NCBI C++ ToolKit
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CBioseqIndex Class Reference

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#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 CBioseqGetBioseq (void) const
 
CBioseq_Handle GetOrigBioseqHandle (void) const
 
CRef< CSeqsetIndexGetParent (void) const
 
CRef< CScopeGetScope (void) const
 
CRef< CSeqVectorGetSeqVector (void) const
 
CWeakRef< CSeqMasterIndexGetSeqMasterIndex (void) const
 
string GetSequence (void)
 
void GetSequence (string &buffer)
 
string GetSequence (int from, int to)
 
void GetSequence (int from, int to, string &buffer)
 
CRef< CFeatureIndexGetFeatIndex (const CMappedFeat &mf)
 
const vector< CRef< CGapIndex > > & GetGapIndices (void)
 
const vector< CRef< CDescriptorIndex > > & GetDescriptorIndices (void)
 
const vector< CRef< CFeatureIndex > > & GetFeatureIndices (void)
 
CRef< CFeatureIndexGetFeatureForProduct (void)
 
CWeakRef< CBioseqIndexGetBioseqForProduct (void)
 
CRef< CFeatureIndexGetBestProteinFeature (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 stringGetAccession (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 stringGetTitle (void)
 
CConstRef< CMolInfoGetMolInfo (void)
 
CMolInfo::TBiomol GetBiomol (void)
 
CMolInfo::TTech GetTech (void)
 
CMolInfo::TCompleteness GetCompleteness (void)
 
CConstRef< CBioSourceGetBioSource (void)
 
const stringGetTaxname (void)
 
const stringGetDescTaxname (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 stringGetCommon (void)
 
const stringGetLineage (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 stringGetOrganelle (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 stringGetComment (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...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 
- Public Member Functions inherited from CWeakObject
 CWeakObject (void)
 
virtual ~CWeakObject (void)
 
CPtrToObjectProxyGetPtrProxy (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
 
CBioseqIndexoperator= (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 CBioseqm_Bsp
 
CBioseq_Handle m_OrigBsh
 
CRef< CSeqsetIndexm_Prnt
 
CSeq_entry_Handle m_Tseh
 
CRef< CScopem_Scope
 
CWeakRef< CSeqMasterIndexm_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< CFeatureIndexm_FeatureForProduct
 
bool m_BestProtFeatInitialized
 
CRef< CFeatureIndexm_BestProteinFeature
 
TFeatIndexMap m_FeatIndexMap
 
CRef< CSeqVectorm_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< CMolInfom_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< CBioSourcem_DescBioSource
 
string m_DescTaxname
 
CConstRef< CBioSourcem_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< Uint8TCounter
 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

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(), data, 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(), 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(), 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  )

◆ GetBiomol()

CMolInfo::TBiomol CBioseqIndex::GetBiomol ( void  )

Definition at line 2386 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  )

◆ 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  )

◆ GetBreed()

CTempString CBioseqIndex::GetBreed ( void  )

◆ GetChromosome()

CTempString CBioseqIndex::GetChromosome ( void  )

◆ GetClone()

CTempString CBioseqIndex::GetClone ( void  )

◆ GetComment()

const string & CBioseqIndex::GetComment ( void  )

Definition at line 2968 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 2516 of file indexer.cpp.

References m_Common, m_SourcesInitialized, and x_InitSource().

◆ GetCompleteness()

CMolInfo::TCompleteness CBioseqIndex::GetCompleteness ( void  )

Definition at line 2406 of file indexer.cpp.

References m_Completeness, m_DescsInitialized, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

◆ GetCultivar()

CTempString CBioseqIndex::GetCultivar ( void  )

◆ GetDescriptorIndices()

const vector< CRef< CDescriptorIndex > > & CBioseqIndex::GetDescriptorIndices ( void  )

Definition at line 3128 of file indexer.cpp.

References m_DescsInitialized, m_SdxList, and x_InitDescs().

◆ GetDescTaxname()

const string & CBioseqIndex::GetDescTaxname ( void  )

◆ GetFeatIndex()

CRef< CFeatureIndex > CBioseqIndex::GetFeatIndex ( const CMappedFeat mf)

◆ GetFeatureForProduct()

CRef< CFeatureIndex > CBioseqIndex::GetFeatureForProduct ( void  )

◆ GetFeatureIndices()

const vector< CRef< CFeatureIndex > > & CBioseqIndex::GetFeatureIndices ( void  )

Definition at line 3138 of file indexer.cpp.

References m_FeatsInitialized, m_SfxList, and x_InitFeats().

◆ GetFirstSuperKingdom()

string CBioseqIndex::GetFirstSuperKingdom ( void  )

Definition at line 2626 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  )

◆ 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  )

◆ GetGenus()

CTempString CBioseqIndex::GetGenus ( void  )

◆ GetIsolate()

CTempString CBioseqIndex::GetIsolate ( void  )

◆ GetLength()

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

◆ GetLineage()

const string & CBioseqIndex::GetLineage ( void  )

Definition at line 2526 of file indexer.cpp.

References m_Lineage, m_SourcesInitialized, and x_InitSource().

◆ GetLinkageGroup()

CTempString CBioseqIndex::GetLinkageGroup ( void  )

◆ GetMap()

CTempString CBioseqIndex::GetMap ( void  )

◆ GetMetaGenomeSource()

CTempString CBioseqIndex::GetMetaGenomeSource ( void  )

◆ GetMolInfo()

CConstRef< CMolInfo > CBioseqIndex::GetMolInfo ( void  )

Definition at line 2376 of file indexer.cpp.

