CBioseqIndex Class Reference

Search Toolkit Book for CBioseqIndex

#include <objmgr/util/indexer.hpp>

Inheritance diagram for CBioseqIndex:

Collaboration diagram for CBioseqIndex:

Public Member Functions
	CBioseqIndex (CBioseq_Handle bsh, const CBioseq &bsp, CBioseq_Handle obsh, CRef< CSeqsetIndex > prnt, CSeq_entry_Handle tseh, CRef< CScope > scope, CSeqMasterIndex &idx, CSeqEntryIndex::EPolicy policy, CSeqEntryIndex::TFlags flags)
	~CBioseqIndex (void)
template<typename Fnc >
size_t	IterateGaps (Fnc m)
template<typename Fnc >
size_t	IterateDescriptors (Fnc m)
template<typename Fnc >
size_t	IterateFeatures (Fnc m)
template<typename Fnc >
size_t	IterateFeatures (CSeq_loc &slp, Fnc m)
CBioseq_Handle	GetBioseqHandle (void) const
const CBioseq &	GetBioseq (void) const
CBioseq_Handle	GetOrigBioseqHandle (void) const
CRef< CSeqsetIndex >	GetParent (void) const
CRef< CScope >	GetScope (void) const
CRef< CSeqVector >	GetSeqVector (void) const
CWeakRef< CSeqMasterIndex >	GetSeqMasterIndex (void) const
string	GetSequence (void)
void	GetSequence (string &buffer)
string	GetSequence (int from, int to)
void	GetSequence (int from, int to, string &buffer)
CRef< CFeatureIndex >	GetFeatIndex (const CMappedFeat &mf)
const vector< CRef< CGapIndex > > &	GetGapIndices (void)
const vector< CRef< CDescriptorIndex > > &	GetDescriptorIndices (void)
const vector< CRef< CFeatureIndex > > &	GetFeatureIndices (void)
CRef< CFeatureIndex >	GetFeatureForProduct (void)
CWeakRef< CBioseqIndex >	GetBioseqForProduct (void)
CRef< CFeatureIndex >	GetBestProteinFeature (void)
bool	IsFetchFailure (void) const
void	SetFetchFailure (bool fails)
void	GetSelector (SAnnotSelector &sel)
bool	IsNA (void) const
bool	IsAA (void) const
CSeq_inst::TTopology	GetTopology (void) const
CSeq_inst::TLength	GetLength (void) const
bool	IsDelta (void) const
bool	IsDeltaLitOnly (void) const
bool	IsVirtual (void) const
bool	IsMap (void) const
const string &	GetAccession (void) const
bool	IsRefSeq (void) const
bool	IsNC (void) const
bool	IsNM (void) const
bool	IsNR (void) const
bool	IsNZ (void) const
bool	IsPatent (void) const
bool	IsPDB (void) const
bool	IsWP (void) const
bool	IsThirdParty (void) const
bool	IsWGSMaster (void) const
bool	IsTSAMaster (void) const
bool	IsTLSMaster (void) const
string	GetGeneralStr (void) const
int	GetGeneralId (void) const
string	GetPatentCountry (void) const
string	GetPatentNumber (void) const
int	GetPatentSequence (void) const
int	GetPDBChain (void) const
string	GetPDBChainID (void) const
const string &	GetTitle (void)
CConstRef< CMolInfo >	GetMolInfo (void)
CMolInfo::TBiomol	GetBiomol (void)
CMolInfo::TTech	GetTech (void)
CMolInfo::TCompleteness	GetCompleteness (void)
CConstRef< CBioSource >	GetBioSource (void)
const string &	GetTaxname (void)
const string &	GetDescTaxname (void)
bool	IsHTGTech (void)
bool	IsHTGSUnfinished (void)
bool	IsTLS (void)
bool	IsTSA (void)
bool	IsWGS (void)
bool	IsEST_STS_GSS (void)
bool	IsUseBiosrc (void)
const string &	GetCommon (void)
const string &	GetLineage (void)
TTaxId	GetTaxid (void)
bool	IsUsingAnamorph (void)
CTempString	GetGenus (void)
CTempString	GetSpecies (void)
bool	IsMultispecies (void)
CBioSource::TGenome	GetGenome (void)
bool	IsPlasmid (void)
bool	IsChromosome (void)
const string &	GetOrganelle (void)
string	GetFirstSuperKingdom (void)
string	GetSecondSuperKingdom (void)
bool	IsCrossKingdom (void)
CTempString	GetChromosome (void)
CTempString	GetLinkageGroup (void)
CTempString	GetClone (void)
bool	HasClone (void)
CTempString	GetMap (void)
CTempString	GetPlasmid (void)
CTempString	GetSegment (void)
CTempString	GetBreed (void)
CTempString	GetCultivar (void)
CTempString	GetSpecimenVoucher (void)
CTempString	GetIsolate (void)
CTempString	GetStrain (void)
CTempString	GetSubstrain (void)
CTempString	GetMetaGenomeSource (void)
bool	IsHTGSCancelled (void)
bool	IsHTGSDraft (void)
bool	IsHTGSPooled (void)
bool	IsTPAExp (void)
bool	IsTPAInf (void)
bool	IsTPAReasm (void)
bool	IsUnordered (void)
CTempString	GetPDBCompound (void)
bool	IsForceOnlyNearFeats (void)
bool	IsUnverified (void)
bool	IsUnverifiedFeature (void)
bool	IsUnverifiedOrganism (void)
bool	IsUnverifiedMisassembled (void)
bool	IsUnverifiedContaminant (void)
bool	IsUnreviewed (void)
bool	IsUnreviewedUnannotated (void)
CTempString	GetTargetedLocus (void)
const string &	GetComment (void)
bool	IsPseudogene (void)
bool	HasOperon (void)
bool	HasGene (void)
bool	HasMultiIntervalGenes (void)
bool	HasSource (void)
string	GetrEnzyme (void)
Public Member Functions inherited from CObjectEx
	CObjectEx (void)
virtual	~CObjectEx (void)
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
Public Member Functions inherited from CWeakObject
	CWeakObject (void)
virtual	~CWeakObject (void)
CPtrToObjectProxy *	GetPtrProxy (void) const
	Get pointer to proxy object containing pointer to this object. More...

Private Types
typedef map< CMappedFeat, CRef< CFeatureIndex > >	TFeatIndexMap

Private Member Functions
	CBioseqIndex (const CBioseqIndex &)=delete
CBioseqIndex &	operator= (const CBioseqIndex &)=delete
void	x_InitGaps (void)
void	x_InitDescs (void)
void	x_InitFeats (void)
void	x_InitFeats (CSeq_loc &slp)
void	x_DefaultSelector (SAnnotSelector &sel, CSeqEntryIndex::EPolicy policy, CSeqEntryIndex::TFlags flags, bool onlyNear, CScope &scope)
void	x_InitFeats (CSeq_loc *slpp)
void	x_InitSource (void)

Private Attributes
CBioseq_Handle	m_Bsh
const CBioseq &	m_Bsp
CBioseq_Handle	m_OrigBsh
CRef< CSeqsetIndex >	m_Prnt
CSeq_entry_Handle	m_Tseh
CRef< CScope >	m_Scope
CWeakRef< CSeqMasterIndex >	m_Idx
bool	m_GapsInitialized
vector< CRef< CGapIndex > >	m_GapList
bool	m_DescsInitialized
vector< CRef< CDescriptorIndex > >	m_SdxList
bool	m_FeatsInitialized
vector< CRef< CFeatureIndex > >	m_SfxList
bool	m_SourcesInitialized
bool	m_FeatForProdInitialized
CRef< CFeatureIndex >	m_FeatureForProduct
bool	m_BestProtFeatInitialized
CRef< CFeatureIndex >	m_BestProteinFeature
TFeatIndexMap	m_FeatIndexMap
CRef< CSeqVector >	m_SeqVec
CSeqEntryIndex::EPolicy	m_Policy
CSeqEntryIndex::TFlags	m_Flags
bool	m_FetchFailure
bool	m_IsNA
bool	m_IsAA
CSeq_inst::TTopology	m_Topology
CSeq_inst::TLength	m_Length
bool	m_IsDelta
bool	m_IsDeltaLitOnly
bool	m_IsVirtual
bool	m_IsMap
string	m_Accession
bool	m_IsRefSeq
bool	m_IsNC
bool	m_IsNM
bool	m_IsNR
bool	m_IsNZ
bool	m_IsPatent
bool	m_IsPDB
bool	m_IsWP
bool	m_ThirdParty
bool	m_WGSMaster
bool	m_TSAMaster
bool	m_TLSMaster
string	m_GeneralStr
int	m_GeneralId
string	m_PatentCountry
string	m_PatentNumber
int	m_PatentSequence
int	m_PDBChain
string	m_PDBChainID
string	m_Title
CConstRef< CMolInfo >	m_MolInfo
CMolInfo::TBiomol	m_Biomol
CMolInfo::TTech	m_Tech
CMolInfo::TCompleteness	m_Completeness
bool	m_HTGTech
bool	m_HTGSUnfinished
bool	m_IsTLS
bool	m_IsTSA
bool	m_IsWGS
bool	m_IsEST_STS_GSS
bool	m_UseBiosrc
CConstRef< CBioSource >	m_DescBioSource
string	m_DescTaxname
CConstRef< CBioSource >	m_BioSource
string	m_Taxname
string	m_Common
string	m_Lineage
TTaxId	m_Taxid
bool	m_UsingAnamorph
CTempString	m_Genus
CTempString	m_Species
bool	m_Multispecies
CBioSource::TGenome	m_Genome
bool	m_IsPlasmid
bool	m_IsChromosome
string	m_Organelle
string	m_FirstSuperKingdom
string	m_SecondSuperKingdom
bool	m_IsCrossKingdom
CTempString	m_Chromosome
CTempString	m_LinkageGroup
CTempString	m_Clone
bool	m_has_clone
CTempString	m_Map
CTempString	m_Plasmid
CTempString	m_Segment
CTempString	m_Breed
CTempString	m_Cultivar
CTempString	m_SpecimenVoucher
CTempString	m_Isolate
CTempString	m_Strain
CTempString	m_Substrain
CTempString	m_MetaGenomeSource
bool	m_HTGSCancelled
bool	m_HTGSDraft
bool	m_HTGSPooled
bool	m_TPAExp
bool	m_TPAInf
bool	m_TPAReasm
bool	m_Unordered
CTempString	m_PDBCompound
bool	m_ForceOnlyNearFeats
bool	m_IsUnverified
bool	m_IsUnverifiedFeature
bool	m_IsUnverifiedOrganism
bool	m_IsUnverifiedMisassembled
bool	m_IsUnverifiedContaminant
CTempString	m_UnverifiedPrefix
bool	m_IsUnreviewed
bool	m_IsUnreviewedUnannotated
CTempString	m_UnreviewedPrefix
CTempString	m_TargetedLocus
string	m_Comment
bool	m_IsPseudogene
bool	m_HasGene
bool	m_HasMultiIntervalGenes
bool	m_HasSource
string	m_rEnzyme

Additional Inherited Members
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...
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...
Protected Member Functions inherited from CWeakObject
void	CleanWeakRefs (void) const
	Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More...

