NCBI C++ ToolKit
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CBioseqContext Class Reference

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#include <objtools/format/context.hpp>

+ Inheritance diagram for CBioseqContext:
+ Collaboration diagram for CBioseqContext:

Public Types

enum  FUnverified {
  fUnverified_None = 0 , fUnverified_Organism = 1 << 0 , fUnverified_SequenceOrAnnotation = 1 << 1 , fUnverified_Misassembled = 1 << 2 ,
  fUnverified_Contaminant = 1 << 3
}
 
enum  FUnreviewed { fUnreviewed_None = 0 , fUnreviewed_Unannotated = 1 << 0 }
 
typedef CRef< CReferenceItemTRef
 
typedef vector< TRefTReferences
 
typedef CRange< TSeqPosTRange
 
typedef Int8 TUnverified
 
typedef Int8 TUnreviewed
 
- 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

 CBioseqContext (const CBioseq_Handle &seq, CFlatFileContext &ffctx, CMasterContext *mctx=nullptr, CTopLevelSeqEntryContext *tlsec=nullptr)
 
 CBioseqContext (const CBioseq_Handle &prev_seq, const CBioseq_Handle &seq, const CBioseq_Handle &next_seq, CFlatFileContext &ffctx, CMasterContext *mctx=nullptr, CTopLevelSeqEntryContext *tlsec=nullptr)
 
 ~CBioseqContext (void)
 
CBioseq_HandleGetPrevHandle (void)
 
CBioseq_HandleGetHandle (void)
 
const CBioseq_HandleGetHandle (void) const
 
CBioseq_HandleGetNextHandle (void)
 
CScopeGetScope (void) const
 
feature::CFeatTree & GetFeatTree (void)
 
bool UsingSeqEntryIndex (void) const
 
const CRef< CSeqEntryIndexGetSeqEntryIndex (void) const
 
CSeq_idGetPrimaryId (void)
 
CSeq_id_Handle GetPreferredSynonym (const CSeq_id &id) const
 
const stringGetAccession (void) const
 
TGi GetGI (void) const
 
bool IsProt (void) const
 
bool IsNuc (void) const
 
CSeq_inst::TRepr GetRepr (void) const
 
CSeq_inst::TMol GetMol (void) const
 
const CMolInfoGetMolinfo (void) const
 
CMolInfo::TTech GetTech (void) const
 
CMolInfo::TBiomol GetBiomol (void) const
 
const CBioseq::TIdGetBioseqIds (void) const
 
bool IsSegmented (void) const
 
bool HasParts (void) const
 
bool IsPart (void) const
 
SIZE_TYPE GetPartNumber (void) const
 
SIZE_TYPE GetTotalNumParts (void) const
 
CMasterContextGetMaster (void)
 
bool CanGetMaster (void) const
 
void SetMaster (CMasterContext &mctx)
 
CTopLevelSeqEntryContextGetTLSeqEntryCtx (void)
 
bool CanGetTLSeqEntryCtx (void) const
 
bool IsBioseqInSameTopLevelSeqEntry (const CBioseq_Handle &seq)
 
bool IsSeqIdInSameTopLevelSeqEntry (const CSeq_id &seq_id)
 
bool IsDelta (void) const
 
bool IsDeltaLitOnly (void) const
 
bool IsWGS (void) const
 
bool IsWGSMaster (void) const
 
const stringGetWGSMasterAccn (void) const
 
const stringGetWGSMasterName (void) const
 
bool IsTSA (void) const
 
bool IsTSAMaster (void) const
 
const stringGetTSAMasterAccn (void) const
 
const stringGetTSAMasterName (void) const
 
bool IsTLS (void) const
 
bool IsTLSMaster (void) const
 
const stringGetTLSMasterAccn (void) const
 
const stringGetTLSMasterName (void) const
 
TReferencesSetReferences (void)
 
const TReferencesGetReferences (void) const
 
const CSeq_locGetLocation (void) const
 
CSeq_loc_MapperGetMapper (void)
 
bool DoContigStyle (void) const
 
bool ShowGBBSource (void) const
 
bool IsInSGS (void) const
 
bool IsInGPS (void) const
 
bool IsInNucProt (void) const
 
bool IsGED (void) const
 
bool IsGenbank (void) const
 
bool IsEMBL (void) const
 
bool IsDDBJ (void) const
 
bool IsPDB (void) const
 
bool IsSP (void) const
 
bool IsTPA (void) const
 
bool IsJournalScan (void) const
 
bool IsPatent (void) const
 
bool IsGbGenomeProject (void) const
 
bool IsNcbiCONDiv (void) const
 
bool IsNcbiGenomes (void) const
 
bool IsRefSeq (void) const
 
bool IsRSCompleteGenomic (void) const
 
bool IsRSIncompleteGenomic (void) const
 
bool IsRSMRna (void) const
 
bool IsRSNonCodingRna (void) const
 
bool IsRSProtein (void) const
 
bool IsRSContig (void) const
 
bool IsRSIntermedWGS (void) const
 
bool IsRSPredictedMRna (void) const
 
bool IsRSPredictedNCRna (void) const
 
bool IsRSPredictedProtein (void) const
 
bool IsRSWGSNuc (void) const
 
bool IsRSWGSProt (void) const
 
bool IsRSUniqueProt (void) const
 
bool IsEncode (void) const
 
const CUser_objectGetEncode (void) const
 
const stringGetFinishingStatus (void) const
 
bool IsGenomeAssembly (void) const
 
bool IsCrossKingdom (void) const
 
bool UsePDBCompoundForComment (void) const
 
void SetPDBCompoundForComment (bool value)
 
bool IsUnverified (void) const
 
TUnverified GetUnverifiedType (void) const
 
TUnreviewed GetUnreviewedType (void) const
 
bool ShowAnnotCommentAsCOMMENT () const
 
bool IsHup (void) const
 
int GetPatentSeqId (void) const
 
const CSubmit_blockGetSubmitBlock (void) const
 
const CSeq_entry_HandleGetTopLevelEntry (void) const
 
const CFlatFileConfigConfig (void) const
 
const SAnnotSelectorGetAnnotSelector (void) const
 
SAnnotSelectorSetAnnotSelector (void)
 
const CSeq_locGetMasterLocation (void) const
 
bool GetSGS (void) const
 
bool IsGenbankFormat (void) const
 
bool HasOperon (void) const
 
bool HasMultiIntervalGenes (void) const
 
void ThrowIfCanceled (void) const
 Checks if CFlatFileConfig has an ICanceled, and throws if it indicates cancellation. More...
 
const stringGetTaxname (void) const
 Empty string if unavailable. More...
 
const stringGetFiletrackURL (void) const
 Empty if no Filetrack URL. More...
 
const vector< string > & GetBasemodURLs (void) const
 Empty if no Basemod URLs. More...
 
