CBioseqContext Class Reference

Search Toolkit Book for CBioseqContext

#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< CReferenceItem >	TRef
typedef vector< TRef >	TReferences
typedef CRange< TSeqPos >	TRange
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< Uint8 >	TCounter
	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_Handle &	GetPrevHandle (void)
CBioseq_Handle &	GetHandle (void)
const CBioseq_Handle &	GetHandle (void) const
CBioseq_Handle &	GetNextHandle (void)
CScope &	GetScope (void) const
feature::CFeatTree &	GetFeatTree (void)
bool	UsingSeqEntryIndex (void) const
const CRef< CSeqEntryIndex >	GetSeqEntryIndex (void) const
CSeq_id *	GetPrimaryId (void)
CSeq_id_Handle	GetPreferredSynonym (const CSeq_id &id) const
const string &	GetAccession (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 CMolInfo *	GetMolinfo (void) const
CMolInfo::TTech	GetTech (void) const
CMolInfo::TBiomol	GetBiomol (void) const
const CBioseq::TId &	GetBioseqIds (void) const
bool	IsSegmented (void) const
bool	HasParts (void) const
bool	IsPart (void) const
SIZE_TYPE	GetPartNumber (void) const
SIZE_TYPE	GetTotalNumParts (void) const
CMasterContext &	GetMaster (void)
bool	CanGetMaster (void) const
void	SetMaster (CMasterContext &mctx)
CTopLevelSeqEntryContext &	GetTLSeqEntryCtx (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 string &	GetWGSMasterAccn (void) const
const string &	GetWGSMasterName (void) const
bool	IsTSA (void) const
bool	IsTSAMaster (void) const
const string &	GetTSAMasterAccn (void) const
const string &	GetTSAMasterName (void) const
bool	IsTLS (void) const
bool	IsTLSMaster (void) const
const string &	GetTLSMasterAccn (void) const
const string &	GetTLSMasterName (void) const
TReferences &	SetReferences (void)
const TReferences &	GetReferences (void) const
const CSeq_loc &	GetLocation (void) const
CSeq_loc_Mapper *	GetMapper (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_object &	GetEncode (void) const
const string &	GetFinishingStatus (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_block *	GetSubmitBlock (void) const
const CSeq_entry_Handle &	GetTopLevelEntry (void) const
const CFlatFileConfig &	Config (void) const
const SAnnotSelector *	GetAnnotSelector (void) const
SAnnotSelector &	SetAnnotSelector (void)
const CSeq_loc *	GetMasterLocation (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 string &	GetTaxname (void) const
	Empty string if unavailable. More...
const string &	GetFiletrackURL (void) const
	Empty if no Filetrack URL. More...
const vector< string > &	GetBasemodURLs (void) const
	Empty if no Basemod URLs. More...
const string &	GetAuthorizedAccess (void) const
const CPacked_seqpnt *	GetOpticalMapPoints (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...
CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...
bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...
bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...
bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...
bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...
void	AddReference (void) const
	Add reference to object. More...
void	RemoveReference (void) const
	Remove reference to object. More...
void	ReleaseReference (void) const
	Remove reference without deleting object. More...
virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...
virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...
void *	operator new (size_t size)
	Define new operator for memory allocation. More...
void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...
void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...
void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...
void *	operator new (size_t size, void *place)
	Define new operator. More...
void	operator delete (void *ptr, void *place)
	Define delete operator. More...
void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...
void	operator delete (void *ptr, CObjectMemoryPool *place)
	Define delete operator. More...
virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...
Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)
virtual	~CDebugDumpable (void)
void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
void	DumpToConsole (void) const

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 CMolInfo *	x_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_id >	m_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< string >	m_BasemodURLs
string	m_AuthorizedAccess
const CPacked_seqpnt *	m_pOpticalMapPoints
unique_ptr< CPacked_seqpnt >	m_pOpticalMapPointsDestroyer
CSeq_inst::TRepr	m_Repr
CSeq_inst::TMol	m_Mol
CConstRef< CMolInfo >	m_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_object >	m_Encode
TReferences	m_References
CConstRef< CSeq_loc >	m_Location
CRef< CSeq_loc_Mapper >	m_Mapper
CBioseq_Handle	m_Virtual
CFlatFileContext &	m_FFCtx
vector< string > *	m_RefCache
CRef< CMasterContext >	m_Master
CRef< CTopLevelSeqEntryContext >	m_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

typedef CRange<TSeqPos> CBioseqContext::TRange

Definition at line 78 of file context.hpp.