Detailed Description

Definition at line 394 of file indexer.hpp.

Member Typedef Documentation

TFeatIndexMap

typedef map<CMappedFeat, CRef<CFeatureIndex> > CBioseqIndex::TFeatIndexMap

private

Definition at line 644 of file indexer.hpp.

Constructor & Destructor Documentation

CBioseqIndex() [1/2]

CBioseqIndex::CBioseqIndex	(	CBioseq_Handle	bsh,
		const CBioseq &	bsp,
		CBioseq_Handle	obsh,
		CRef< CSeqsetIndex >	prnt,
		CSeq_entry_Handle	tseh,
		CRef< CScope >	scope,
		CSeqMasterIndex &	idx,
		CSeqEntryIndex::EPolicy	policy,
		CSeqEntryIndex::TFlags	flags
	)

Definition at line 783 of file indexer.cpp.

References CTempString::clear(), CMolInfo_Base::eBiomol_unknown, CMolInfo_Base::eCompleteness_unknown, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_map, CSeq_inst_Base::eRepr_virtual, CMolInfo_Base::eTech_unknown, CSeq_inst_Base::eTopology_not_set, CSeq_id::fAcc_master, CDelta_ext_Base::Get(), CMap_ext_Base::Get(), CTextseq_id_Base::GetAccession(), CBioseq_Handle::GetBioseqLength(), CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CPatent_seq_id_Base::GetCit(), CId_pat_Base::GetCountry(), CSeq_feat_Base::GetData(), CSeq_ext_Base::GetDelta(), CObject_id_Base::GetId(), CBioseq_Handle::GetId(), CBioseq_Handle::GetInst_Ext(), CBioseq_Handle::GetInst_Length(), CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::GetInst_Topology(), CSeq_ext_Base::GetMap(), CSeqFeatData_Base::GetRsite(), CPatent_seq_id_Base::GetSeqid(), CId_pat::GetSomeNumber(), CObject_id_Base::GetStr(), CRsite_ref_Base::GetStr(), CDbtag_Base::GetTag(), CSeq_id::IdentifyAccession(), CBioseq_Handle::IsAa(), CSeq_ext_Base::IsDelta(), CObject_id_Base::IsId(), CSeq_ext_Base::IsMap(), CBioseq_Handle::IsNa(), CSeq_loc_Base::IsNull(), CSeqFeatData_Base::IsRsite(), CMap_ext_Base::IsSet(), CTextseq_id_Base::IsSetAccession(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CPatent_seq_id_Base::IsSetCit(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Ext(), CBioseq_Handle::IsSetInst_Length(), CBioseq_Handle::IsSetInst_Repr(), CBioseq_Handle::IsSetInst_Topology(), CPatent_seq_id_Base::IsSetSeqid(), CDbtag_Base::IsSetTag(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), CRsite_ref_Base::IsStr(), ITERATE, m_Accession, m_BestProtFeatInitialized, m_Biomol, m_BioSource, m_Breed, m_Bsh, m_Chromosome, m_Clone, m_Comment, m_Common, m_Completeness, m_Cultivar, m_DescBioSource, m_DescsInitialized, m_DescTaxname, m_FeatForProdInitialized, m_FeatsInitialized, m_FetchFailure, m_FirstSuperKingdom, m_ForceOnlyNearFeats, m_GapsInitialized, m_GeneralId, m_GeneralStr, m_Genome, m_Genus, m_has_clone, m_HasGene, m_HasMultiIntervalGenes, m_HasSource, m_HTGSCancelled, m_HTGSDraft, m_HTGSPooled, m_HTGSUnfinished, m_HTGTech, m_IsAA, m_IsChromosome, m_IsCrossKingdom, m_IsDelta, m_IsDeltaLitOnly, m_IsEST_STS_GSS, m_IsMap, m_IsNA, m_IsNC, m_IsNM, m_IsNR, m_IsNZ, m_Isolate, m_IsPatent, m_IsPDB, m_IsPlasmid, m_IsPseudogene, m_IsRefSeq, m_IsTLS, m_IsTSA, m_IsUnreviewed, m_IsUnreviewedUnannotated, m_IsUnverified, m_IsUnverifiedContaminant, m_IsUnverifiedFeature, m_IsUnverifiedMisassembled, m_IsUnverifiedOrganism, m_IsVirtual, m_IsWGS, m_IsWP, m_Length, m_Lineage, m_LinkageGroup, m_Map, m_MetaGenomeSource, m_MolInfo, m_Multispecies, m_Organelle, m_PatentCountry, m_PatentNumber, m_PatentSequence, m_PDBChain, m_PDBChainID, m_PDBCompound, m_Plasmid, m_rEnzyme, m_SecondSuperKingdom, m_Segment, m_SourcesInitialized, m_Species, m_SpecimenVoucher, m_Strain, m_Substrain, m_TargetedLocus, m_Taxid, m_Taxname, m_Tech, m_ThirdParty, m_Title, m_TLSMaster, m_Topology, m_TPAExp, m_TPAInf, m_TPAReasm, m_TSAMaster, m_Unordered, m_UseBiosrc, m_UsingAnamorph, m_WGSMaster, NCBI_ACCN, NCBI_GENOME, NCBI_SEQID, NCBI_SEQTOPOLOGY, CConstRef< C, Locker >::Reset(), and ZERO_TAX_ID.

~CBioseqIndex()

CBioseqIndex::~CBioseqIndex

(

void

)

Definition at line 1101 of file indexer.cpp.

CBioseqIndex() [2/2]

CBioseqIndex::CBioseqIndex ( const CBioseqIndex &  )

privatedelete

Member Function Documentation

GetAccession()

const string& CBioseqIndex::GetAccession ( void  ) const

inline

Definition at line 482 of file indexer.hpp.

References m_Accession.

Referenced by CExploreProcess::DoOneBioseq(), and CSeqMasterIndex::x_InitSeqs().

GetBestProteinFeature()

CRef< CFeatureIndex > CBioseqIndex::GetBestProteinFeature

(

void

)

Definition at line 2352 of file indexer.cpp.

References m_BestProteinFeature, m_BestProtFeatInitialized, m_FeatsInitialized, and x_InitFeats().

Referenced by CExploreProcess::DoOneBioseq(), CFeatureItem::x_GetAssociatedProtInfoIdx(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

GetBiomol()

CMolInfo::TBiomol CBioseqIndex::GetBiomol

(

void

)

Definition at line 2385 of file indexer.cpp.

References m_Biomol, m_DescsInitialized, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetBioseq()

const CBioseq& CBioseqIndex::GetBioseq ( void  ) const

inline

Definition at line 429 of file indexer.hpp.

References m_Bsp.

GetBioseqForProduct()

CWeakRef< CBioseqIndex > CBioseqIndex::GetBioseqForProduct

(

void

)

Definition at line 2340 of file indexer.cpp.

References CFeatureIndex::GetBioseqIndex(), and GetFeatureForProduct().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), and CDeflineGenerator::x_AdjustProteinTitleSuffixIdx().

GetBioseqHandle()

CBioseq_Handle CBioseqIndex::GetBioseqHandle ( void  ) const

inline

Definition at line 428 of file indexer.hpp.

References m_Bsh.

Referenced by x_DefaultSelector().

GetBioSource()

CConstRef< CBioSource > CBioseqIndex::GetBioSource

(

void

)

Definition at line 2485 of file indexer.cpp.

References m_BioSource, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), x_GetDivisionProcIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetBreed()

CTempString CBioseqIndex::GetBreed

(

void

)

Definition at line 2725 of file indexer.cpp.

References m_Breed, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetChromosome()

CTempString CBioseqIndex::GetChromosome

(

void

)

Definition at line 2655 of file indexer.cpp.

References m_Chromosome, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetClone()

CTempString CBioseqIndex::GetClone

(

void

)

Definition at line 2675 of file indexer.cpp.

References m_Clone, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetComment()

const string & CBioseqIndex::GetComment

(

void

)

Definition at line 2967 of file indexer.cpp.

References m_Comment, m_DescsInitialized, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetCommon()

const string & CBioseqIndex::GetCommon

(

void

)

Definition at line 2515 of file indexer.cpp.

References m_Common, m_SourcesInitialized, and x_InitSource().

GetCompleteness()

CMolInfo::TCompleteness CBioseqIndex::GetCompleteness

(

void

)

Definition at line 2405 of file indexer.cpp.

References m_Completeness, m_DescsInitialized, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetCultivar()

CTempString CBioseqIndex::GetCultivar

(

void

)

Definition at line 2735 of file indexer.cpp.

References m_Cultivar, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetDescriptorIndices()

const vector< CRef< CDescriptorIndex > > & CBioseqIndex::GetDescriptorIndices

(

void

)

Definition at line 3127 of file indexer.cpp.