const stringGetAuthorizedAccess (void) const
 
const CPacked_seqpntGetOpticalMapPoints (void) const
 Empty or NULL if no points or if this bioseq isn't an optical map. More...
 
vector< string > * GetRefCache (void) const
 
void SetRefCache (vector< string > *rc)
 
- 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
 

Private Member Functions

void x_Init (const CBioseq_Handle &seq, const CSeq_loc *user_loc)
 
void x_SetId (void)
 
bool x_HasParts (void) const
 
bool x_IsDeltaLitOnly (void) const
 
bool x_IsPart (void) const
 
CBioseq_Handle x_GetMasterForPart (void) const
 
SIZE_TYPE x_GetPartNumber (void)
 
bool x_IsInSGS (void) const
 
bool x_IsInGPS (void) const
 
bool x_IsInNucProt (void) const
 
void x_SetLocation (const CSeq_loc *user_loc=nullptr)
 
void x_SetMapper (const CSeq_loc &loc)
 
void x_SetHasMultiIntervalGenes (void) const
 
void x_SetDataFromUserObjects (void)
 
void x_CheckForShowComments () const
 
void x_SetTaxname (void) const
 
void x_SetFiletrackURL (const CUser_object &uo)
 
void x_SetAuthorizedAccess (const CUser_object &uo)
 
void x_SetOpticalMapPoints (void)
 
void x_SetEncode (const CUser_object &uo)
 
CSeq_inst::TRepr x_GetRepr (void) const
 
const CMolInfox_GetMolInfo (void) const
 
bool x_HasOperon (void) const
 

Private Attributes

CBioseq_Handle m_PrevHandle
 
CBioseq_Handle m_Handle
 
CBioseq_Handle m_NextHandle
 
feature::CFeatTree m_FeatTree
 
CRef< CSeq_idm_PrimaryId
 
string m_Accession
 
string m_WGSMasterAccn
 
string m_WGSMasterName
 
string m_TSAMasterAccn
 
string m_TSAMasterName
 
string m_TLSMasterAccn
 
string m_TLSMasterName
 
string m_FinishingStatus
 
string m_Taxname
 
string m_FiletrackURL
 
vector< stringm_BasemodURLs
 
string m_AuthorizedAccess
 
const CPacked_seqpntm_pOpticalMapPoints
 
unique_ptr< CPacked_seqpntm_pOpticalMapPointsDestroyer
 
CSeq_inst::TRepr m_Repr
 
CSeq_inst::TMol m_Mol
 
CConstRef< CMolInfom_Molinfo
 
bool m_HasParts
 
bool m_IsPart
 
SIZE_TYPE m_PartNumber
 
bool m_IsDeltaLitOnly
 
bool m_IsProt
 
bool m_IsInSGS
 
bool m_IsInGPS
 
bool m_IsInNucProt
 
bool m_IsGED
 
bool m_IsGenbank
 
bool m_IsEMBL
 
bool m_IsDDBJ
 
bool m_IsPDB
 
bool m_IsSP
 
bool m_IsTPA
 
bool m_IsJournalScan
 
bool m_IsRefSeq
 
unsigned int m_RefseqInfo
 
bool m_IsGbGenomeProject
 
bool m_IsNcbiCONDiv
 
bool m_IsNcbiGenomes
 
bool m_IsPatent
 
bool m_IsGI
 
bool m_IsWGS
 
bool m_IsWGSMaster
 
bool m_IsTSA
 
bool m_IsTSAMaster
 
bool m_IsTLS
 
bool m_IsTLSMaster
 
bool m_IsHup
 
TGi m_Gi
 
bool m_ShowGBBSource
 
int m_PatSeqid
 
bool m_HasOperon
 
bool m_HasMultiIntervalGenes
 
bool m_IsGenomeAssembly
 
bool m_IsCrossKingdom
 
bool m_UsePDBCompoundForComment
 
TUnverified m_fUnverified
 
TUnreviewed m_fUnreviewed
 
bool m_ShowAnnotCommentAsCOMMENT
 
bool m_ShowAnnotCommentAsCOMMENT_checked
 
CConstRef< CUser_objectm_Encode
 
TReferences m_References
 
CConstRef< CSeq_locm_Location
 
CRef< CSeq_loc_Mapperm_Mapper
 
CBioseq_Handle m_Virtual
 
CFlatFileContextm_FFCtx
 
vector< string > * m_RefCache
 
CRef< CMasterContextm_Master
 
CRef< CTopLevelSeqEntryContextm_TLSeqEntryCtx
 

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

Definition at line 72 of file context.hpp.

Member Typedef Documentation

◆ TRange

Definition at line 78 of file context.hpp.

◆ TRef

Definition at line 76 of file context.hpp.

◆ TReferences

Definition at line 77 of file context.hpp.

◆ TUnreviewed

Definition at line 239 of file context.hpp.

◆ TUnverified

Definition at line 230 of file context.hpp.

Member Enumeration Documentation

◆ FUnreviewed

Enumerator
fUnreviewed_None 
fUnreviewed_Unannotated 

Definition at line 232 of file context.hpp.

◆ FUnverified

Enumerator
fUnverified_None 
fUnverified_Organism 
fUnverified_SequenceOrAnnotation 
fUnverified_Misassembled 
fUnverified_Contaminant 

Definition at line 220 of file context.hpp.

Constructor & Destructor Documentation

◆ CBioseqContext() [1/2]

CBioseqContext::CBioseqContext ( const CBioseq_Handle seq,
CFlatFileContext ffctx,
CMasterContext mctx = nullptr,
CTopLevelSeqEntryContext tlsec = nullptr 
)

Definition at line 77 of file context.cpp.

◆ CBioseqContext() [2/2]

CBioseqContext::CBioseqContext ( const CBioseq_Handle prev_seq,
const CBioseq_Handle seq,
const CBioseq_Handle next_seq,
CFlatFileContext ffctx,
CMasterContext mctx = nullptr,
CTopLevelSeqEntryContext tlsec = nullptr 
)

Definition at line 137 of file context.cpp.

References CFlatFileContext::GetLocation(), m_FFCtx, and x_Init().

◆ ~CBioseqContext()

CBioseqContext::~CBioseqContext ( void  )

Member Function Documentation

◆ CanGetMaster()

bool CBioseqContext::CanGetMaster ( void  ) const
inline

Definition at line 133 of file context.hpp.

References m_Master, and CRef< C, Locker >::NotNull().

◆ CanGetTLSeqEntryCtx()

bool CBioseqContext::CanGetTLSeqEntryCtx ( void  ) const
inline

Definition at line 138 of file context.hpp.

References m_TLSeqEntryCtx, and CRef< C, Locker >::NotNull().