References m_DescsInitialized, m_MolInfo, and x_InitDescs().

◆ GetOrganelle()

const string & CBioseqIndex::GetOrganelle ( void  )

◆ 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 2868 of file indexer.cpp.

References m_DescsInitialized, m_PDBCompound, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

◆ GetPlasmid()

CTempString CBioseqIndex::GetPlasmid ( void  )

◆ GetrEnzyme()

string CBioseqIndex::GetrEnzyme ( void  )

Definition at line 3034 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  )

◆ GetSegment()

CTempString CBioseqIndex::GetSegment ( void  )

◆ GetSelector()

void CBioseqIndex::GetSelector ( SAnnotSelector sel)

◆ 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 3092 of file indexer.cpp.

References buffer, and GetSequence().

◆ GetSequence() [2/4]

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

◆ GetSequence() [3/4]

void CBioseqIndex::GetSequence ( string buffer)

Definition at line 3102 of file indexer.cpp.

References buffer, and GetSequence().

◆ GetSequence() [4/4]

string CBioseqIndex::GetSequence ( void  )

Definition at line 3108 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  )

◆ GetSpecimenVoucher()

CTempString CBioseqIndex::GetSpecimenVoucher ( void  )

◆ GetStrain()

CTempString CBioseqIndex::GetStrain ( void  )

◆ GetSubstrain()

CTempString CBioseqIndex::GetSubstrain ( void  )

◆ GetTargetedLocus()

CTempString CBioseqIndex::GetTargetedLocus ( void  )

Definition at line 2958 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 2536 of file indexer.cpp.

References m_SourcesInitialized, m_Taxid, and x_InitSource().

◆ GetTaxname()

const string & CBioseqIndex::GetTaxname ( void  )

◆ GetTech()

CMolInfo::TTech CBioseqIndex::GetTech ( void  )

Definition at line 2396 of file indexer.cpp.

References m_DescsInitialized, m_Tech, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

◆ GetTitle()

const string & CBioseqIndex::GetTitle ( void  )

◆ 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  )

◆ HasGene()

bool CBioseqIndex::HasGene ( void  )

Definition at line 3004 of file indexer.cpp.

References m_FeatsInitialized, m_HasGene, and x_InitFeats().

◆ HasMultiIntervalGenes()

bool CBioseqIndex::HasMultiIntervalGenes ( void  )

◆ HasOperon()

bool CBioseqIndex::HasOperon ( void  )

◆ HasSource()

bool CBioseqIndex::HasSource ( void  )

Definition at line 3024 of file indexer.cpp.

References m_FeatsInitialized, m_HasSource, and x_InitFeats().

◆ IsAA()

bool CBioseqIndex::IsAA ( void  ) const
inline

◆ IsChromosome()

bool CBioseqIndex::IsChromosome ( void  )

◆ IsCrossKingdom()

bool CBioseqIndex::IsCrossKingdom ( void  )

◆ 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 2466 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 2878 of file indexer.cpp.

References m_DescsInitialized, m_ForceOnlyNearFeats, and x_InitDescs().

◆ IsHTGSCancelled()

bool CBioseqIndex::IsHTGSCancelled ( void  )

Definition at line 2798 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 2808 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 2818 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 2426 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 2416 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  )

◆ IsNA()

bool CBioseqIndex::IsNA ( void  ) const
inline

◆ 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  )

◆ IsPseudogene()

bool CBioseqIndex::IsPseudogene ( void  )

Definition at line 2978 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 2436 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 2828 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 2838 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 2848 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 2446 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 2858 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 2938 of file indexer.cpp.

References m_DescsInitialized, m_IsUnreviewed, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

◆ IsUnreviewedUnannotated()

bool CBioseqIndex::IsUnreviewedUnannotated ( void  )

◆ IsUnverified()

bool CBioseqIndex::IsUnverified ( void  )

Definition at line 2888 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverified, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

◆ IsUnverifiedContaminant()

bool CBioseqIndex::IsUnverifiedContaminant ( void  )

◆ IsUnverifiedFeature()

bool CBioseqIndex::IsUnverifiedFeature ( void  )

Definition at line 2898 of file indexer.cpp.

References m_DescsInitialized, m_IsUnverifiedFeature, and x_InitDescs().

Referenced by CDeflineGenerator::x_SetFlagsIdx().

◆ IsUnverifiedMisassembled()

bool CBioseqIndex::IsUnverifiedMisassembled ( void  )

◆ IsUnverifiedOrganism()

bool CBioseqIndex::IsUnverifiedOrganism ( void  )

Definition at line 2908 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 2476 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 2546 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 2456 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

◆ 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

◆ 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 2292 of file indexer.cpp.

References x_InitFeats().

◆ x_InitFeats() [2/3]

void CBioseqIndex::x_InitFeats ( CSeq_loc slpp)
private

Definition at line 2062 of file indexer.cpp.

References CSeq_id::Assign(), CSeq_id_Handle::AsString(), data, 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(), CSeq_loc_Base::Which(), x_DefaultSelector(), and x_InitDescs().

◆ x_InitFeats() [3/3]

void CBioseqIndex::x_InitFeats ( void  )
private

◆ x_InitGaps()

void CBioseqIndex::x_InitGaps ( void  )
private

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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

◆ 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().


The documentation for this class was generated from the following files:
Modified on Tue May 28 05:54:33 2024 by modify_doxy.py rev. 669887