References m_DescsInitialized, m_SdxList, and x_InitDescs().

GetDescTaxname()

const string & CBioseqIndex::GetDescTaxname

(

void

)

Definition at line 2505 of file indexer.cpp.

References m_DescTaxname, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx().

GetFeatIndex()

CRef< CFeatureIndex > CBioseqIndex::GetFeatIndex

(

const CMappedFeat &

mf

)

Definition at line 3043 of file indexer.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and m_FeatIndexMap.

Referenced by CFeatureItem::x_AddQualsIdx().

GetFeatureForProduct()

CRef< CFeatureIndex > CBioseqIndex::GetFeatureForProduct

(

void

)

Definition at line 2298 of file indexer.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, fi, CScope::GetBioseqHandle(), CMappedFeat::GetLocationId(), GetSeqMasterIndex(), CBioseq_Handle::GetTSE_Handle(), CWeakRef< C, Locker >::Lock(), m_Bsh, m_FeatForProdInitialized, m_FeatsInitialized, m_FeatureForProduct, m_Scope, and x_InitFeats().

Referenced by CExploreProcess::DoOneBioseq(), GetBioseqForProduct(), CFeatureItem::x_AddQualsIdx(), x_GetDivisionProcIdx(), x_InitSource(), CDeflineGenerator::x_SetPrefix(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

GetFeatureIndices()

const vector< CRef< CFeatureIndex > > & CBioseqIndex::GetFeatureIndices

(

void

)

Definition at line 3137 of file indexer.cpp.

References m_FeatsInitialized, m_SfxList, and x_InitFeats().

GetFirstSuperKingdom()

string CBioseqIndex::GetFirstSuperKingdom

(

void

)

Definition at line 2625 of file indexer.cpp.

References m_FirstSuperKingdom, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetGapIndices()

const vector< CRef< CGapIndex > > & CBioseqIndex::GetGapIndices

(

void

)

Definition at line 3117 of file indexer.cpp.

References m_GapList, m_GapsInitialized, and x_InitGaps().

Referenced by CExploreProcess::DoOneBioseq(), and CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().

GetGeneralId()

int CBioseqIndex::GetGeneralId ( void  ) const

inline

Definition at line 498 of file indexer.hpp.

References m_GeneralId.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetGeneralStr()

string CBioseqIndex::GetGeneralStr ( void  ) const

inline

Definition at line 497 of file indexer.hpp.

References m_GeneralStr.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetGenome()

CBioSource::TGenome CBioseqIndex::GetGenome

(

void

)

Definition at line 2585 of file indexer.cpp.

References m_Genome, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetGenus()

CTempString CBioseqIndex::GetGenus

(

void

)

Definition at line 2555 of file indexer.cpp.

References m_Genus, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetIsolate()

CTempString CBioseqIndex::GetIsolate

(

void

)

Definition at line 2757 of file indexer.cpp.

References m_Isolate, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetLength()

CSeq_inst::TLength CBioseqIndex::GetLength ( void  ) const

inline

Definition at line 474 of file indexer.hpp.

References m_Length.

Referenced by CExploreProcess::DoOneBioseq(), x_DefaultSelector(), and CDeflineGenerator::x_SetFlagsIdx().

GetLineage()

const string & CBioseqIndex::GetLineage

(

void

)

Definition at line 2525 of file indexer.cpp.

References m_Lineage, m_SourcesInitialized, and x_InitSource().

GetLinkageGroup()

CTempString CBioseqIndex::GetLinkageGroup

(

void

)

Definition at line 2665 of file indexer.cpp.

References m_LinkageGroup, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetMap()

CTempString CBioseqIndex::GetMap

(

void

)

Definition at line 2695 of file indexer.cpp.

References m_Map, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetMetaGenomeSource()

CTempString CBioseqIndex::GetMetaGenomeSource

(

void

)

Definition at line 2787 of file indexer.cpp.

References m_MetaGenomeSource, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetMolInfo()

CConstRef< CMolInfo > CBioseqIndex::GetMolInfo

(

void

)

Definition at line 2375 of file indexer.cpp.

References m_DescsInitialized, m_MolInfo, and x_InitDescs().

GetOrganelle()

const string & CBioseqIndex::GetOrganelle

(

void

)

Definition at line 2615 of file indexer.cpp.

References m_Organelle, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetOrigBioseqHandle()

CBioseq_Handle CBioseqIndex::GetOrigBioseqHandle ( void  ) const

inline

Definition at line 430 of file indexer.hpp.

References m_OrigBsh.

GetParent()

CRef<CSeqsetIndex> CBioseqIndex::GetParent ( void  ) const

inline

Definition at line 431 of file indexer.hpp.

References m_Prnt.

Referenced by CExploreProcess::DoOneBioseq().

GetPatentCountry()

string CBioseqIndex::GetPatentCountry ( void  ) const

inline

Definition at line 500 of file indexer.hpp.

References m_PatentCountry.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetPatentNumber()

string CBioseqIndex::GetPatentNumber ( void  ) const

inline

Definition at line 501 of file indexer.hpp.

References m_PatentNumber.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetPatentSequence()

int CBioseqIndex::GetPatentSequence ( void  ) const

inline

Definition at line 502 of file indexer.hpp.

References m_PatentSequence.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetPDBChain()

int CBioseqIndex::GetPDBChain ( void  ) const

inline

Definition at line 504 of file indexer.hpp.

References m_PDBChain.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetPDBChainID()

string CBioseqIndex::GetPDBChainID ( void  ) const

inline

Definition at line 505 of file indexer.hpp.

References m_PDBChainID.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetPDBCompound()

CTempString CBioseqIndex::GetPDBCompound

(

void

)

Definition at line 2867 of file indexer.cpp.

References m_DescsInitialized, m_PDBCompound, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetPlasmid()

CTempString CBioseqIndex::GetPlasmid

(

void

)

Definition at line 2705 of file indexer.cpp.

References m_Plasmid, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetrEnzyme()

string CBioseqIndex::GetrEnzyme

(

void

)

Definition at line 3033 of file indexer.cpp.

References m_DescsInitialized, m_rEnzyme, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetScope()

CRef<CScope> CBioseqIndex::GetScope ( void  ) const

inline

Definition at line 432 of file indexer.hpp.

References m_Scope.

GetSecondSuperKingdom()

string CBioseqIndex::GetSecondSuperKingdom

(

void

)

Definition at line 2635 of file indexer.cpp.

References m_SecondSuperKingdom, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetSegment()

CTempString CBioseqIndex::GetSegment

(

void

)

Definition at line 2715 of file indexer.cpp.

References m_Segment, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetSelector()

void CBioseqIndex::GetSelector

(

SAnnotSelector &

sel

)

Definition at line 2054 of file indexer.cpp.

References m_Flags, m_ForceOnlyNearFeats, m_Policy, m_Scope, and x_DefaultSelector().

Referenced by CFlatGatherer::x_GatherFeaturesOnRangeIdx().

GetSeqMasterIndex()

CWeakRef<CSeqMasterIndex> CBioseqIndex::GetSeqMasterIndex ( void  ) const

inline

Definition at line 436 of file indexer.hpp.

References m_Idx.

Referenced by GetFeatureForProduct(), HasOperon(), x_DefaultSelector(), x_InitFeats(), and x_InitGaps().

GetSequence() [1/4]

string CBioseqIndex::GetSequence	(	int	from,
		int	to
	)

Definition at line 3091 of file indexer.cpp.

References buffer, and GetSequence().

GetSequence() [2/4]

void CBioseqIndex::GetSequence	(	int	from,
		int	to,
		string &	buffer
	)

Definition at line 3056 of file indexer.cpp.

References buffer, CSeqVector::CanGetRange(), CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, ERR_POST_X, Error(), CSeqVector::GetSeqData(), IsAA(), m_Bsh, m_FetchFailure, m_SeqVec, CSeqVector::SetCoding(), CSeqVector::size(), and CException::what().

GetSequence() [3/4]

void CBioseqIndex::GetSequence

(

string &

buffer

)

Definition at line 3101 of file indexer.cpp.

References buffer, and GetSequence().

GetSequence() [4/4]

string CBioseqIndex::GetSequence

(

void

)

Definition at line 3107 of file indexer.cpp.

References buffer.

Referenced by CExploreProcess::DoOneBioseq(), and GetSequence().

GetSeqVector()

CRef<CSeqVector> CBioseqIndex::GetSeqVector ( void  ) const

inline

Definition at line 433 of file indexer.hpp.

References m_SeqVec.

GetSpecies()

CTempString CBioseqIndex::GetSpecies

(

void

)

Definition at line 2565 of file indexer.cpp.

References m_SourcesInitialized, m_Species, and x_InitSource().

Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetSpecimenVoucher()

CTempString CBioseqIndex::GetSpecimenVoucher

(

void

)

Definition at line 2746 of file indexer.cpp.

References m_SourcesInitialized, m_SpecimenVoucher, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetStrain()

CTempString CBioseqIndex::GetStrain

(

void

)

Definition at line 2767 of file indexer.cpp.

References m_SourcesInitialized, m_Strain, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetSubstrain()

CTempString CBioseqIndex::GetSubstrain

(

void

)

Definition at line 2777 of file indexer.cpp.

References m_SourcesInitialized, m_Substrain, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetTargetedLocus()

CTempString CBioseqIndex::GetTargetedLocus

(

void

)

Definition at line 2957 of file indexer.cpp.

References m_DescsInitialized, m_TargetedLocus, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetTaxid()

TTaxId CBioseqIndex::GetTaxid

(

void

)

Definition at line 2535 of file indexer.cpp.

References m_SourcesInitialized, m_Taxid, and x_InitSource().

GetTaxname()

const string & CBioseqIndex::GetTaxname

(

void

)

Definition at line 2495 of file indexer.cpp.

References m_SourcesInitialized, m_Taxname, and x_InitSource().