◆ Config()

const CFlatFileConfig & CBioseqContext::Config ( void  ) const
inline

◆ DoContigStyle()

bool CBioseqContext::DoContigStyle ( void  ) const

◆ GetAccession()

const string& CBioseqContext::GetAccession ( void  ) const
inline

◆ GetAnnotSelector()

const SAnnotSelector * CBioseqContext::GetAnnotSelector ( void  ) const
inline

Definition at line 707 of file context.hpp.

References CFlatFileContext::GetAnnotSelector(), and m_FFCtx.

◆ GetAuthorizedAccess()

const string& CBioseqContext::GetAuthorizedAccess ( void  ) const
inline

Definition at line 275 of file context.hpp.

References m_AuthorizedAccess.

◆ GetBasemodURLs()

const vector< string >& CBioseqContext::GetBasemodURLs ( void  ) const
inline

Empty if no Basemod URLs.

Definition at line 272 of file context.hpp.

References m_BasemodURLs.

◆ GetBiomol()

CMolInfo::TBiomol CBioseqContext::GetBiomol ( void  ) const
inline

◆ GetBioseqIds()

const CBioseq::TId & CBioseqContext::GetBioseqIds ( void  ) const
inline

Definition at line 525 of file context.hpp.

References CBioseq_Handle::GetBioseqCore(), CBioseq_Base::GetId(), and m_Handle.

◆ GetEncode()

const CUser_object & CBioseqContext::GetEncode ( void  ) const
inline

Definition at line 639 of file context.hpp.

References _ASSERT, IsEncode(), and m_Encode.

◆ GetFeatTree()

feature::CFeatTree& CBioseqContext::GetFeatTree ( void  )
inline

Definition at line 103 of file context.hpp.

References m_FeatTree.

Referenced by CFlatFeatureRetrieveJob::x_Run().

◆ GetFiletrackURL()

const string& CBioseqContext::GetFiletrackURL ( void  ) const
inline

Empty if no Filetrack URL.

Definition at line 269 of file context.hpp.

References m_FiletrackURL.

◆ GetFinishingStatus()

const string & CBioseqContext::GetFinishingStatus ( void  ) const
inline

Definition at line 646 of file context.hpp.

References m_FinishingStatus.

◆ GetGI()

TGi CBioseqContext::GetGI ( void  ) const
inline

Definition at line 111 of file context.hpp.

References m_Gi.

Referenced by s_GetLinkFeatureKey().

◆ GetHandle() [1/2]

CBioseq_Handle& CBioseqContext::GetHandle ( void  )
inline

Definition at line 99 of file context.hpp.

References m_Handle.

Referenced by CFlatGatherer::x_GatherCDSReferences(), and CFlatGatherer::x_MergeEqualBioSources().

◆ GetHandle() [2/2]

const CBioseq_Handle& CBioseqContext::GetHandle ( void  ) const
inline

Definition at line 100 of file context.hpp.

References m_Handle.

◆ GetLocation()

const CSeq_loc& CBioseqContext::GetLocation ( void  ) const
inline

◆ GetMapper()

CSeq_loc_Mapper* CBioseqContext::GetMapper ( void  )
inline

Definition at line 170 of file context.hpp.

References m_Mapper.

◆ GetMaster()

CMasterContext& CBioseqContext::GetMaster ( void  )
inline

Definition at line 132 of file context.hpp.

References m_Master.

◆ GetMasterLocation()

const CSeq_loc * CBioseqContext::GetMasterLocation ( void  ) const
inline

Definition at line 719 of file context.hpp.

References CFlatFileContext::GetLocation(), and m_FFCtx.

◆ GetMol()

CSeq_inst::TMol CBioseqContext::GetMol ( void  ) const
inline

Definition at line 118 of file context.hpp.

References m_Mol.

◆ GetMolinfo()

const CMolInfo* CBioseqContext::GetMolinfo ( void  ) const
inline

Definition at line 119 of file context.hpp.

References m_Molinfo.

◆ GetNextHandle()

CBioseq_Handle& CBioseqContext::GetNextHandle ( void  )
inline

Definition at line 101 of file context.hpp.

References m_NextHandle.

◆ GetOpticalMapPoints()

const CPacked_seqpnt* CBioseqContext::GetOpticalMapPoints ( void  ) const
inline

Empty or NULL if no points or if this bioseq isn't an optical map.

Definition at line 278 of file context.hpp.

References m_pOpticalMapPoints.

◆ GetPartNumber()

SIZE_TYPE CBioseqContext::GetPartNumber ( void  ) const
inline

Definition at line 130 of file context.hpp.

References m_PartNumber.

◆ GetPatentSeqId()

int CBioseqContext::GetPatentSeqId ( void  ) const
inline

Definition at line 246 of file context.hpp.

References m_PatSeqid.

◆ GetPreferredSynonym()

CSeq_id_Handle CBioseqContext::GetPreferredSynonym ( const CSeq_id id) const

◆ GetPrevHandle()

CBioseq_Handle& CBioseqContext::GetPrevHandle ( void  )
inline

Definition at line 98 of file context.hpp.

References m_PrevHandle.

◆ GetPrimaryId()

CSeq_id* CBioseqContext::GetPrimaryId ( void  )
inline

Definition at line 108 of file context.hpp.

References m_PrimaryId.

Referenced by CFlatGatherer::x_GatherCDSReferences().

◆ GetRefCache()

vector<string>* CBioseqContext::GetRefCache ( void  ) const
inline

Definition at line 281 of file context.hpp.

References m_RefCache.

◆ GetReferences()

const TReferences& CBioseqContext::GetReferences ( void  ) const
inline

Definition at line 165 of file context.hpp.

References m_References.

◆ GetRepr()

CSeq_inst::TRepr CBioseqContext::GetRepr ( void  ) const
inline

◆ GetScope()

CScope& CBioseqContext::GetScope ( void  ) const
inline

◆ GetSeqEntryIndex()

const CRef< CSeqEntryIndex > CBioseqContext::GetSeqEntryIndex ( void  ) const
inline

◆ GetSGS()

bool CBioseqContext::GetSGS ( void  ) const
inline

Definition at line 726 of file context.hpp.

References CFlatFileContext::GetSGS(), and m_FFCtx.

◆ GetSubmitBlock()

const CSubmit_block * CBioseqContext::GetSubmitBlock ( void  ) const
inline

Definition at line 695 of file context.hpp.

References CFlatFileContext::GetSubmitBlock(), and m_FFCtx.

Referenced by CFlatGatherer::x_GatherReferences().

◆ GetTaxname()

const string & CBioseqContext::GetTaxname ( void  ) const

◆ GetTech()

CMolInfo::TTech CBioseqContext::GetTech ( void  ) const
inline

Definition at line 732 of file context.hpp.

References CMolInfo_Base::eTech_unknown, CMolInfo_Base::GetTech(), and m_Molinfo.

Referenced by x_SetId().