TRef

typedef CRef<CReferenceItem> CBioseqContext::TRef

Definition at line 76 of file context.hpp.

TReferences

typedef vector<TRef> CBioseqContext::TReferences

Definition at line 77 of file context.hpp.

TUnreviewed

typedef Int8 CBioseqContext::TUnreviewed

Definition at line 239 of file context.hpp.

TUnverified

typedef Int8 CBioseqContext::TUnverified

Definition at line 230 of file context.hpp.

Member Enumeration Documentation

FUnreviewed

enum CBioseqContext::FUnreviewed

Enumerator
fUnreviewed_None
fUnreviewed_Unannotated

Definition at line 232 of file context.hpp.

FUnverified

enum CBioseqContext::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

)

Definition at line 202 of file context.cpp.

References CBioseq_Handle::GetEditHandle(), m_Virtual, and CBioseq_EditHandle::Remove().

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

Definition at line 689 of file context.hpp.

References CFlatFileContext::GetConfig(), and m_FFCtx.

Referenced by DoContigStyle(), CGenbankFormatter::FormatAccession(), CGenbankFormatter::FormatDBSource(), CGenbankFormatter::FormatGenomeProject(), CGenbankFormatter::FormatKeywords(), CGenbankFormatter::FormatPrimary(), CGenbankFormatter::FormatTSA(), CGenbankFormatter::FormatWGS(), IsGenbankFormat(), s_FormatRegularSequencePiece(), s_GetLinkFeatureKey(), ThrowIfCanceled(), CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddFTableRnaQuals(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualProteinId(), CGenbankFormatter::x_Authors(), CGenbankFormatter::x_Consortium(), CDBSourceItem::x_FormatDBSourceID(), CFeatureItem::x_FormatNoteQuals(), CDBSourceItem::x_FormatPDBSource(), CFeatureItem::x_FormatQuals(), CFlatGatherer::x_GatherSourceFeatures(), CGenbankFormatter::x_Journal(), CGenbankFormatter::x_Reference(), CGenbankFormatter::x_SmartWrapQuals(), and CGenbankFormatter::x_Title().

DoContigStyle()

bool CBioseqContext::DoContigStyle

(

void

)

const

Definition at line 1076 of file context.cpp.

References Config(), HasParts(), IsDelta(), IsDeltaLitOnly(), IsSegmented(), CFlatFileConfig::IsStyleContig(), and CFlatFileConfig::IsStyleNormal().

GetAccession()

const string& CBioseqContext::GetAccession ( void  ) const

inline

Definition at line 110 of file context.hpp.

References m_Accession.

Referenced by CGBSeqFormatter::FormatGap(), CGenbankFormatter::FormatSequence(), s_FormatRegularSequencePiece(), and x_SetMapper().

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

Definition at line 739 of file context.hpp.

References CMolInfo_Base::eBiomol_unknown, CMolInfo_Base::GetBiomol(), and m_Molinfo.

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

Definition at line 169 of file context.hpp.

References m_Location.

Referenced by CGenbankFormatter::FormatAccession(), CGenbankGatherer::x_DoSingleSection(), CFlatGatherer::x_GatherReferences(), and CFlatGatherer::x_GatherSequence().

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

Definition at line 210 of file context.cpp.

References eGetId_Best, CSeq_id_Handle::GetHandle(), GetId(), CBioseq_Handle::GetScope(), m_Gi, m_Handle, and m_PrimaryId.

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

Definition at line 117 of file context.hpp.

References m_Repr.

Referenced by x_CheckForShowComments(), CFlatGatherer::x_GatherCDSReferences(), and x_SetOpticalMapPoints().