Referenced by CExploreProcess::DoOneBioseq(), CBioseqContext::GetTaxname(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

GetTech()

CMolInfo::TTech CBioseqIndex::GetTech

(

void

)

Definition at line 2395 of file indexer.cpp.

References m_DescsInitialized, m_Tech, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

GetTitle()

const string & CBioseqIndex::GetTitle

(

void

)

Definition at line 2365 of file indexer.cpp.

References m_DescsInitialized, m_Title, and x_InitDescs().

Referenced by CExploreProcess::DoOneBioseq(), and CDeflineGenerator::x_SetFlagsIdx().

GetTopology()

CSeq_inst::TTopology CBioseqIndex::GetTopology ( void  ) const

inline

Definition at line 473 of file indexer.hpp.

References m_Topology.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

HasClone()

bool CBioseqIndex::HasClone

(

void

)

Definition at line 2685 of file indexer.cpp.

References m_has_clone, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

HasGene()

bool CBioseqIndex::HasGene

(

void

)

Definition at line 3003 of file indexer.cpp.

References m_FeatsInitialized, m_HasGene, and x_InitFeats().

HasMultiIntervalGenes()

bool CBioseqIndex::HasMultiIntervalGenes

(

void

)

Definition at line 3013 of file indexer.cpp.

References m_FeatsInitialized, m_HasMultiIntervalGenes, and x_InitFeats().

Referenced by CBioseqContext::HasMultiIntervalGenes().

HasOperon()

bool CBioseqIndex::HasOperon

(

void

)

Definition at line 2987 of file indexer.cpp.

References GetSeqMasterIndex(), CWeakRef< C, Locker >::Lock(), m_FeatsInitialized, and x_InitFeats().

Referenced by CBioseqContext::HasOperon(), and CFeatureItem::x_AddQualsIdx().

HasSource()

bool CBioseqIndex::HasSource

(

void

)

Definition at line 3023 of file indexer.cpp.

References m_FeatsInitialized, m_HasSource, and x_InitFeats().

IsAA()

bool CBioseqIndex::IsAA ( void  ) const

inline

Definition at line 472 of file indexer.hpp.

References m_IsAA.

Referenced by CExploreProcess::DoOneBioseq(), GetSequence(), CExploreProcess::SeqEntryProcess(), x_InitFeats(), and CDeflineGenerator::x_SetFlagsIdx().

IsChromosome()

bool CBioseqIndex::IsChromosome

(

void

)

Definition at line 2605 of file indexer.cpp.

References m_IsChromosome, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

IsCrossKingdom()

bool CBioseqIndex::IsCrossKingdom

(

void

)

Definition at line 2645 of file indexer.cpp.

References m_IsCrossKingdom, m_SourcesInitialized, and x_InitSource().

Referenced by CBioseqContext::IsCrossKingdom(), and CDeflineGenerator::x_SetFlagsIdx().

IsDelta()

bool CBioseqIndex::IsDelta ( void  ) const

inline

Definition at line 476 of file indexer.hpp.

References m_IsDelta.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsDeltaLitOnly()

bool CBioseqIndex::IsDeltaLitOnly ( void  ) const

inline

Definition at line 477 of file indexer.hpp.

References m_IsDeltaLitOnly.

IsEST_STS_GSS()

bool CBioseqIndex::IsEST_STS_GSS

(

void

)

Definition at line 2465 of file indexer.cpp.

References m_DescsInitialized, m_IsEST_STS_GSS, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsFetchFailure()

bool CBioseqIndex::IsFetchFailure ( void  ) const

inline

Definition at line 464 of file indexer.hpp.

References m_FetchFailure.

IsForceOnlyNearFeats()

bool CBioseqIndex::IsForceOnlyNearFeats

(

void

)

Definition at line 2877 of file indexer.cpp.

References m_DescsInitialized, m_ForceOnlyNearFeats, and x_InitDescs().

IsHTGSCancelled()

bool CBioseqIndex::IsHTGSCancelled

(

void

)

Definition at line 2797 of file indexer.cpp.

References m_DescsInitialized, m_HTGSCancelled, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsHTGSDraft()

bool CBioseqIndex::IsHTGSDraft

(

void

)

Definition at line 2807 of file indexer.cpp.

References m_DescsInitialized, m_HTGSDraft, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsHTGSPooled()

bool CBioseqIndex::IsHTGSPooled

(

void

)

Definition at line 2817 of file indexer.cpp.

References m_DescsInitialized, m_HTGSPooled, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsHTGSUnfinished()

bool CBioseqIndex::IsHTGSUnfinished

(

void

)

Definition at line 2425 of file indexer.cpp.

References m_DescsInitialized, m_HTGSUnfinished, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsHTGTech()

bool CBioseqIndex::IsHTGTech

(

void

)

Definition at line 2415 of file indexer.cpp.

References m_DescsInitialized, m_HTGTech, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsMap()

bool CBioseqIndex::IsMap ( void  ) const

inline

Definition at line 479 of file indexer.hpp.

References m_IsMap.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsMultispecies()

bool CBioseqIndex::IsMultispecies

(

void

)

Definition at line 2575 of file indexer.cpp.

References m_Multispecies, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

IsNA()

bool CBioseqIndex::IsNA ( void  ) const

inline

Definition at line 471 of file indexer.hpp.

References m_IsNA.

Referenced by CExploreProcess::DoOneBioseq(), CExploreProcess::SeqEntryProcess(), x_InitFeats(), and CDeflineGenerator::x_SetFlagsIdx().

IsNC()

bool CBioseqIndex::IsNC ( void  ) const

inline

Definition at line 485 of file indexer.hpp.

References m_IsNC.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsNM()

bool CBioseqIndex::IsNM ( void  ) const

inline

Definition at line 486 of file indexer.hpp.

References m_IsNM.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsNR()

bool CBioseqIndex::IsNR ( void  ) const

inline

Definition at line 487 of file indexer.hpp.

References m_IsNR.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsNZ()

bool CBioseqIndex::IsNZ ( void  ) const

inline

Definition at line 488 of file indexer.hpp.

References m_IsNZ.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsPatent()

bool CBioseqIndex::IsPatent ( void  ) const

inline

Definition at line 489 of file indexer.hpp.

References m_IsPatent.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsPDB()

bool CBioseqIndex::IsPDB ( void  ) const

inline

Definition at line 490 of file indexer.hpp.

References m_IsPDB.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsPlasmid()

bool CBioseqIndex::IsPlasmid

(

void

)

Definition at line 2595 of file indexer.cpp.

References m_IsPlasmid, m_SourcesInitialized, and x_InitSource().

Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().

IsPseudogene()

bool CBioseqIndex::IsPseudogene

(

void

)

Definition at line 2977 of file indexer.cpp.

References m_DescsInitialized, m_IsPseudogene, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsRefSeq()

bool CBioseqIndex::IsRefSeq ( void  ) const

inline

Definition at line 484 of file indexer.hpp.

References m_IsRefSeq.

IsThirdParty()

bool CBioseqIndex::IsThirdParty ( void  ) const

inline

Definition at line 492 of file indexer.hpp.

References m_ThirdParty.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTLS()

bool CBioseqIndex::IsTLS

(

void

)

Definition at line 2435 of file indexer.cpp.

References m_DescsInitialized, m_IsTLS, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTLSMaster()

bool CBioseqIndex::IsTLSMaster ( void  ) const

inline

Definition at line 495 of file indexer.hpp.

References m_TLSMaster.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTPAExp()

bool CBioseqIndex::IsTPAExp

(

void

)

Definition at line 2827 of file indexer.cpp.

References m_DescsInitialized, m_TPAExp, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTPAInf()

bool CBioseqIndex::IsTPAInf

(

void

)

Definition at line 2837 of file indexer.cpp.

References m_DescsInitialized, m_TPAInf, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTPAReasm()

bool CBioseqIndex::IsTPAReasm

(

void

)

Definition at line 2847 of file indexer.cpp.

References m_DescsInitialized, m_TPAReasm, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTSA()

bool CBioseqIndex::IsTSA

(

void

)

Definition at line 2445 of file indexer.cpp.

References m_DescsInitialized, m_IsTSA, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsTSAMaster()

bool CBioseqIndex::IsTSAMaster ( void  ) const

inline

Definition at line 494 of file indexer.hpp.

References m_TSAMaster.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnordered()

bool CBioseqIndex::IsUnordered

(

void

)

Definition at line 2857 of file indexer.cpp.

References m_DescsInitialized, m_Unordered, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnreviewed()

bool CBioseqIndex::IsUnreviewed

(

void

)

Definition at line 2937 of file indexer.cpp.

References m_DescsInitialized, m_IsUnreviewed, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnreviewedUnannotated()

bool CBioseqIndex::IsUnreviewedUnannotated

(

void

)

Definition at line 2947 of file indexer.cpp.

References m_DescsInitialized, m_IsUnreviewedUnannotated, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnverified()

bool CBioseqIndex::IsUnverified

(

void

)

Definition at line 2887 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverified, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnverifiedContaminant()

bool CBioseqIndex::IsUnverifiedContaminant

(

void

)

Definition at line 2927 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverifiedContaminant, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnverifiedFeature()

bool CBioseqIndex::IsUnverifiedFeature

(

void

)

Definition at line 2897 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverifiedFeature, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnverifiedMisassembled()

bool CBioseqIndex::IsUnverifiedMisassembled

(

void

)

Definition at line 2917 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverifiedMisassembled, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUnverifiedOrganism()

bool CBioseqIndex::IsUnverifiedOrganism

(

void

)

Definition at line 2907 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverifiedOrganism, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUseBiosrc()

bool CBioseqIndex::IsUseBiosrc

(

void

)

Definition at line 2475 of file indexer.cpp.

References m_DescsInitialized, m_UseBiosrc, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsUsingAnamorph()

bool CBioseqIndex::IsUsingAnamorph

(

void

)

Definition at line 2545 of file indexer.cpp.

References m_SourcesInitialized, m_UsingAnamorph, and x_InitSource().