◆ GetTLSeqEntryCtx()

CTopLevelSeqEntryContext& CBioseqContext::GetTLSeqEntryCtx ( void  )
inline

Definition at line 137 of file context.hpp.

References m_TLSeqEntryCtx.

◆ GetTLSMasterAccn()

const string& CBioseqContext::GetTLSMasterAccn ( void  ) const
inline

Definition at line 161 of file context.hpp.

References m_TLSMasterAccn.

◆ GetTLSMasterName()

const string& CBioseqContext::GetTLSMasterName ( void  ) const
inline

Definition at line 162 of file context.hpp.

References m_TLSMasterName.

Referenced by CGenbankFormatter::FormatTSA().

◆ GetTopLevelEntry()

const CSeq_entry_Handle & CBioseqContext::GetTopLevelEntry ( void  ) const
inline

Definition at line 701 of file context.hpp.

References CFlatFileContext::GetEntry(), and m_FFCtx.

Referenced by CFlatGatherer::x_GatherReferences(), and x_IsPart().

◆ GetTotalNumParts()

SIZE_TYPE CBioseqContext::GetTotalNumParts ( void  ) const
inline

Definition at line 531 of file context.hpp.

References CMasterContext::GetNumParts(), and m_Master.

◆ GetTSAMasterAccn()

const string& CBioseqContext::GetTSAMasterAccn ( void  ) const
inline

Definition at line 155 of file context.hpp.

References m_TSAMasterAccn.

◆ GetTSAMasterName()

const string& CBioseqContext::GetTSAMasterName ( void  ) const
inline

Definition at line 156 of file context.hpp.

References m_TSAMasterName.

Referenced by CGenbankFormatter::FormatTSA().

◆ GetUnreviewedType()

CBioseqContext::TUnreviewed CBioseqContext::GetUnreviewedType ( void  ) const
inline

Definition at line 670 of file context.hpp.

References m_fUnreviewed.

◆ GetUnverifiedType()

CBioseqContext::TUnverified CBioseqContext::GetUnverifiedType ( void  ) const
inline

Definition at line 664 of file context.hpp.

References m_fUnverified.

◆ GetWGSMasterAccn()

const string& CBioseqContext::GetWGSMasterAccn ( void  ) const
inline

Definition at line 149 of file context.hpp.

References m_WGSMasterAccn.

◆ GetWGSMasterName()

const string& CBioseqContext::GetWGSMasterName ( void  ) const
inline

Definition at line 150 of file context.hpp.

References m_WGSMasterName.

◆ HasMultiIntervalGenes()

bool CBioseqContext::HasMultiIntervalGenes ( void  ) const

◆ HasOperon()

bool CBioseqContext::HasOperon ( void  ) const

◆ HasParts()

bool CBioseqContext::HasParts ( void  ) const
inline

Definition at line 126 of file context.hpp.

References m_HasParts.

Referenced by DoContigStyle().

◆ IsBioseqInSameTopLevelSeqEntry()

bool CBioseqContext::IsBioseqInSameTopLevelSeqEntry ( const CBioseq_Handle seq)
inline

Definition at line 542 of file context.hpp.

References CBioseq_Handle::GetTopLevelEntry(), and m_Handle.

◆ IsCrossKingdom()

bool CBioseqContext::IsCrossKingdom ( void  ) const

◆ IsDDBJ()

bool CBioseqContext::IsDDBJ ( void  ) const
inline

Definition at line 183 of file context.hpp.

References m_IsDDBJ.

Referenced by CFeatureItem::x_AddQualsGene().

◆ IsDelta()

bool CBioseqContext::IsDelta ( void  ) const
inline

Definition at line 143 of file context.hpp.

References CSeq_inst_Base::eRepr_delta, and m_Repr.

Referenced by DoContigStyle(), x_Init(), and x_IsDeltaLitOnly().

◆ IsDeltaLitOnly()

bool CBioseqContext::IsDeltaLitOnly ( void  ) const
inline

Definition at line 144 of file context.hpp.

References m_IsDeltaLitOnly.

Referenced by DoContigStyle().

◆ IsEMBL()

bool CBioseqContext::IsEMBL ( void  ) const
inline

Definition at line 182 of file context.hpp.

References m_IsEMBL.

Referenced by CFeatureItem::x_AddQualsGene().

◆ IsEncode()

bool CBioseqContext::IsEncode ( void  ) const
inline

Definition at line 633 of file context.hpp.

References m_Encode, and CConstRef< C, Locker >::NotEmpty().

Referenced by GetEncode().

◆ IsGbGenomeProject()

bool CBioseqContext::IsGbGenomeProject ( void  ) const
inline

Definition at line 189 of file context.hpp.

References m_IsGbGenomeProject.

◆ IsGED()

bool CBioseqContext::IsGED ( void  ) const
inline

Definition at line 180 of file context.hpp.

References m_IsGED.

◆ IsGenbank()

bool CBioseqContext::IsGenbank ( void  ) const
inline

Definition at line 181 of file context.hpp.

References m_IsGenbank.

◆ IsGenbankFormat()

bool CBioseqContext::IsGenbankFormat ( void  ) const
inline

Definition at line 746 of file context.hpp.

References Config().

◆ IsGenomeAssembly()

bool CBioseqContext::IsGenomeAssembly ( void  ) const
inline

Definition at line 652 of file context.hpp.

References m_IsGenomeAssembly.

◆ IsHup()

bool CBioseqContext::IsHup ( void  ) const
inline

Definition at line 243 of file context.hpp.

References m_IsHup.

◆ IsInGPS()

bool CBioseqContext::IsInGPS ( void  ) const
inline

Definition at line 176 of file context.hpp.

References m_IsInGPS.

◆ IsInNucProt()

bool CBioseqContext::IsInNucProt ( void  ) const
inline

Definition at line 177 of file context.hpp.

References m_IsInNucProt.

◆ IsInSGS()

bool CBioseqContext::IsInSGS ( void  ) const
inline

Definition at line 175 of file context.hpp.

References m_IsInSGS.

◆ IsJournalScan()

bool CBioseqContext::IsJournalScan ( void  ) const
inline

Definition at line 187 of file context.hpp.

References m_IsJournalScan.

◆ IsNcbiCONDiv()

bool CBioseqContext::IsNcbiCONDiv ( void  ) const
inline

Definition at line 190 of file context.hpp.

References m_IsNcbiCONDiv.

◆ IsNcbiGenomes()

bool CBioseqContext::IsNcbiGenomes ( void  ) const
inline

Definition at line 191 of file context.hpp.

References m_IsNcbiGenomes.

◆ IsNuc()

bool CBioseqContext::IsNuc ( void  ) const
inline

Definition at line 115 of file context.hpp.

References m_IsProt.

◆ IsPart()

bool CBioseqContext::IsPart ( void  ) const
inline

Definition at line 129 of file context.hpp.

References m_IsPart.