GetScope()

CScope& CBioseqContext::GetScope ( void  ) const

inline

Definition at line 102 of file context.hpp.

References CBioseq_Handle::GetScope(), and m_Handle.

Referenced by IsSeqIdInSameTopLevelSeqEntry(), s_CombineRefs(), CFeatureItem::x_AddQualSeqfeatNote(), CFlatGatherer::x_BiosourcesEqualForMergingPurposes(), CGenbankGatherer::x_DoSingleSection(), CFlatGatherer::x_GatherCDSReferences(), CFlatGatherer::x_GatherReferences(), CFlatGatherer::x_GatherReferencesIdx(), CFlatGatherer::x_GatherSequence(), CFlatGatherer::x_MergeEqualBioSources(), x_SetMapper(), and CFlatGatherer::x_SubtractFromFocus().

GetSeqEntryIndex()

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

inline

Definition at line 682 of file context.hpp.

References CFlatFileContext::GetSeqEntryIndex(), and m_FFCtx.

Referenced by GetTaxname(), HasMultiIntervalGenes(), HasOperon(), and IsCrossKingdom().

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

Empty string if unavailable.

Definition at line 447 of file context.cpp.

References CSeqEntryIndex::GetBioseqIndex(), GetSeqEntryIndex(), CBioseqIndex::GetTaxname(), m_Handle, m_Taxname, UsingSeqEntryIndex(), and x_SetTaxname().

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

Definition at line 358 of file context.cpp.

References CSeqEntryIndex::GetBioseqIndex(), GetSeqEntryIndex(), CBioseqIndex::HasMultiIntervalGenes(), m_Handle, m_HasMultiIntervalGenes, UsingSeqEntryIndex(), and x_SetHasMultiIntervalGenes().

HasOperon()

bool CBioseqContext::HasOperon

(

void

)

const

Definition at line 751 of file context.cpp.

References CSeqEntryIndex::GetBioseqIndex(), GetSeqEntryIndex(), CBioseqIndex::HasOperon(), m_Handle, m_HasOperon, UsingSeqEntryIndex(), and x_HasOperon().

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

Definition at line 466 of file context.cpp.

References CSeqEntryIndex::GetBioseqIndex(), GetSeqEntryIndex(), CBioseqIndex::IsCrossKingdom(), m_Handle, m_IsCrossKingdom, UsingSeqEntryIndex(), and x_SetTaxname().

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

Definition at line 114 of file context.hpp.

References m_IsProt.

Referenced by CGenbankFormatter::FormatSequence(), CFlatGatherer::x_GatherCDSReferences(), and CFlatGatherer::x_GatherReferences().

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 rapidjson::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

Definition at line 676 of file context.cpp.

References m_ShowAnnotCommentAsCOMMENT, m_ShowAnnotCommentAsCOMMENT_checked, and x_CheckForShowComments().

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

Definition at line 676 of file context.hpp.

References m_FFCtx, and CFlatFileContext::UsingSeqEntryIndex().

Referenced by GetTaxname(), HasMultiIntervalGenes(), HasOperon(), and IsCrossKingdom().

x_CheckForShowComments()

void CBioseqContext::x_CheckForShowComments ( ) const

private

Definition at line 685 of file context.cpp.

References CSeq_annot_Base::C_Data::e_Ftable, CSeq_inst_Base::eRepr_map, CAnnot_descr_Base::Get(), CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::GetLabel(), GetRepr(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CAnnotdesc_Base::GetUser(), CUser_field_Base::IsSetData(), CUser_object_Base::IsSetData(), CUser_field_Base::IsSetLabel(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), CAnnotdesc_Base::IsUser(), ITERATE, m_Handle, m_ShowAnnotCommentAsCOMMENT, m_ShowAnnotCommentAsCOMMENT_checked, CSeq_annot_Handle::Seq_annot_GetDesc(), CSeq_annot_Handle::Seq_annot_IsSetDesc(), and SAnnotSelector::SetAnnotType().

Referenced by ShowAnnotCommentAsCOMMENT().