IsVirtual()

bool CBioseqIndex::IsVirtual ( void  ) const

inline

Definition at line 478 of file indexer.hpp.

References m_IsVirtual.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsWGS()

bool CBioseqIndex::IsWGS

(

void

)

Definition at line 2455 of file indexer.cpp.

References m_DescsInitialized, m_IsWGS, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsWGSMaster()

bool CBioseqIndex::IsWGSMaster ( void  ) const

inline

Definition at line 493 of file indexer.hpp.

References m_WGSMaster.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IsWP()

bool CBioseqIndex::IsWP ( void  ) const

inline

Definition at line 491 of file indexer.hpp.

References m_IsWP.

Referenced by CDeflineGenerator::x_SetFlagsIdx().

IterateDescriptors()

template<typename Fnc >

size_t CBioseqIndex::IterateDescriptors ( Fnc  m )

inline

Definition at line 1058 of file indexer.hpp.

References ERR_POST, Error(), m_DescsInitialized, m_SdxList, CException::what(), and x_InitDescs().

Referenced by CFlatGatherer::x_GatherReferencesIdx().

IterateFeatures() [1/2]

template<typename Fnc >

size_t CBioseqIndex::IterateFeatures ( CSeq_loc &  slp, Fnc  m  )

inline

Definition at line 1105 of file indexer.hpp.

References ERR_POST, Error(), m_SfxList, CException::what(), and x_InitFeats().

IterateFeatures() [2/2]

template<typename Fnc >

size_t CBioseqIndex::IterateFeatures ( Fnc  m )

inline

Definition at line 1082 of file indexer.hpp.

References ERR_POST, Error(), m_FeatsInitialized, m_SfxList, CException::what(), and x_InitFeats().

Referenced by CExploreProcess::DoOneBioseq(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), and CValidError_bioseq::x_ValidateCDSVDJCmatch().

IterateGaps()

template<typename Fnc >

size_t CBioseqIndex::IterateGaps ( Fnc  m )

inline

Definition at line 1034 of file indexer.hpp.

References ERR_POST, Error(), m_GapList, m_GapsInitialized, CException::what(), and x_InitGaps().

operator=()

CBioseqIndex& CBioseqIndex::operator= ( const CBioseqIndex &  )

privatedelete

SetFetchFailure()

void CBioseqIndex::SetFetchFailure ( bool  fails )

inline

Definition at line 466 of file indexer.hpp.

References m_FetchFailure.

x_DefaultSelector()

void CBioseqIndex::x_DefaultSelector ( SAnnotSelector &  sel, CSeqEntryIndex::EPolicy  policy, CSeqEntryIndex::TFlags  flags, bool  onlyNear, CScope &  scope  )

private

Definition at line 1849 of file indexer.cpp.

References CSeqFeatData_Base::e_Biosrc, CSeqFeatData_Base::e_Bond, CSeqFeatData_Base::e_Comment, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Site, CSeqEntryIndex::eAdaptive, CSeqEntryIndex::eExhaustive, CSeqEntryIndex::eExternal, CSeqEntryIndex::eFtp, CSeqEntryIndex::eGenomes, CSeqEntryIndex::eInternal, SAnnotSelector::eMaxSearchSegmentsSilent, CSeqFeatData::eSubtype_assembly_gap, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gap, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_pub, CSeqFeatData::eSubtype_rsite, CSeqFeatData::eSubtype_seq, CSeqFeatData::eSubtype_STS, CSeqEntryIndex::eWeb, SAnnotSelector::ExcludeFeatSubtype(), SAnnotSelector::ExcludeFeatType(), SAnnotSelector::ExcludeNamedAnnotAccession(), SAnnotSelector::ExcludeNamedAnnots(), CSeqEntryIndex::fHideCDDFeats, CSeqEntryIndex::fHideExonFeats, CSeqEntryIndex::fHideGapFeats, CSeqEntryIndex::fHideImpFeats, CSeqEntryIndex::fHideIntronFeats, CSeqEntryIndex::fHideMiscFeats, CSeqEntryIndex::fHideSNPFeats, CSeqEntryIndex::fHideSTSFeats, flags, CSeqEntryIndex::fShowCDDFeats, CSeqEntryIndex::fShowSNPFeats, GetBioseqHandle(), GetLength(), GetSeqMasterIndex(), SAnnotSelector::IncludeNamedAnnotAccession(), kMax_Int, CWeakRef< C, Locker >::Lock(), m_IsDeltaLitOnly, m_IsRefSeq, SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetExcludeExternal(), SAnnotSelector::SetFailUnresolved(), SAnnotSelector::SetFeatComparator(), SAnnotSelector::SetMaxSearchSegments(), SAnnotSelector::SetMaxSearchSegmentsAction(), SAnnotSelector::SetMaxSearchTime(), SAnnotSelector::SetResolveAll(), and SAnnotSelector::SetResolveDepth().

Referenced by GetSelector(), and x_InitFeats().

x_InitDescs()

void CBioseqIndex::x_InitDescs ( void  )

private

Definition at line 1590 of file indexer.cpp.

References _ASSERT, CSeqdesc_Base::e_Comment, CSeqdesc_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Pdb, CSeqdesc_Base::e_Source, CSeqdesc_Base::e_Title, CSeqdesc_Base::e_User, CTempString::empty(), NStr::EqualNocase(), ERR_POST_X, Error(), FIELD_IS_SET_AND_IS, NStr::Find(), FOR_EACH_COMPOUND_ON_PDBBLOCK, FOR_EACH_STRING_IN_LIST, FOR_EACH_USERFIELD_ON_USEROBJECT, NStr::fSplit_Tokenize, CPartialOrgName_Base::Get(), GET_FIELD, CMolInfo_Base::GetBiomol(), CSeqdesc_Base::GetComment(), CMolInfo_Base::GetCompleteness(), CUser_field_Base::GetData(), CTaxElement_Base::GetFixed_level(), CEMBL_block_Base::GetKeywords(), CGB_block_Base::GetKeywords(), CUser_field_Base::GetLabel(), CTaxElement_Base::GetLevel(), CSeqdesc_Base::GetMolinfo(), COrgName_Base::GetName(), CTaxElement_Base::GetName(), CBioSource::GetOrgname(), COrgName_Base::C_Name::GetPartial(), CSeqdesc_Base::GetSource(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CMolInfo_Base::GetTech(), CSeqdesc_Base::GetTitle(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), COrgName_Base::C_Name::IsPartial(), CPartialOrgName_Base::IsSet(), CUser_field_Base::IsSetData(), CTaxElement_Base::IsSetFixed_level(), CEMBL_block_Base::IsSetKeywords(), CGB_block_Base::IsSetKeywords(), CUser_field_Base::IsSetLabel(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetName(), CTaxElement_Base::IsSetName(), CBioSource::IsSetOrgname(), 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_Biomol, m_BioSource, m_Comment, m_Completeness, m_DescBioSource, m_DescsInitialized, m_FirstSuperKingdom, m_ForceOnlyNearFeats, m_HTGSCancelled, m_HTGSDraft, m_HTGSPooled, m_HTGSUnfinished, m_HTGTech, m_IsCrossKingdom, m_IsEST_STS_GSS, m_IsNA, m_IsPDB, m_IsPseudogene, m_IsTLS, m_IsTSA, m_IsUnreviewed, m_IsUnreviewedUnannotated, m_IsUnverified, m_IsUnverifiedContaminant, m_IsUnverifiedFeature, m_IsUnverifiedMisassembled, m_IsUnverifiedOrganism, m_IsVirtual, m_IsWGS, m_IsWP, m_MolInfo, m_OrigBsh, m_PDBCompound, m_SdxList, m_SecondSuperKingdom, m_TargetedLocus, m_Tech, m_ThirdParty, m_Title, m_TLSMaster, m_TPAExp, m_TPAInf, m_TPAReasm, m_TSAMaster, m_Unordered, m_UseBiosrc, NCBI_TECH, NULL, CConstRef< C, Locker >::Reset(), NStr::Split(), str(), CException::what(), and CSeqdesc_Base::Which().

Referenced by GetBiomol(), GetComment(), GetCompleteness(), GetDescriptorIndices(), GetMolInfo(), GetPDBCompound(), GetrEnzyme(), GetTargetedLocus(), GetTech(), GetTitle(), IsEST_STS_GSS(), IsForceOnlyNearFeats(), IsHTGSCancelled(), IsHTGSDraft(), IsHTGSPooled(), IsHTGSUnfinished(), IsHTGTech(), IsPseudogene(), IsTLS(), IsTPAExp(), IsTPAInf(), IsTPAReasm(), IsTSA(), IsUnordered(), IsUnreviewed(), IsUnreviewedUnannotated(), IsUnverified(), IsUnverifiedContaminant(), IsUnverifiedFeature(), IsUnverifiedMisassembled(), IsUnverifiedOrganism(), IsUseBiosrc(), IsWGS(), IterateDescriptors(), x_InitFeats(), and x_InitSource().

x_InitFeats() [1/3]

void CBioseqIndex::x_InitFeats ( CSeq_loc &  slp )

private

Definition at line 2291 of file indexer.cpp.

References x_InitFeats().

x_InitFeats() [2/3]

void CBioseqIndex::x_InitFeats ( CSeq_loc *  slpp )

private

Definition at line 2061 of file indexer.cpp.