◆ IsPatent()

bool CBioseqContext::IsPatent ( void  ) const
inline

Definition at line 188 of file context.hpp.

References m_IsPatent.

◆ IsPDB()

bool CBioseqContext::IsPDB ( void  ) const
inline

Definition at line 184 of file context.hpp.

References m_IsPDB.

◆ IsProt()

bool CBioseqContext::IsProt ( void  ) const
inline

◆ IsRefSeq()

bool CBioseqContext::IsRefSeq ( void  ) const
inline

Definition at line 194 of file context.hpp.

References m_IsRefSeq.

Referenced by x_Init().

◆ IsRSCompleteGenomic()

bool CBioseqContext::IsRSCompleteGenomic ( void  ) const
inline

Definition at line 554 of file context.hpp.

References CSeq_id::eAcc_refseq_chromosome, and m_RefseqInfo.

◆ IsRSContig()

bool CBioseqContext::IsRSContig ( void  ) const
inline

Definition at line 584 of file context.hpp.

References CSeq_id::eAcc_refseq_contig, and m_RefseqInfo.

◆ IsRSIncompleteGenomic()

bool CBioseqContext::IsRSIncompleteGenomic ( void  ) const
inline

Definition at line 560 of file context.hpp.

References CSeq_id::eAcc_refseq_genomic, and m_RefseqInfo.

◆ IsRSIntermedWGS()

bool CBioseqContext::IsRSIntermedWGS ( void  ) const
inline

Definition at line 590 of file context.hpp.

References CSeq_id::eAcc_refseq_wgs_intermed, and m_RefseqInfo.

◆ IsRSMRna()

bool CBioseqContext::IsRSMRna ( void  ) const
inline

Definition at line 566 of file context.hpp.

References CSeq_id::eAcc_refseq_mrna, and m_RefseqInfo.

◆ IsRSNonCodingRna()

bool CBioseqContext::IsRSNonCodingRna ( void  ) const
inline

Definition at line 572 of file context.hpp.

References CSeq_id::eAcc_refseq_ncrna, and m_RefseqInfo.

◆ IsRSPredictedMRna()

bool CBioseqContext::IsRSPredictedMRna ( void  ) const
inline

Definition at line 596 of file context.hpp.

References CSeq_id::eAcc_refseq_mrna_predicted, and m_RefseqInfo.

◆ IsRSPredictedNCRna()

bool CBioseqContext::IsRSPredictedNCRna ( void  ) const
inline

Definition at line 602 of file context.hpp.

References CSeq_id::eAcc_refseq_ncrna_predicted, and m_RefseqInfo.

◆ IsRSPredictedProtein()

bool CBioseqContext::IsRSPredictedProtein ( void  ) const
inline

Definition at line 608 of file context.hpp.

References CSeq_id::eAcc_refseq_prot_predicted, and m_RefseqInfo.

◆ IsRSProtein()

bool CBioseqContext::IsRSProtein ( void  ) const
inline

Definition at line 578 of file context.hpp.

References CSeq_id::eAcc_refseq_prot, and m_RefseqInfo.

◆ IsRSUniqueProt()

bool CBioseqContext::IsRSUniqueProt ( void  ) const
inline

Definition at line 627 of file context.hpp.

References CSeq_id::eAcc_refseq_unique_prot.

◆ IsRSWGSNuc()

bool CBioseqContext::IsRSWGSNuc ( void  ) const
inline

Definition at line 614 of file context.hpp.

References CSeq_id::eAcc_refseq_wgs_nuc, CSeq_id::fAcc_master, and m_RefseqInfo.

◆ IsRSWGSProt()

bool CBioseqContext::IsRSWGSProt ( void  ) const
inline

Definition at line 621 of file context.hpp.

References CSeq_id::eAcc_refseq_wgs_prot, and m_RefseqInfo.

◆ IsSegmented()

bool CBioseqContext::IsSegmented ( void  ) const
inline

Definition at line 125 of file context.hpp.

References CSeq_inst_Base::eRepr_seg, and m_Repr.

Referenced by DoContigStyle(), x_HasParts(), and x_Init().

◆ IsSeqIdInSameTopLevelSeqEntry()

bool CBioseqContext::IsSeqIdInSameTopLevelSeqEntry ( const CSeq_id seq_id)
inline

Definition at line 548 of file context.hpp.

References CScope::GetBioseqHandleFromTSE(), GetScope(), and m_Handle.

◆ IsSP()

bool CBioseqContext::IsSP ( void  ) const
inline

Definition at line 185 of file context.hpp.

References m_IsSP.

◆ IsTLS()

bool CBioseqContext::IsTLS ( void  ) const
inline

Definition at line 159 of file context.hpp.

References m_IsTLS.

◆ IsTLSMaster()

bool CBioseqContext::IsTLSMaster ( void  ) const
inline

Definition at line 160 of file context.hpp.

References m_IsTLSMaster.

◆ IsTPA()

bool CBioseqContext::IsTPA ( void  ) const
inline

Definition at line 186 of file context.hpp.

References m_IsTPA.

◆ IsTSA()

bool CBioseqContext::IsTSA ( void  ) const
inline

Definition at line 153 of file context.hpp.

References m_IsTSA.

◆ IsTSAMaster()

bool CBioseqContext::IsTSAMaster ( void  ) const
inline

Definition at line 154 of file context.hpp.

References m_IsTSAMaster.

◆ IsUnverified()

bool CBioseqContext::IsUnverified ( void  ) const
inline

Definition at line 658 of file context.hpp.

References fUnverified_None, and m_fUnverified.

◆ IsWGS()

bool CBioseqContext::IsWGS ( void  ) const
inline

Definition at line 147 of file context.hpp.

References m_IsWGS.

◆ IsWGSMaster()

bool CBioseqContext::IsWGSMaster ( void  ) const
inline

Definition at line 148 of file context.hpp.

References m_IsWGSMaster.

◆ SetAnnotSelector()

SAnnotSelector & CBioseqContext::SetAnnotSelector ( void  )
inline

Definition at line 713 of file context.hpp.

References m_FFCtx, and CFlatFileContext::SetAnnotSelector().

Referenced by CFlatGatherer::x_GatherReferences(), and x_Init().

◆ SetMaster()

void CBioseqContext::SetMaster ( CMasterContext mctx)
inline

Definition at line 537 of file context.hpp.

References m_Master, and CRef< C, Locker >::Reset().

◆ SetPDBCompoundForComment()

void CBioseqContext::SetPDBCompoundForComment ( bool  value)

Definition at line 491 of file context.cpp.

References m_UsePDBCompoundForComment, and value.

◆ SetRefCache()

void CBioseqContext::SetRefCache ( vector< string > *  rc)
inline

Definition at line 282 of file context.hpp.

References m_RefCache.

Referenced by CFlatGatherer::x_DoMultipleSections(), and CFlatGatherer::x_GatherBioseq().