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

Definition at line 949 of file context.cpp.

References CSeq_inst_Base::eRepr_not_set, CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::IsSetInst_Repr(), and m_Handle.

Referenced by x_Init().

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

Definition at line 988 of file context.cpp.

References _ASSERT, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CBioseq_Handle::GetExactComplexityLevel(), IsSegmented(), and m_Handle.

Referenced by x_Init().

x_Init()

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

private

Definition at line 224 of file context.cpp.

References _ASSERT, CBioseq_Handle::GetInst_Mol(), CSeq_inst::IsAa(), IsDelta(), IsRefSeq(), IsSegmented(), CBioseq_Handle::IsSetInst(), m_FFCtx, m_HasParts, m_IsDeltaLitOnly, m_IsInGPS, m_IsInNucProt, m_IsInSGS, m_IsPart, m_IsProt, m_Master, m_Mol, m_Molinfo, m_PartNumber, m_Repr, m_ShowAnnotCommentAsCOMMENT, m_ShowAnnotCommentAsCOMMENT_checked, CConstRef< C, Locker >::Reset(), SetAnnotSelector(), CFlatFileContext::SetConfig(), CFlatFileConfig::SetRefSeqConventions(), SAnnotSelector::SetResolveAll(), x_GetMolInfo(), x_GetPartNumber(), x_GetRepr(), x_HasParts(), x_IsDeltaLitOnly(), x_IsInGPS(), x_IsInNucProt(), x_IsInSGS(), x_IsPart(), x_SetDataFromUserObjects(), x_SetId(), x_SetLocation(), and x_SetOpticalMapPoints().

Referenced by CBioseqContext().

x_IsDeltaLitOnly()

bool CBioseqContext::x_IsDeltaLitOnly ( void  ) const

private

Definition at line 1026 of file context.cpp.

References _ASSERT, CDelta_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CBioseq_Handle::GetInst_Ext(), CSeq_ext_Base::IsDelta(), IsDelta(), CSeq_loc_Base::IsNull(), CBioseq_Handle::IsSetInst_Ext(), ITERATE, and m_Handle.

Referenced by x_Init().

x_IsInGPS()

bool CBioseqContext::x_IsInGPS ( void  ) const

private

Definition at line 1060 of file context.cpp.

References CBioseq_set_Base::eClass_gen_prod_set, CBioseq_Handle::GetExactComplexityLevel(), and m_Handle.

Referenced by x_Init().

x_IsInNucProt()

bool CBioseqContext::x_IsInNucProt ( void  ) const

private

Definition at line 1068 of file context.cpp.

References CBioseq_set_Base::eClass_nuc_prot, CBioseq_Handle::GetExactComplexityLevel(), and m_Handle.

Referenced by x_Init().

x_IsInSGS()

bool CBioseqContext::x_IsInSGS ( void  ) const

private

Definition at line 1052 of file context.cpp.

References CBioseq_set_Base::eClass_small_genome_set, CBioseq_Handle::GetExactComplexityLevel(), and m_Handle.

Referenced by x_Init().

x_IsPart()

bool CBioseqContext::x_IsPart ( void  ) const

private

Definition at line 963 of file context.cpp.

References _ASSERT, CBioseq_set_Base::eClass_parts, CSeq_inst_Base::eRepr_const, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_virtual, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CSeq_entry_Handle::GetSet(), GetTopLevelEntry(), CSeq_entry_Handle::IsSeq(), CSeq_entry_Handle::IsSet(), CBioseq_set_Handle::IsSetClass(), m_Handle, and m_Repr.

Referenced by x_Init().

x_SetAuthorizedAccess()

void CBioseqContext::x_SetAuthorizedAccess ( const CUser_object &  uo )

private

Definition at line 537 of file context.cpp.

References NStr::EqualNocase(), FIELD_IS_SET_AND_IS, CUser_field_Base::GetData(), CUser_object::GetFieldRef(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), m_AuthorizedAccess, and Type.

Referenced by x_SetDataFromUserObjects().

x_SetDataFromUserObjects()

void CBioseqContext::x_SetDataFromUserObjects ( void  )

private

Definition at line 602 of file context.cpp.