References CSeq_id::Assign(), CSeq_id_Handle::AsString(), CSeqFeatData_Base::e_Biosrc, CSeqFeatData_Base::e_Cdregion, 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, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, eDiagFilter_All, eExtreme_Positional, CProt_ref_Base::eProcessed_not_set, ERR_POST_X, Error(), CSeqFeatData::eSubtype_gap, CSeqFeatData::eSubtype_operon, CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr, CSeqEntryIndex::fGeneRNACDSOnly, CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Handle::GetData(), GetLength(), CMappedFeat::GetLocation(), CProt_ref_Base::GetProcessed(), CMappedFeat::GetProductId(), CSeqFeatData_Base::GetProt(), CMappedFeat::GetSeq_feat_Handle(), CBioseq_Handle::GetSeqId(), GetSeqMasterIndex(), CSeq_loc::GetStart(), CFeatureIndex::GetSubtype(), CFeatureIndex::GetType(), IsAA(), IsNA(), CSeq_feat_Handle::IsSetData(), CProt_ref_Base::IsSetProcessed(), CWeakRef< C, Locker >::Lock(), m_BestProteinFeature, m_BestProtFeatInitialized, m_BioSource, m_Bsh, m_DescsInitialized, m_FeatForProdInitialized, m_FeatIndexMap, m_FeatsInitialized, m_FeatureForProduct, m_FetchFailure, m_Flags, m_ForceOnlyNearFeats, m_HasGene, m_HasMultiIntervalGenes, m_HasSource, m_Length, m_Policy, m_Scope, m_SfxList, CSeq_loc_Mapper_Base::Map(), CConstRef< C, Locker >::Reset(), SetDiagFilter(), CSeq_loc_Mapper_Base::SetFuzzOption(), SAnnotSelector::SetIgnoreStrand(), CSeq_loc::SetInt(), str(), CSeq_loc_Mapper_Base::TruncateNonmappingRanges(), CException::what(), CSeqFeatData_Base::Which(), CSeq_loc_Base::Which(), x_DefaultSelector(), and x_InitDescs().

x_InitFeats() [3/3]

void CBioseqIndex::x_InitFeats ( void  )

private

Definition at line 2285 of file indexer.cpp.

Referenced by GetBestProteinFeature(), GetFeatureForProduct(), GetFeatureIndices(), HasGene(), HasMultiIntervalGenes(), HasOperon(), HasSource(), IterateFeatures(), and x_InitFeats().

x_InitGaps()

void CBioseqIndex::x_InitGaps ( void  )

private

Definition at line 1107 of file indexer.cpp.

References ERR_POST_X, Error(), CSeqMap::fFindGap, CFastaOstream::SGapModText::gap_linkage_evidences, CFastaOstream::SGapModText::gap_type, CSeq_data_Base::GetGap(), CFastaOstream::GetGapModText(), GetSeqMasterIndex(), CSeq_data_Base::IsGap(), CWeakRef< C, Locker >::Lock(), m_GapList, m_GapsInitialized, m_IsDelta, m_OrigBsh, NULL, SSeqMapSelector::SetFlags(), SSeqMapSelector::SetResolveCount(), and CException::what().

Referenced by GetGapIndices(), and IterateGaps().

x_InitSource()

void CBioseqIndex::x_InitSource ( void  )

private

Definition at line 1305 of file indexer.cpp.

References COrgName_Base::CanGetLineage(), CBioSource_Base::CanGetOrg(), CTempString::empty(), NStr::EqualNocase(), ERR_POST_X, Error(), NStr::FindNoCase(), FOR_EACH_ORGMOD_ON_BIOSOURCE, FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CPartialOrgName_Base::Get(), COrgName_Base::C_Name::GetBinomial(), CSeqFeatData_Base::GetBiosrc(), CBioSource::GetCommon(), CSeq_feat_Handle::GetData(), GetFeatureForProduct(), CTaxElement_Base::GetFixed_level(), CBioSource_Base::GetGenome(), CBinomialOrgName_Base::GetGenus(), CTaxElement_Base::GetLevel(), COrgName_Base::GetLineage(), CFeatureIndex::GetMappedFeat(), COrgName_Base::GetName(), CSubSource_Base::GetName(), CBioSource_Base::GetOrg(), CBioSource::GetOrgname(), CFeatureIndex::GetOverlappingSource(), COrgName_Base::C_Name::GetPartial(), CBinomialOrgName_Base::GetSpecies(), COrgMod_Base::GetSubname(), COrg_ref::GetTaxId(), CBioSource::GetTaxname(), COrgName_Base::C_Name::IsBinomial(), COrgName_Base::C_Name::IsPartial(), CPartialOrgName_Base::IsSet(), CBioSource::IsSetCommon(), CTaxElement_Base::IsSetFixed_level(), CBioSource_Base::IsSetGenome(), CBinomialOrgName_Base::IsSetGenus(), CTaxElement_Base::IsSetLevel(), COrgName_Base::IsSetName(), CSubSource_Base::IsSetName(), CBioSource::IsSetOrgname(), CBinomialOrgName_Base::IsSetSpecies(), COrgMod_Base::IsSetSubname(), CBioSource::IsSetTaxname(), ITERATE, m_BioSource, m_Breed, m_Chromosome, m_Clone, m_Common, m_Cultivar, m_DescBioSource, m_DescsInitialized, m_DescTaxname, m_Genome, m_Genus, m_has_clone, m_IsAA, m_IsChromosome, m_Isolate, m_IsPlasmid, m_IsWGS, m_Lineage, m_LinkageGroup, m_Map, m_MetaGenomeSource, m_Multispecies, m_Organelle, m_Plasmid, m_Segment, m_SourcesInitialized, m_Species, m_SpecimenVoucher, m_Strain, m_Substrain, m_Taxid, m_Taxname, m_UsingAnamorph, NCBI_GENOME, NCBI_ORGMOD, NCBI_SUBSOURCE, CConstRef< C, Locker >::NotEmpty(), NPOS, NULL, CConstRef< C, Locker >::Reset(), s_BlankOrNotSpecialTaxname(), str(), SWITCH_ON_ORGMOD_CHOICE, SWITCH_ON_SUBSOURCE_CHOICE, CException::what(), x_InitDescs(), and x_OrganelleName().

Referenced by GetBioSource(), GetBreed(), GetChromosome(), GetClone(), GetCommon(), GetCultivar(), GetDescTaxname(), GetFirstSuperKingdom(), GetGenome(), GetGenus(), GetIsolate(), GetLineage(), GetLinkageGroup(), GetMap(), GetMetaGenomeSource(), GetOrganelle(), GetPlasmid(), GetSecondSuperKingdom(), GetSegment(), GetSpecies(), GetSpecimenVoucher(), GetStrain(), GetSubstrain(), GetTaxid(), GetTaxname(), HasClone(), IsChromosome(), IsCrossKingdom(), IsMultispecies(), IsPlasmid(), and IsUsingAnamorph().

Member Data Documentation

m_Accession

string CBioseqIndex::m_Accession

private

Definition at line 667 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetAccession().

m_BestProteinFeature

CRef<CFeatureIndex> CBioseqIndex::m_BestProteinFeature

private

Definition at line 641 of file indexer.hpp.

Referenced by GetBestProteinFeature(), and x_InitFeats().

m_BestProtFeatInitialized

bool CBioseqIndex::m_BestProtFeatInitialized

private

Definition at line 640 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBestProteinFeature(), and x_InitFeats().

m_Biomol

CMolInfo::TBiomol CBioseqIndex::m_Biomol

private

Definition at line 697 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBiomol(), and x_InitDescs().

m_BioSource

CConstRef<CBioSource> CBioseqIndex::m_BioSource

private

Definition at line 714 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBioSource(), x_InitDescs(), x_InitFeats(), and x_InitSource().

m_Breed

CTempString CBioseqIndex::m_Breed

private

Definition at line 745 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBreed(), and x_InitSource().

m_Bsh

CBioseq_Handle CBioseqIndex::m_Bsh

private

Definition at line 617 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBioseqHandle(), GetFeatureForProduct(), GetSequence(), and x_InitFeats().

m_Bsp

const CBioseq& CBioseqIndex::m_Bsp

private

Definition at line 618 of file indexer.hpp.

Referenced by GetBioseq().

m_Chromosome

CTempString CBioseqIndex::m_Chromosome

private

Definition at line 736 of file indexer.hpp.

Referenced by CBioseqIndex(), GetChromosome(), and x_InitSource().

m_Clone

CTempString CBioseqIndex::m_Clone

private

Definition at line 738 of file indexer.hpp.

Referenced by CBioseqIndex(), GetClone(), and x_InitSource().

m_Comment

string CBioseqIndex::m_Comment

private

Definition at line 781 of file indexer.hpp.

Referenced by CBioseqIndex(), GetComment(), and x_InitDescs().

m_Common

string CBioseqIndex::m_Common

private

Definition at line 717 of file indexer.hpp.

Referenced by CBioseqIndex(), GetCommon(), and x_InitSource().

m_Completeness

CMolInfo::TCompleteness CBioseqIndex::m_Completeness

private

Definition at line 699 of file indexer.hpp.

Referenced by CBioseqIndex(), GetCompleteness(), and x_InitDescs().

m_Cultivar

CTempString CBioseqIndex::m_Cultivar

private

Definition at line 746 of file indexer.hpp.

Referenced by CBioseqIndex(), GetCultivar(), and x_InitSource().

m_DescBioSource

CConstRef<CBioSource> CBioseqIndex::m_DescBioSource

private

Definition at line 711 of file indexer.hpp.

Referenced by CBioseqIndex(), x_InitDescs(), and x_InitSource().

m_DescsInitialized

bool CBioseqIndex::m_DescsInitialized

private

Definition at line 629 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBiomol(), GetComment(), GetCompleteness(), GetDescriptorIndices(), GetMolInfo(), GetPDBCompound(), GetrEnzyme(), GetTargetedLocus(), GetTech(), GetTitle(), IsEST_STS_GSS(), IsForceOnlyNearFeats(), IsHTGSCancelled(), IsHTGSDraft(), IsHTGSPooled(), IsHTGSUnfinished(), IsHTGTech(), IsPseudogene(), IsTLS(), IsTPAExp(), IsTPAInf(), IsTPAReasm(), IsTSA(), IsUnordered(), IsUnreviewed(), IsUnreviewedUnannotated(), IsUnverified(), IsUnverifiedContaminant(), IsUnverifiedFeature(), IsUnverifiedMisassembled(), IsUnverifiedOrganism(), IsUseBiosrc(), IsWGS(), IterateDescriptors(), x_InitDescs(), x_InitFeats(), and x_InitSource().

m_DescTaxname

string CBioseqIndex::m_DescTaxname

private

Definition at line 712 of file indexer.hpp.