◆ SetReferences()

TReferences& CBioseqContext::SetReferences ( void  )
inline

Definition at line 164 of file context.hpp.

References m_References.

Referenced by CFlatGatherer::x_GatherReferences().

◆ ShowAnnotCommentAsCOMMENT()

bool CBioseqContext::ShowAnnotCommentAsCOMMENT ( ) const

◆ ShowGBBSource()

bool CBioseqContext::ShowGBBSource ( void  ) const
inline

Definition at line 173 of file context.hpp.

References m_ShowGBBSource.

◆ ThrowIfCanceled()

void CBioseqContext::ThrowIfCanceled ( void  ) const
inline

Checks if CFlatFileConfig has an ICanceled, and throws if it indicates cancellation.

Definition at line 755 of file context.hpp.

References Config(), and CFlatFileConfig::ThrowIfCanceled().

◆ UsePDBCompoundForComment()

bool CBioseqContext::UsePDBCompoundForComment ( void  ) const

Definition at line 485 of file context.cpp.

References m_UsePDBCompoundForComment.

◆ UsingSeqEntryIndex()

bool CBioseqContext::UsingSeqEntryIndex ( void  ) const
inline

◆ x_CheckForShowComments()

void CBioseqContext::x_CheckForShowComments ( ) const
private

◆ x_GetMasterForPart()

CBioseq_Handle CBioseqContext::x_GetMasterForPart ( void  ) const
private

◆ x_GetMolInfo()

const CMolInfo * CBioseqContext::x_GetMolInfo ( void  ) const
private

Definition at line 956 of file context.cpp.

References CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::GetMolinfo(), and m_Handle.

Referenced by x_Init().

◆ x_GetPartNumber()

SIZE_TYPE CBioseqContext::x_GetPartNumber ( void  )
private

Definition at line 1046 of file context.cpp.

References CMasterContext::GetPartNumber(), m_Handle, and m_Master.

Referenced by x_Init().

◆ x_GetRepr()

CSeq_inst::TRepr CBioseqContext::x_GetRepr ( void  ) const
private

◆ x_HasOperon()

bool CBioseqContext::x_HasOperon ( void  ) const
private

Definition at line 744 of file context.cpp.

References CSeqFeatData::eSubtype_operon, CBioseq_Handle::GetScope(), m_Handle, and m_Location.

Referenced by HasOperon().

◆ x_HasParts()

bool CBioseqContext::x_HasParts ( void  ) const
private

◆ x_Init()

void CBioseqContext::x_Init ( const CBioseq_Handle seq,
const CSeq_loc user_loc 
)
private

◆ x_IsDeltaLitOnly()

bool CBioseqContext::x_IsDeltaLitOnly ( void  ) const
private

◆ x_IsInGPS()

bool CBioseqContext::x_IsInGPS ( void  ) const
private

◆ x_IsInNucProt()

bool CBioseqContext::x_IsInNucProt ( void  ) const
private

◆ x_IsInSGS()

bool CBioseqContext::x_IsInSGS ( void  ) const
private

◆ x_IsPart()

bool CBioseqContext::x_IsPart ( void  ) const
private

◆ x_SetAuthorizedAccess()

void CBioseqContext::x_SetAuthorizedAccess ( const CUser_object uo)
private

◆ x_SetDataFromUserObjects()

void CBioseqContext::x_SetDataFromUserObjects ( void  )
private

◆ x_SetEncode()

void CBioseqContext::x_SetEncode ( const CUser_object uo)
private

◆ x_SetFiletrackURL()

void CBioseqContext::x_SetFiletrackURL ( const CUser_object uo)
private

◆ x_SetHasMultiIntervalGenes()

void CBioseqContext::x_SetHasMultiIntervalGenes ( void  ) const
private

◆ x_SetId()

void CBioseqContext::x_SetId ( void  )
private

Definition at line 767 of file context.cpp.

References CSeq_id::Assign(), CTextseq_id_Base::CanGetAccession(), CTextseq_id_Base::CanGetName(), NStr::CompareCase(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeqdesc_Base::e_User, CSeq_id::eAcc_division_mask, CSeq_id::eAcc_gb_con, CSeq_id::eAcc_gb_genome, CSeq_id::eAcc_gb_segset, CSeq_id::eAcc_gsdb_dirsub, CSeq_id::eAcc_wgs, CSeq_id::eContent, eGetId_Best, NStr::Equal(), CSeq_inst_Base::eRepr_virtual, CMolInfo_Base::eTech_targeted, CMolInfo_Base::eTech_tsa, CSeq_id::fAcc_master, CTextseq_id_Base::GetAccession(), CBioseq_Handle::GetBioseqCore(), GetId(), CBioseq_Base::GetId(), CSeq_id::GetLabel(), CTextseq_id_Base::GetName(), GetSeqId(), CObject_id_Base::GetStr(), GetTech(), CUser_object_Base::GetType(), CObject_id_Base::IsStr(), ITERATE, kEmptyStr, m_Accession, m_Gi, m_Handle, m_IsDDBJ, m_IsEMBL, m_IsGbGenomeProject, m_IsGED, m_IsGenbank, m_IsGI, m_IsJournalScan, m_IsNcbiCONDiv, m_IsNcbiGenomes, m_IsPatent, m_IsPDB, m_IsRefSeq, m_IsSP, m_IsTLS, m_IsTLSMaster, m_IsTPA, m_IsTSA, m_IsTSAMaster, m_IsWGS, m_IsWGSMaster, m_PatSeqid, m_PrimaryId, m_RefseqInfo, m_Repr, m_ShowGBBSource, m_TLSMasterAccn, m_TLSMasterName, m_TSAMasterAccn, m_TSAMasterName, m_WGSMasterAccn, m_WGSMasterName, and CRef< C, Locker >::Reset().

Referenced by x_Init().

◆ x_SetLocation()

void CBioseqContext::x_SetLocation ( const CSeq_loc user_loc = nullptr)
private

◆ x_SetMapper()

void CBioseqContext::x_SetMapper ( const CSeq_loc loc)
private

◆ x_SetOpticalMapPoints()

void CBioseqContext::x_SetOpticalMapPoints ( void  )
private

◆ x_SetTaxname()

void CBioseqContext::x_SetTaxname ( void  ) const
private

Member Data Documentation

◆ m_Accession

string CBioseqContext::m_Accession
private

Definition at line 316 of file context.hpp.

Referenced by GetAccession(), and x_SetId().

◆ m_AuthorizedAccess

string CBioseqContext::m_AuthorizedAccess
private

Definition at line 327 of file context.hpp.

Referenced by GetAuthorizedAccess(), and x_SetAuthorizedAccess().

◆ m_BasemodURLs

vector< string > CBioseqContext::m_BasemodURLs
private

Definition at line 326 of file context.hpp.

