and SetMasterDescr().

◆ m_MasterEntry

CRef<CSeq_entry> CWGSDb_Impl::m_MasterEntry
private

Definition at line 633 of file wgsread.hpp.

Referenced by GetMasterDescrEntry(), GetMasterGi(), and GetMasterSeq_entry().

◆ m_Mgr

CVDBMgr CWGSDb_Impl::m_Mgr
private

Definition at line 582 of file wgsread.hpp.

◆ m_PatentId

CRef<CSeq_id> CWGSDb_Impl::m_PatentId
private

Definition at line 635 of file wgsread.hpp.

Referenced by GetPatentId(), GetPatentSeq_id(), HasPatentId(), and SetPatentId().

◆ m_ProductNameIndex

CVDBTableIndex CWGSDb_Impl::m_ProductNameIndex
private

Definition at line 622 of file wgsread.hpp.

Referenced by OpenProductNameIndex(), and ProductNameIndex().

◆ m_ProductNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ProductNameIndexIsOpened
private

Definition at line 603 of file wgsread.hpp.

Referenced by GetProductNameRowId(), OpenProductNameIndex(), and ProductNameIndex().

◆ m_ProjectGBState

NCBI_gb_state CWGSDb_Impl::m_ProjectGBState
private

Definition at line 636 of file wgsread.hpp.

Referenced by GetProjectGBState(), and x_InitIdParams().

◆ m_Prot

CVDBObjectCache<SProtTableCursor> CWGSDb_Impl::m_Prot
private

Definition at line 614 of file wgsread.hpp.

Referenced by Prot(), and Put().

◆ m_Prot0

CVDBObjectCache<SProt0TableCursor> CWGSDb_Impl::m_Prot0
private

Definition at line 613 of file wgsread.hpp.

Referenced by Prot0(), and Put().

◆ m_ProtAccIndex

CVDBTableIndex CWGSDb_Impl::m_ProtAccIndex
private

Definition at line 618 of file wgsread.hpp.

Referenced by OpenProtAccIndex(), and ProtAccIndex().

◆ m_ProtAccIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ProtAccIndexIsOpened
private

Definition at line 599 of file wgsread.hpp.

Referenced by OpenProtAccIndex(), and ProtAccIndex().

◆ m_ProteinNameIndex

CVDBTableIndex CWGSDb_Impl::m_ProteinNameIndex
private

Definition at line 621 of file wgsread.hpp.

Referenced by OpenProteinNameIndex(), and ProteinNameIndex().

◆ m_ProteinNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ProteinNameIndexIsOpened
private

Definition at line 602 of file wgsread.hpp.

Referenced by GetProteinNameRowId(), OpenProteinNameIndex(), and ProteinNameIndex().

◆ m_ProtIdx

CVDBObjectCache<SProtIdxTableCursor> CWGSDb_Impl::m_ProtIdx
private

Definition at line 617 of file wgsread.hpp.

Referenced by ProtIdx(), and Put().

◆ m_ProtIdxTable

CVDBTable CWGSDb_Impl::m_ProtIdxTable
private

Definition at line 608 of file wgsread.hpp.

Referenced by OpenProtIdxTable(), and ProtIdxTable().

◆ m_ProtIdxTableIsOpened

atomic<bool> CWGSDb_Impl::m_ProtIdxTableIsOpened
private

Definition at line 598 of file wgsread.hpp.

Referenced by OpenProtIdxTable(), and ProtIdxTable().

◆ m_ProtTable

CVDBTable CWGSDb_Impl::m_ProtTable
private

Definition at line 605 of file wgsread.hpp.

Referenced by OpenProtTable(), and ProtTable().

◆ m_ProtTableIsOpened

atomic<bool> CWGSDb_Impl::m_ProtTableIsOpened
private

Definition at line 595 of file wgsread.hpp.

Referenced by OpenProtTable(), and ProtTable().

◆ m_ReplacedBy

string CWGSDb_Impl::m_ReplacedBy
private

Definition at line 638 of file wgsread.hpp.

Referenced by GetReplacedBy(), IsReplaced(), and x_InitIdParams().

◆ m_ScaffoldNameIndex

CVDBTableIndex CWGSDb_Impl::m_ScaffoldNameIndex
private

Definition at line 620 of file wgsread.hpp.

Referenced by OpenScaffoldNameIndex(), and ScaffoldNameIndex().

◆ m_ScaffoldNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ScaffoldNameIndexIsOpened
private

Definition at line 601 of file wgsread.hpp.

Referenced by GetScaffoldNameRowId(), OpenScaffoldNameIndex(), and ScaffoldNameIndex().

◆ m_Scf

CVDBObjectCache<SScfTableCursor> CWGSDb_Impl::m_Scf
private

Definition at line 612 of file wgsread.hpp.

Referenced by Put(), and Scf().

◆ m_ScfTable

CVDBTable CWGSDb_Impl::m_ScfTable
private

Definition at line 604 of file wgsread.hpp.

Referenced by OpenScfTable(), and ScfTable().

◆ m_ScfTableIsOpened

atomic<bool> CWGSDb_Impl::m_ScfTableIsOpened
private

Definition at line 594 of file wgsread.hpp.

Referenced by OpenScfTable(), and ScfTable().

◆ m_Seq

CVDBObjectCache<SSeqTableCursor> CWGSDb_Impl::m_Seq
private

Definition at line 611 of file wgsread.hpp.

Referenced by Put(), and Seq().

◆ m_Seq0

CVDBObjectCache<SSeq0TableCursor> CWGSDb_Impl::m_Seq0
private

Definition at line 610 of file wgsread.hpp.

Referenced by Put(), and Seq0().

◆ m_SeqIdType

CSeq_id::E_Choice CWGSDb_Impl::m_SeqIdType
private

Definition at line 637 of file wgsread.hpp.

Referenced by GetAccSeq_id(), and x_InitIdParams().

◆ m_SeqTable

CVDBTable CWGSDb_Impl::m_SeqTable
private

Definition at line 585 of file wgsread.hpp.

Referenced by CWGSDb_Impl(), and SeqTable().

◆ m_TableMutex

CFastMutex CWGSDb_Impl::m_TableMutex
private

Definition at line 593 of file wgsread.hpp.

Referenced by GetMasterDescrEntry(), OpenIndex(), and OpenTable().

◆ m_WGSPath

string CWGSDb_Impl::m_WGSPath
private

Definition at line 583 of file wgsread.hpp.

Referenced by CWGSDb_Impl(), and GetWGSPath().


The documentation for this class was generated from the following files:
Modified on Tue May 21 10:55:04 2024 by modify_doxy.py rev. 669887