Referenced by CBioseqIndex(), GetDescTaxname(), and x_InitSource().

m_FeatForProdInitialized

bool CBioseqIndex::m_FeatForProdInitialized

private

Definition at line 637 of file indexer.hpp.

Referenced by CBioseqIndex(), GetFeatureForProduct(), and x_InitFeats().

m_FeatIndexMap

TFeatIndexMap CBioseqIndex::m_FeatIndexMap

private

Definition at line 645 of file indexer.hpp.

Referenced by GetFeatIndex(), and x_InitFeats().

m_FeatsInitialized

bool CBioseqIndex::m_FeatsInitialized

private

Definition at line 632 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBestProteinFeature(), GetFeatureForProduct(), GetFeatureIndices(), HasGene(), HasMultiIntervalGenes(), HasOperon(), HasSource(), IterateFeatures(), and x_InitFeats().

m_FeatureForProduct

CRef<CFeatureIndex> CBioseqIndex::m_FeatureForProduct

private

Definition at line 638 of file indexer.hpp.

Referenced by GetFeatureForProduct(), and x_InitFeats().

m_FetchFailure

bool CBioseqIndex::m_FetchFailure

private

Definition at line 652 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSequence(), IsFetchFailure(), SetFetchFailure(), and x_InitFeats().

m_FirstSuperKingdom

string CBioseqIndex::m_FirstSuperKingdom

private

Definition at line 731 of file indexer.hpp.

Referenced by CBioseqIndex(), GetFirstSuperKingdom(), and x_InitDescs().

m_Flags

CSeqEntryIndex::TFlags CBioseqIndex::m_Flags

private

Definition at line 650 of file indexer.hpp.

Referenced by GetSelector(), and x_InitFeats().

m_ForceOnlyNearFeats

bool CBioseqIndex::m_ForceOnlyNearFeats

private

Definition at line 766 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSelector(), IsForceOnlyNearFeats(), x_InitDescs(), and x_InitFeats().

m_GapList

vector<CRef<CGapIndex> > CBioseqIndex::m_GapList

private

Definition at line 627 of file indexer.hpp.

Referenced by GetGapIndices(), IterateGaps(), and x_InitGaps().

m_GapsInitialized

bool CBioseqIndex::m_GapsInitialized

private

Definition at line 626 of file indexer.hpp.

Referenced by CBioseqIndex(), GetGapIndices(), IterateGaps(), and x_InitGaps().

m_GeneralId

int CBioseqIndex::m_GeneralId

private

Definition at line 683 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetGeneralId().

m_GeneralStr

string CBioseqIndex::m_GeneralStr

private

Definition at line 682 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetGeneralStr().

m_Genome

CBioSource::TGenome CBioseqIndex::m_Genome

private

Definition at line 725 of file indexer.hpp.

Referenced by CBioseqIndex(), GetGenome(), and x_InitSource().

m_Genus

CTempString CBioseqIndex::m_Genus

private

Definition at line 722 of file indexer.hpp.

Referenced by CBioseqIndex(), GetGenus(), and x_InitSource().

m_has_clone

bool CBioseqIndex::m_has_clone

private

Definition at line 739 of file indexer.hpp.

Referenced by CBioseqIndex(), HasClone(), and x_InitSource().

m_HasGene

bool CBioseqIndex::m_HasGene

private

Definition at line 785 of file indexer.hpp.

Referenced by CBioseqIndex(), HasGene(), and x_InitFeats().

m_HasMultiIntervalGenes

bool CBioseqIndex::m_HasMultiIntervalGenes

private

Definition at line 786 of file indexer.hpp.

Referenced by CBioseqIndex(), HasMultiIntervalGenes(), and x_InitFeats().

m_HasSource

bool CBioseqIndex::m_HasSource

private

Definition at line 787 of file indexer.hpp.

Referenced by CBioseqIndex(), HasSource(), and x_InitFeats().

m_HTGSCancelled

bool CBioseqIndex::m_HTGSCancelled

private

Definition at line 754 of file indexer.hpp.

Referenced by CBioseqIndex(), IsHTGSCancelled(), and x_InitDescs().

m_HTGSDraft

bool CBioseqIndex::m_HTGSDraft

private

Definition at line 755 of file indexer.hpp.

Referenced by CBioseqIndex(), IsHTGSDraft(), and x_InitDescs().

m_HTGSPooled

bool CBioseqIndex::m_HTGSPooled

private

Definition at line 756 of file indexer.hpp.

Referenced by CBioseqIndex(), IsHTGSPooled(), and x_InitDescs().

m_HTGSUnfinished

bool CBioseqIndex::m_HTGSUnfinished

private

Definition at line 702 of file indexer.hpp.

Referenced by CBioseqIndex(), IsHTGSUnfinished(), and x_InitDescs().

m_HTGTech

bool CBioseqIndex::m_HTGTech

private

Definition at line 701 of file indexer.hpp.

Referenced by CBioseqIndex(), IsHTGTech(), and x_InitDescs().

m_Idx

CWeakRef<CSeqMasterIndex> CBioseqIndex::m_Idx

private

Definition at line 624 of file indexer.hpp.

Referenced by GetSeqMasterIndex().

m_IsAA

bool CBioseqIndex::m_IsAA

private

Definition at line 657 of file indexer.hpp.

Referenced by CBioseqIndex(), IsAA(), and x_InitSource().

m_IsChromosome

bool CBioseqIndex::m_IsChromosome

private

Definition at line 727 of file indexer.hpp.

Referenced by CBioseqIndex(), IsChromosome(), and x_InitSource().

m_IsCrossKingdom

bool CBioseqIndex::m_IsCrossKingdom

private

Definition at line 733 of file indexer.hpp.

Referenced by CBioseqIndex(), IsCrossKingdom(), and x_InitDescs().

m_IsDelta

bool CBioseqIndex::m_IsDelta

private

Definition at line 661 of file indexer.hpp.

Referenced by CBioseqIndex(), IsDelta(), and x_InitGaps().

m_IsDeltaLitOnly

bool CBioseqIndex::m_IsDeltaLitOnly

private

Definition at line 662 of file indexer.hpp.

Referenced by CBioseqIndex(), IsDeltaLitOnly(), and x_DefaultSelector().

m_IsEST_STS_GSS

bool CBioseqIndex::m_IsEST_STS_GSS

private

Definition at line 706 of file indexer.hpp.

Referenced by CBioseqIndex(), IsEST_STS_GSS(), and x_InitDescs().

m_IsMap

bool CBioseqIndex::m_IsMap

private

Definition at line 664 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsMap().

m_IsNA

bool CBioseqIndex::m_IsNA

private

Definition at line 656 of file indexer.hpp.

Referenced by CBioseqIndex(), IsNA(), and x_InitDescs().

m_IsNC

bool CBioseqIndex::m_IsNC

private

Definition at line 670 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsNC().

m_IsNM

bool CBioseqIndex::m_IsNM

private

Definition at line 671 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsNM().

m_IsNR

bool CBioseqIndex::m_IsNR

private

Definition at line 672 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsNR().

m_IsNZ

bool CBioseqIndex::m_IsNZ

private

Definition at line 673 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsNZ().

m_Isolate

CTempString CBioseqIndex::m_Isolate

private

Definition at line 748 of file indexer.hpp.

Referenced by CBioseqIndex(), GetIsolate(), and x_InitSource().

m_IsPatent

bool CBioseqIndex::m_IsPatent

private

Definition at line 674 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsPatent().

m_IsPDB

bool CBioseqIndex::m_IsPDB

private

Definition at line 675 of file indexer.hpp.

Referenced by CBioseqIndex(), IsPDB(), and x_InitDescs().

m_IsPlasmid

bool CBioseqIndex::m_IsPlasmid

private

Definition at line 726 of file indexer.hpp.

Referenced by CBioseqIndex(), IsPlasmid(), and x_InitSource().

m_IsPseudogene

bool CBioseqIndex::m_IsPseudogene

private

Definition at line 782 of file indexer.hpp.

Referenced by CBioseqIndex(), IsPseudogene(), and x_InitDescs().

m_IsRefSeq

bool CBioseqIndex::m_IsRefSeq

private

Definition at line 669 of file indexer.hpp.

Referenced by CBioseqIndex(), IsRefSeq(), and x_DefaultSelector().

m_IsTLS

bool CBioseqIndex::m_IsTLS

private

Definition at line 703 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTLS(), and x_InitDescs().

m_IsTSA

bool CBioseqIndex::m_IsTSA

private

Definition at line 704 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTSA(), and x_InitDescs().

m_IsUnreviewed

bool CBioseqIndex::m_IsUnreviewed

private

Definition at line 775 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnreviewed(), and x_InitDescs().

m_IsUnreviewedUnannotated

bool CBioseqIndex::m_IsUnreviewedUnannotated

private

Definition at line 776 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnreviewedUnannotated(), and x_InitDescs().

m_IsUnverified

bool CBioseqIndex::m_IsUnverified

private

Definition at line 768 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnverified(), and x_InitDescs().

m_IsUnverifiedContaminant

bool CBioseqIndex::m_IsUnverifiedContaminant

private

Definition at line 772 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnverifiedContaminant(), and x_InitDescs().

m_IsUnverifiedFeature

bool CBioseqIndex::m_IsUnverifiedFeature

private

Definition at line 769 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnverifiedFeature(), and x_InitDescs().

m_IsUnverifiedMisassembled

bool CBioseqIndex::m_IsUnverifiedMisassembled

private

Definition at line 771 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnverifiedMisassembled(), and x_InitDescs().

m_IsUnverifiedOrganism

bool CBioseqIndex::m_IsUnverifiedOrganism

private

Definition at line 770 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnverifiedOrganism(), and x_InitDescs().

m_IsVirtual

bool CBioseqIndex::m_IsVirtual

private

Definition at line 663 of file indexer.hpp.