Referenced by GetBasemodURLs(), and x_SetFiletrackURL().

◆ m_Encode

CConstRef<CUser_object> CBioseqContext::m_Encode
private

Definition at line 384 of file context.hpp.

Referenced by GetEncode(), IsEncode(), and x_SetEncode().

◆ m_FeatTree

feature::CFeatTree CBioseqContext::m_FeatTree
private

Definition at line 314 of file context.hpp.

Referenced by GetFeatTree().

◆ m_FFCtx

CFlatFileContext& CBioseqContext::m_FFCtx
private

◆ m_FiletrackURL

string CBioseqContext::m_FiletrackURL
private

Definition at line 325 of file context.hpp.

Referenced by GetFiletrackURL(), and x_SetFiletrackURL().

◆ m_FinishingStatus

string CBioseqContext::m_FinishingStatus
private

Definition at line 323 of file context.hpp.

Referenced by GetFinishingStatus(), and x_SetDataFromUserObjects().

◆ m_fUnreviewed

TUnreviewed CBioseqContext::m_fUnreviewed
private

Definition at line 380 of file context.hpp.

Referenced by GetUnreviewedType(), and x_SetDataFromUserObjects().

◆ m_fUnverified

TUnverified CBioseqContext::m_fUnverified
private

Definition at line 379 of file context.hpp.

Referenced by GetUnverifiedType(), IsUnverified(), and x_SetDataFromUserObjects().

◆ m_Gi

TGi CBioseqContext::m_Gi
private

Definition at line 371 of file context.hpp.

Referenced by GetGI(), GetPreferredSynonym(), and x_SetId().

◆ m_Handle

CBioseq_Handle CBioseqContext::m_Handle
private

◆ m_HasMultiIntervalGenes

bool CBioseqContext::m_HasMultiIntervalGenes
mutableprivate

Definition at line 375 of file context.hpp.

Referenced by HasMultiIntervalGenes(), and x_SetHasMultiIntervalGenes().

◆ m_HasOperon

bool CBioseqContext::m_HasOperon
mutableprivate

Definition at line 374 of file context.hpp.

Referenced by HasOperon().

◆ m_HasParts

bool CBioseqContext::m_HasParts
private

Definition at line 338 of file context.hpp.

Referenced by HasParts(), and x_Init().

◆ m_IsCrossKingdom

bool CBioseqContext::m_IsCrossKingdom
mutableprivate

Definition at line 377 of file context.hpp.

Referenced by IsCrossKingdom(), and x_SetTaxname().

◆ m_IsDDBJ

bool CBioseqContext::m_IsDDBJ
private

Definition at line 352 of file context.hpp.

Referenced by IsDDBJ(), and x_SetId().

◆ m_IsDeltaLitOnly

bool CBioseqContext::m_IsDeltaLitOnly
private

Definition at line 343 of file context.hpp.

Referenced by IsDeltaLitOnly(), and x_Init().

◆ m_IsEMBL

bool CBioseqContext::m_IsEMBL
private

Definition at line 351 of file context.hpp.

Referenced by IsEMBL(), and x_SetId().

◆ m_IsGbGenomeProject

bool CBioseqContext::m_IsGbGenomeProject
private

Definition at line 359 of file context.hpp.

Referenced by IsGbGenomeProject(), and x_SetId().

◆ m_IsGED

bool CBioseqContext::m_IsGED
private

Definition at line 349 of file context.hpp.

Referenced by IsGED(), and x_SetId().

◆ m_IsGenbank

bool CBioseqContext::m_IsGenbank
private

Definition at line 350 of file context.hpp.

Referenced by IsGenbank(), and x_SetId().

◆ m_IsGenomeAssembly

bool CBioseqContext::m_IsGenomeAssembly
private

Definition at line 376 of file context.hpp.

Referenced by IsGenomeAssembly(), and x_SetDataFromUserObjects().

◆ m_IsGI

bool CBioseqContext::m_IsGI
private

Definition at line 363 of file context.hpp.

Referenced by x_SetId().

◆ m_IsHup

bool CBioseqContext::m_IsHup
private

Definition at line 370 of file context.hpp.

Referenced by IsHup().

◆ m_IsInGPS

bool CBioseqContext::m_IsInGPS
private

Definition at line 347 of file context.hpp.

Referenced by IsInGPS(), and x_Init().

◆ m_IsInNucProt

bool CBioseqContext::m_IsInNucProt
private

Definition at line 348 of file context.hpp.

Referenced by IsInNucProt(), and x_Init().

◆ m_IsInSGS

bool CBioseqContext::m_IsInSGS
private

Definition at line 346 of file context.hpp.

Referenced by IsInSGS(), and x_Init().

◆ m_IsJournalScan

bool CBioseqContext::m_IsJournalScan
private

Definition at line 356 of file context.hpp.

Referenced by IsJournalScan(), and x_SetId().

◆ m_IsNcbiCONDiv

bool CBioseqContext::m_IsNcbiCONDiv
private

Definition at line 360 of file context.hpp.

Referenced by IsNcbiCONDiv(), and x_SetId().

◆ m_IsNcbiGenomes

bool CBioseqContext::m_IsNcbiGenomes
private

Definition at line 361 of file context.hpp.

Referenced by IsNcbiGenomes(), and x_SetId().

◆ m_IsPart

bool CBioseqContext::m_IsPart
private

Definition at line 340 of file context.hpp.

Referenced by IsPart(), and x_Init().

◆ m_IsPatent

bool CBioseqContext::m_IsPatent
private

Definition at line 362 of file context.hpp.

Referenced by IsPatent(), and x_SetId().

◆ m_IsPDB

bool CBioseqContext::m_IsPDB
private

Definition at line 353 of file context.hpp.

Referenced by IsPDB(), and x_SetId().

◆ m_IsProt

bool CBioseqContext::m_IsProt
private

Definition at line 345 of file context.hpp.

Referenced by IsNuc(), IsProt(), and x_Init().

◆ m_IsRefSeq

bool CBioseqContext::m_IsRefSeq
private

Definition at line 357 of file context.hpp.

Referenced by IsRefSeq(), and x_SetId().

◆ m_IsSP

bool CBioseqContext::m_IsSP
private

Definition at line 354 of file context.hpp.

Referenced by IsSP(), and x_SetId().

◆ m_IsTLS

bool CBioseqContext::m_IsTLS
private

Definition at line 368 of file context.hpp.

Referenced by IsTLS(), and x_SetId().

◆ m_IsTLSMaster

bool CBioseqContext::m_IsTLSMaster
private

Definition at line 369 of file context.hpp.

Referenced by IsTLSMaster(), and x_SetId().

◆ m_IsTPA

bool CBioseqContext::m_IsTPA
private

Definition at line 355 of file context.hpp.

Referenced by IsTPA(), and x_SetId().