References DEFINE_STATIC_ARRAY_MAP, CSeqdesc_Base::e_User, CUser_object::eObjectType_FileTrack, CUser_object::eObjectType_StructuredComment, CUser_object::eObjectType_Unreviewed, CUser_object::eObjectType_Unverified, NStr::EqualNocase(), fUnreviewed_Unannotated, fUnverified_Contaminant, fUnverified_Misassembled, fUnverified_None, fUnverified_Organism, fUnverified_SequenceOrAnnotation, CUser_field_Base::GetData(), CUser_object_Base::GetData(), CUser_field_Base::GetLabel(), CUser_object::GetObjectType(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CUser_field_Base::IsSetData(), CUser_object_Base::IsSetData(), CUser_field_Base::IsSetLabel(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), CUser_object::IsUnreviewedUnannotated(), CUser_object::IsUnverifiedContaminant(), CUser_object::IsUnverifiedFeature(), CUser_object::IsUnverifiedMisassembled(), CUser_object::IsUnverifiedOrganism(), ITERATE, m_FinishingStatus, m_fUnreviewed, m_fUnverified, m_Handle, m_IsGenomeAssembly, x_SetAuthorizedAccess(), x_SetEncode(), and x_SetFiletrackURL().

Referenced by x_Init().

x_SetEncode()

void CBioseqContext::x_SetEncode ( const CUser_object &  uo )

private

Definition at line 1092 of file context.cpp.

References NStr::EqualNocase(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), m_Encode, and CConstRef< C, Locker >::Reset().

Referenced by x_SetDataFromUserObjects().

x_SetFiletrackURL()

void CBioseqContext::x_SetFiletrackURL ( const CUser_object &  uo )

private

Definition at line 497 of file context.cpp.

References NStr::EqualNocase(), FIELD_IS_SET_AND_IS, FOR_EACH_STRING_IN_VECTOR, CUser_field_Base::GetData(), CUser_object::GetFieldRef(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_field_Base::C_Data::GetStrs(), CUser_object_Base::GetType(), m_BasemodURLs, m_FiletrackURL, str(), and Type.

Referenced by x_SetDataFromUserObjects().

x_SetHasMultiIntervalGenes()

void CBioseqContext::x_SetHasMultiIntervalGenes ( void  ) const

private

Definition at line 333 of file context.cpp.

References CSeq_loc_Base::e_Equiv, CSeqFeatData_Base::e_Gene, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CMappedFeat::GetLocation(), m_Handle, m_HasMultiIntervalGenes, and CSeq_loc_Base::Which().

Referenced by HasMultiIntervalGenes().

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

Definition at line 276 of file context.cpp.

References CSeq_loc::Assign(), CSeq_loc_Mapper::eSeqMap_Up, CSeq_id_Handle::GetHandle(), GetIdHandle(), CBioseq_Handle::GetInst_Length(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqId(), CSeq_loc::GetStrand(), CSeq_loc::GetTotalRange(), CSeq_loc_Base::IsInt(), IsReverse(), IsSameBioseq(), CSeq_loc_Base::IsWhole(), m_Handle, m_Location, m_PrimaryId, CSeq_loc_Mapper_Base::Map(), compile_time_bits::range(), CRef< C, Locker >::Reset(), CSeq_loc::SetWhole(), and x_SetMapper().

Referenced by x_Init().

x_SetMapper()

void CBioseqContext::x_SetMapper ( const CSeq_loc &  loc )

private

Definition at line 316 of file context.cpp.

References _ASSERT, CScope::AddBioseq(), CSeq_inst_Base::eRepr_virtual, CSeq_loc_Mapper::eSeqMap_Up, GetAccession(), GetBioseqFromSeqLoc(), GetScope(), m_Handle, m_Mapper, CRef< C, Locker >::Reset(), CSeq_loc_Mapper_Base::SetGapRemove(), CBioseq_Base::SetInst(), and CSeq_loc_Mapper_Base::SetMergeAbutting().