Referenced by CBioseqIndex(), IsVirtual(), and x_InitDescs().

m_IsWGS

bool CBioseqIndex::m_IsWGS

private

Definition at line 705 of file indexer.hpp.

Referenced by CBioseqIndex(), IsWGS(), x_InitDescs(), and x_InitSource().

m_IsWP

bool CBioseqIndex::m_IsWP

private

Definition at line 676 of file indexer.hpp.

Referenced by CBioseqIndex(), IsWP(), and x_InitDescs().

m_Length

CSeq_inst::TLength CBioseqIndex::m_Length

private

Definition at line 659 of file indexer.hpp.

Referenced by CBioseqIndex(), GetLength(), and x_InitFeats().

m_Lineage

string CBioseqIndex::m_Lineage

private

Definition at line 718 of file indexer.hpp.

Referenced by CBioseqIndex(), GetLineage(), and x_InitSource().

m_LinkageGroup

CTempString CBioseqIndex::m_LinkageGroup

private

Definition at line 737 of file indexer.hpp.

Referenced by CBioseqIndex(), GetLinkageGroup(), and x_InitSource().

m_Map

CTempString CBioseqIndex::m_Map

private

Definition at line 740 of file indexer.hpp.

Referenced by CBioseqIndex(), GetMap(), and x_InitSource().

m_MetaGenomeSource

CTempString CBioseqIndex::m_MetaGenomeSource

private

Definition at line 751 of file indexer.hpp.

Referenced by CBioseqIndex(), GetMetaGenomeSource(), and x_InitSource().

m_MolInfo

CConstRef<CMolInfo> CBioseqIndex::m_MolInfo

private

Definition at line 696 of file indexer.hpp.

Referenced by CBioseqIndex(), GetMolInfo(), and x_InitDescs().

m_Multispecies

bool CBioseqIndex::m_Multispecies

private

Definition at line 724 of file indexer.hpp.

Referenced by CBioseqIndex(), IsMultispecies(), and x_InitSource().

m_Organelle

string CBioseqIndex::m_Organelle

private

Definition at line 729 of file indexer.hpp.

Referenced by CBioseqIndex(), GetOrganelle(), and x_InitSource().

m_OrigBsh

CBioseq_Handle CBioseqIndex::m_OrigBsh

private

Definition at line 619 of file indexer.hpp.

Referenced by GetOrigBioseqHandle(), x_InitDescs(), and x_InitGaps().

m_PatentCountry

string CBioseqIndex::m_PatentCountry

private

Definition at line 685 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetPatentCountry().

m_PatentNumber

string CBioseqIndex::m_PatentNumber

private

Definition at line 686 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetPatentNumber().

m_PatentSequence

int CBioseqIndex::m_PatentSequence

private

Definition at line 687 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetPatentSequence().

m_PDBChain

int CBioseqIndex::m_PDBChain

private

Definition at line 689 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetPDBChain().

m_PDBChainID

string CBioseqIndex::m_PDBChainID

private

Definition at line 690 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetPDBChainID().

m_PDBCompound

CTempString CBioseqIndex::m_PDBCompound

private

Definition at line 763 of file indexer.hpp.

Referenced by CBioseqIndex(), GetPDBCompound(), and x_InitDescs().

m_Plasmid

CTempString CBioseqIndex::m_Plasmid

private

Definition at line 741 of file indexer.hpp.

Referenced by CBioseqIndex(), GetPlasmid(), and x_InitSource().

m_Policy

CSeqEntryIndex::EPolicy CBioseqIndex::m_Policy

private

Definition at line 649 of file indexer.hpp.

Referenced by GetSelector(), and x_InitFeats().

m_Prnt

CRef<CSeqsetIndex> CBioseqIndex::m_Prnt

private

Definition at line 620 of file indexer.hpp.

Referenced by GetParent().

m_rEnzyme

string CBioseqIndex::m_rEnzyme

private

Definition at line 790 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetrEnzyme().

m_Scope

CRef<CScope> CBioseqIndex::m_Scope

private

Definition at line 622 of file indexer.hpp.

Referenced by GetFeatureForProduct(), GetScope(), GetSelector(), and x_InitFeats().

m_SdxList

vector<CRef<CDescriptorIndex> > CBioseqIndex::m_SdxList

private

Definition at line 630 of file indexer.hpp.

Referenced by GetDescriptorIndices(), IterateDescriptors(), and x_InitDescs().

m_SecondSuperKingdom

string CBioseqIndex::m_SecondSuperKingdom

private

Definition at line 732 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSecondSuperKingdom(), and x_InitDescs().

m_Segment

CTempString CBioseqIndex::m_Segment

private

Definition at line 742 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSegment(), and x_InitSource().

m_SeqVec

CRef<CSeqVector> CBioseqIndex::m_SeqVec

private

Definition at line 647 of file indexer.hpp.

Referenced by GetSequence(), and GetSeqVector().

m_SfxList

vector<CRef<CFeatureIndex> > CBioseqIndex::m_SfxList

private

Definition at line 633 of file indexer.hpp.

Referenced by GetFeatureIndices(), IterateFeatures(), and x_InitFeats().

m_SourcesInitialized

bool CBioseqIndex::m_SourcesInitialized

private

Definition at line 635 of file indexer.hpp.

Referenced by CBioseqIndex(), GetBioSource(), GetBreed(), GetChromosome(), GetClone(), GetCommon(), GetCultivar(), GetDescTaxname(), GetFirstSuperKingdom(), GetGenome(), GetGenus(), GetIsolate(), GetLineage(), GetLinkageGroup(), GetMap(), GetMetaGenomeSource(), GetOrganelle(), GetPlasmid(), GetSecondSuperKingdom(), GetSegment(), GetSpecies(), GetSpecimenVoucher(), GetStrain(), GetSubstrain(), GetTaxid(), GetTaxname(), HasClone(), IsChromosome(), IsCrossKingdom(), IsMultispecies(), IsPlasmid(), IsUsingAnamorph(), and x_InitSource().

m_Species

CTempString CBioseqIndex::m_Species

private

Definition at line 723 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSpecies(), and x_InitSource().

m_SpecimenVoucher

CTempString CBioseqIndex::m_SpecimenVoucher

private

Definition at line 747 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSpecimenVoucher(), and x_InitSource().

m_Strain

CTempString CBioseqIndex::m_Strain

private

Definition at line 749 of file indexer.hpp.

Referenced by CBioseqIndex(), GetStrain(), and x_InitSource().

m_Substrain

CTempString CBioseqIndex::m_Substrain

private

Definition at line 750 of file indexer.hpp.

Referenced by CBioseqIndex(), GetSubstrain(), and x_InitSource().

m_TargetedLocus

CTempString CBioseqIndex::m_TargetedLocus

private

Definition at line 778 of file indexer.hpp.

Referenced by CBioseqIndex(), GetTargetedLocus(), and x_InitDescs().

m_Taxid

TTaxId CBioseqIndex::m_Taxid

private

Definition at line 719 of file indexer.hpp.

Referenced by CBioseqIndex(), GetTaxid(), and x_InitSource().

m_Taxname

string CBioseqIndex::m_Taxname

private

Definition at line 715 of file indexer.hpp.

Referenced by CBioseqIndex(), GetTaxname(), and x_InitSource().

m_Tech

CMolInfo::TTech CBioseqIndex::m_Tech

private

Definition at line 698 of file indexer.hpp.

Referenced by CBioseqIndex(), GetTech(), and x_InitDescs().

m_ThirdParty

bool CBioseqIndex::m_ThirdParty

private

Definition at line 677 of file indexer.hpp.

Referenced by CBioseqIndex(), IsThirdParty(), and x_InitDescs().

m_Title

string CBioseqIndex::m_Title

private

Definition at line 693 of file indexer.hpp.

Referenced by CBioseqIndex(), GetTitle(), and x_InitDescs().

m_TLSMaster

bool CBioseqIndex::m_TLSMaster

private

Definition at line 680 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTLSMaster(), and x_InitDescs().

m_Topology

CSeq_inst::TTopology CBioseqIndex::m_Topology

private

Definition at line 658 of file indexer.hpp.

Referenced by CBioseqIndex(), and GetTopology().

m_TPAExp

bool CBioseqIndex::m_TPAExp

private

Definition at line 757 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTPAExp(), and x_InitDescs().

m_TPAInf

bool CBioseqIndex::m_TPAInf

private

Definition at line 758 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTPAInf(), and x_InitDescs().

m_TPAReasm

bool CBioseqIndex::m_TPAReasm

private

Definition at line 759 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTPAReasm(), and x_InitDescs().

m_TSAMaster

bool CBioseqIndex::m_TSAMaster

private

Definition at line 679 of file indexer.hpp.

Referenced by CBioseqIndex(), IsTSAMaster(), and x_InitDescs().

m_Tseh

CSeq_entry_Handle CBioseqIndex::m_Tseh

private

Definition at line 621 of file indexer.hpp.

m_Unordered

bool CBioseqIndex::m_Unordered

private

Definition at line 760 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUnordered(), and x_InitDescs().

m_UnreviewedPrefix

CTempString CBioseqIndex::m_UnreviewedPrefix

private

Definition at line 777 of file indexer.hpp.

m_UnverifiedPrefix

CTempString CBioseqIndex::m_UnverifiedPrefix

private

Definition at line 773 of file indexer.hpp.

m_UseBiosrc

bool CBioseqIndex::m_UseBiosrc

private

Definition at line 708 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUseBiosrc(), and x_InitDescs().

m_UsingAnamorph

bool CBioseqIndex::m_UsingAnamorph

private

Definition at line 720 of file indexer.hpp.

Referenced by CBioseqIndex(), IsUsingAnamorph(), and x_InitSource().

m_WGSMaster

bool CBioseqIndex::m_WGSMaster

private

Definition at line 678 of file indexer.hpp.

Referenced by CBioseqIndex(), and IsWGSMaster().

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

• include/objmgr/util/indexer.hpp
• src/objmgr/util/indexer.cpp