◆ m_IsTSA

bool CBioseqContext::m_IsTSA
private

Definition at line 366 of file context.hpp.

Referenced by IsTSA(), and x_SetId().

◆ m_IsTSAMaster

bool CBioseqContext::m_IsTSAMaster
private

Definition at line 367 of file context.hpp.

Referenced by IsTSAMaster(), and x_SetId().

◆ m_IsWGS

bool CBioseqContext::m_IsWGS
private

Definition at line 364 of file context.hpp.

Referenced by IsWGS(), and x_SetId().

◆ m_IsWGSMaster

bool CBioseqContext::m_IsWGSMaster
private

Definition at line 365 of file context.hpp.

Referenced by IsWGSMaster(), and x_SetId().

◆ m_Location

CConstRef<CSeq_loc> CBioseqContext::m_Location
private

Definition at line 387 of file context.hpp.

Referenced by GetLocation(), x_HasOperon(), and x_SetLocation().

◆ m_Mapper

CRef<CSeq_loc_Mapper> CBioseqContext::m_Mapper
private

Definition at line 388 of file context.hpp.

Referenced by GetMapper(), and x_SetMapper().

◆ m_Master

CRef<CMasterContext> CBioseqContext::m_Master
private

◆ m_Mol

CSeq_inst::TMol CBioseqContext::m_Mol
private

Definition at line 334 of file context.hpp.

Referenced by GetMol(), and x_Init().

◆ m_Molinfo

CConstRef<CMolInfo> CBioseqContext::m_Molinfo
private

Definition at line 335 of file context.hpp.

Referenced by GetBiomol(), GetMolinfo(), GetTech(), and x_Init().

◆ m_NextHandle

CBioseq_Handle CBioseqContext::m_NextHandle
private

Definition at line 313 of file context.hpp.

Referenced by GetNextHandle().

◆ m_PartNumber

SIZE_TYPE CBioseqContext::m_PartNumber
private

Definition at line 341 of file context.hpp.

Referenced by GetPartNumber(), and x_Init().

◆ m_PatSeqid

int CBioseqContext::m_PatSeqid
private

Definition at line 373 of file context.hpp.

Referenced by GetPatentSeqId(), and x_SetId().

◆ m_pOpticalMapPoints

const CPacked_seqpnt* CBioseqContext::m_pOpticalMapPoints
private

Definition at line 328 of file context.hpp.

Referenced by GetOpticalMapPoints(), and x_SetOpticalMapPoints().

◆ m_pOpticalMapPointsDestroyer

unique_ptr<CPacked_seqpnt> CBioseqContext::m_pOpticalMapPointsDestroyer
private

Definition at line 331 of file context.hpp.

Referenced by x_SetOpticalMapPoints().

◆ m_PrevHandle

CBioseq_Handle CBioseqContext::m_PrevHandle
private

Definition at line 311 of file context.hpp.

Referenced by GetPrevHandle().

◆ m_PrimaryId

CRef<CSeq_id> CBioseqContext::m_PrimaryId
private

Definition at line 315 of file context.hpp.

Referenced by GetPreferredSynonym(), GetPrimaryId(), x_SetId(), and x_SetLocation().

◆ m_RefCache

vector<string>* CBioseqContext::m_RefCache
mutableprivate

Definition at line 391 of file context.hpp.

Referenced by GetRefCache(), and SetRefCache().

◆ m_References

TReferences CBioseqContext::m_References
private

Definition at line 386 of file context.hpp.

Referenced by GetReferences(), and SetReferences().

◆ m_RefseqInfo

unsigned int CBioseqContext::m_RefseqInfo
private

◆ m_Repr

CSeq_inst::TRepr CBioseqContext::m_Repr
private

Definition at line 333 of file context.hpp.

Referenced by GetRepr(), IsDelta(), IsSegmented(), x_Init(), x_IsPart(), and x_SetId().

◆ m_ShowAnnotCommentAsCOMMENT

bool CBioseqContext::m_ShowAnnotCommentAsCOMMENT
mutableprivate

Definition at line 381 of file context.hpp.

Referenced by ShowAnnotCommentAsCOMMENT(), x_CheckForShowComments(), and x_Init().

◆ m_ShowAnnotCommentAsCOMMENT_checked

bool CBioseqContext::m_ShowAnnotCommentAsCOMMENT_checked
mutableprivate

Definition at line 382 of file context.hpp.

Referenced by ShowAnnotCommentAsCOMMENT(), x_CheckForShowComments(), and x_Init().

◆ m_ShowGBBSource

bool CBioseqContext::m_ShowGBBSource
private

Definition at line 372 of file context.hpp.

Referenced by ShowGBBSource(), and x_SetId().

◆ m_Taxname

string CBioseqContext::m_Taxname
mutableprivate

Definition at line 324 of file context.hpp.

Referenced by GetTaxname(), and x_SetTaxname().

◆ m_TLSeqEntryCtx

CRef<CTopLevelSeqEntryContext> CBioseqContext::m_TLSeqEntryCtx
private

Definition at line 393 of file context.hpp.

Referenced by CanGetTLSeqEntryCtx(), and GetTLSeqEntryCtx().

◆ m_TLSMasterAccn

string CBioseqContext::m_TLSMasterAccn
private

Definition at line 321 of file context.hpp.

Referenced by GetTLSMasterAccn(), and x_SetId().

◆ m_TLSMasterName

string CBioseqContext::m_TLSMasterName
private

Definition at line 322 of file context.hpp.

Referenced by GetTLSMasterName(), and x_SetId().

◆ m_TSAMasterAccn

string CBioseqContext::m_TSAMasterAccn
private

Definition at line 319 of file context.hpp.

Referenced by GetTSAMasterAccn(), and x_SetId().

◆ m_TSAMasterName

string CBioseqContext::m_TSAMasterName
private

Definition at line 320 of file context.hpp.

Referenced by GetTSAMasterName(), and x_SetId().

◆ m_UsePDBCompoundForComment

bool CBioseqContext::m_UsePDBCompoundForComment
mutableprivate

Definition at line 378 of file context.hpp.

Referenced by SetPDBCompoundForComment(), and UsePDBCompoundForComment().

◆ m_Virtual

CBioseq_Handle CBioseqContext::m_Virtual
private

Definition at line 389 of file context.hpp.

Referenced by ~CBioseqContext().

◆ m_WGSMasterAccn

string CBioseqContext::m_WGSMasterAccn
private

Definition at line 317 of file context.hpp.

Referenced by GetWGSMasterAccn(), and x_SetId().

◆ m_WGSMasterName

string CBioseqContext::m_WGSMasterName
private

Definition at line 318 of file context.hpp.

Referenced by GetWGSMasterName(), and x_SetId().


The documentation for this class was generated from the following files:
Modified on Sat Dec 09 04:44:04 2023 by modify_doxy.py rev. 669887