Referenced by x_SetLocation().

x_SetOpticalMapPoints()

void CBioseqContext::x_SetOpticalMapPoints ( void  )

private

Definition at line 555 of file context.cpp.

References ASSIGN_IF_SET_ELSE_RESET, CLONE_IF_SET_ELSE_RESET, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_inst_Base::eRepr_map, FIELD_IS_SET_AND_IS, FOR_EACH_SEQFEAT_ON_MAPEXT, CBioseq_Handle::GetInst_Ext(), CSeq_feat_Base::GetLocation(), CSeq_ext_Base::GetMap(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), GetRepr(), CSeq_feat_Base::IsSetLocation(), CSeq_point_Base::IsSetPoint(), m_Handle, m_pOpticalMapPoints, m_pOpticalMapPointsDestroyer, Map(), and CSeq_loc_Base::Which().

Referenced by x_Init().

x_SetTaxname()

void CBioseqContext::x_SetTaxname ( void  ) const

private

Definition at line 372 of file context.cpp.

References CSeqFeatData_Base::e_Biosrc, CSeqdesc_Base::e_Source, NStr::EqualNocase(), CPartialOrgName_Base::Get(), CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Base::GetData(), CTaxElement_Base::GetFixed_level(), CTaxElement_Base::GetLevel(), COrgName_Base::GetName(), CTaxElement_Base::GetName(), CBioSource::GetOrgname(), COrgName_Base::C_Name::GetPartial(), CMappedFeat::GetSeq_feat(), CSeqdesc_Base::GetSource(), CBioSource::GetTaxname(), CSeqFeatData_Base::IsBiosrc(), COrgName_Base::C_Name::IsPartial(), CPartialOrgName_Base::IsSet(), CSeq_feat_Base::IsSetData(), CTaxElement_Base::IsSetFixed_level(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetName(), CTaxElement_Base::IsSetName(), CBioSource::IsSetOrgname(), CBioSource::IsSetTaxname(), CSeqdesc_Base::IsSource(), ITERATE, m_Handle, m_IsCrossKingdom, m_Taxname, and SAnnotSelector::SetFeatType().

Referenced by GetTaxname(), and IsCrossKingdom().

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

Definition at line 390 of file context.hpp.

Referenced by CBioseqContext(), Config(), GetAnnotSelector(), GetMasterLocation(), GetSeqEntryIndex(), GetSGS(), GetSubmitBlock(), GetTopLevelEntry(), SetAnnotSelector(), UsingSeqEntryIndex(), and x_Init().

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

Definition at line 312 of file context.hpp.

Referenced by GetBioseqIds(), GetHandle(), GetPreferredSynonym(), GetScope(), GetTaxname(), HasMultiIntervalGenes(), HasOperon(), IsBioseqInSameTopLevelSeqEntry(), IsCrossKingdom(), IsSeqIdInSameTopLevelSeqEntry(), x_CheckForShowComments(), x_GetMolInfo(), x_GetPartNumber(), x_GetRepr(), x_HasOperon(), x_HasParts(), x_IsDeltaLitOnly(), x_IsInGPS(), x_IsInNucProt(), x_IsInSGS(), x_IsPart(), x_SetDataFromUserObjects(), x_SetHasMultiIntervalGenes(), x_SetId(), x_SetLocation(), x_SetMapper(), x_SetOpticalMapPoints(), and x_SetTaxname().

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

Definition at line 392 of file context.hpp.

Referenced by CanGetMaster(), GetMaster(), GetTotalNumParts(), SetMaster(), x_GetPartNumber(), and x_Init().

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

Definition at line 358 of file context.hpp.

Referenced by IsRSCompleteGenomic(), IsRSContig(), IsRSIncompleteGenomic(), IsRSIntermedWGS(), IsRSMRna(), IsRSNonCodingRna(), IsRSPredictedMRna(), IsRSPredictedNCRna(), IsRSPredictedProtein(), IsRSProtein(), IsRSWGSNuc(), IsRSWGSProt(), and x_SetId().

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().

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

• include/objtools/format/context.hpp
• src/objtools/format/context.cpp