NCBI C++ ToolKit
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Search Toolkit Book for CBioseqIndex
#include <objmgr/util/indexer.hpp>
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) |
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... | |
Definition at line 394 of file indexer.hpp.
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private |
Definition at line 644 of file indexer.hpp.
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 | ||
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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 | ( | void | ) |
Definition at line 1101 of file indexer.cpp.
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Definition at line 482 of file indexer.hpp.
References m_Accession.
Referenced by CExploreProcess::DoOneBioseq(), and CSeqMasterIndex::x_InitSeqs().
CRef< CFeatureIndex > CBioseqIndex::GetBestProteinFeature | ( | void | ) |
Definition at line 2353 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().
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().
Definition at line 429 of file indexer.hpp.
References m_Bsp.
CWeakRef< CBioseqIndex > CBioseqIndex::GetBioseqForProduct | ( | void | ) |
Definition at line 2341 of file indexer.cpp.
References CFeatureIndex::GetBioseqIndex(), and GetFeatureForProduct().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffix(), CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), and CDeflineGenerator::x_SetPrefix().
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CConstRef< CBioSource > CBioseqIndex::GetBioSource | ( | void | ) |
Definition at line 2486 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().
CTempString CBioseqIndex::GetBreed | ( | void | ) |
Definition at line 2726 of file indexer.cpp.
References m_Breed, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetChromosome | ( | void | ) |
Definition at line 2656 of file indexer.cpp.
References m_Chromosome, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetClone | ( | void | ) |
Definition at line 2676 of file indexer.cpp.
References m_Clone, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
Definition at line 2968 of file indexer.cpp.
References m_Comment, m_DescsInitialized, and x_InitDescs().
Referenced by CDeflineGenerator::x_SetFlagsIdx().
Definition at line 2516 of file indexer.cpp.
References m_Common, m_SourcesInitialized, and x_InitSource().
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().
CTempString CBioseqIndex::GetCultivar | ( | void | ) |
Definition at line 2736 of file indexer.cpp.
References m_Cultivar, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
const vector< CRef< CDescriptorIndex > > & CBioseqIndex::GetDescriptorIndices | ( | void | ) |
Definition at line 3128 of file indexer.cpp.
References m_DescsInitialized, m_SdxList, and x_InitDescs().
Definition at line 2506 of file indexer.cpp.
References m_DescTaxname, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx().
CRef< CFeatureIndex > CBioseqIndex::GetFeatIndex | ( | const CMappedFeat & | mf | ) |
Definition at line 3044 of file indexer.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), and m_FeatIndexMap.
Referenced by CFeatureItem::x_AddQualsIdx().
CRef< CFeatureIndex > CBioseqIndex::GetFeatureForProduct | ( | void | ) |
Definition at line 2299 of file indexer.cpp.
References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, 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().
const vector< CRef< CFeatureIndex > > & CBioseqIndex::GetFeatureIndices | ( | void | ) |
Definition at line 3138 of file indexer.cpp.
References m_FeatsInitialized, m_SfxList, and x_InitFeats().
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().
Definition at line 3118 of file indexer.cpp.
References m_GapList, m_GapsInitialized, and x_InitGaps().
Referenced by CExploreProcess::DoOneBioseq(), and CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx().
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Definition at line 498 of file indexer.hpp.
References m_GeneralId.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 497 of file indexer.hpp.
References m_GeneralStr.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
CBioSource::TGenome CBioseqIndex::GetGenome | ( | void | ) |
Definition at line 2586 of file indexer.cpp.
References m_Genome, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetGenus | ( | void | ) |
Definition at line 2556 of file indexer.cpp.
References m_Genus, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetIsolate | ( | void | ) |
Definition at line 2758 of file indexer.cpp.
References m_Isolate, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 474 of file indexer.hpp.
References m_Length.
Referenced by CExploreProcess::DoOneBioseq(), x_DefaultSelector(), and CDeflineGenerator::x_SetFlagsIdx().
Definition at line 2526 of file indexer.cpp.
References m_Lineage, m_SourcesInitialized, and x_InitSource().
CTempString CBioseqIndex::GetLinkageGroup | ( | void | ) |
Definition at line 2666 of file indexer.cpp.
References m_LinkageGroup, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetMap | ( | void | ) |
Definition at line 2696 of file indexer.cpp.
References m_Map, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetMetaGenomeSource | ( | void | ) |
Definition at line 2788 of file indexer.cpp.
References m_MetaGenomeSource, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
Definition at line 2376 of file indexer.cpp.
References m_DescsInitialized, m_MolInfo, and x_InitDescs().
Definition at line 2616 of file indexer.cpp.
References m_Organelle, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 430 of file indexer.hpp.
References m_OrigBsh.
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Definition at line 431 of file indexer.hpp.
References m_Prnt.
Referenced by CExploreProcess::DoOneBioseq().
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Definition at line 500 of file indexer.hpp.
References m_PatentCountry.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 501 of file indexer.hpp.
References m_PatentNumber.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 502 of file indexer.hpp.
References m_PatentSequence.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 504 of file indexer.hpp.
References m_PDBChain.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 505 of file indexer.hpp.
References m_PDBChainID.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
CTempString CBioseqIndex::GetPlasmid | ( | void | ) |
Definition at line 2706 of file indexer.cpp.
References m_Plasmid, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
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().
Definition at line 432 of file indexer.hpp.
References m_Scope.
string CBioseqIndex::GetSecondSuperKingdom | ( | void | ) |
Definition at line 2636 of file indexer.cpp.
References m_SecondSuperKingdom, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetSegment | ( | void | ) |
Definition at line 2716 of file indexer.cpp.
References m_Segment, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
void CBioseqIndex::GetSelector | ( | SAnnotSelector & | sel | ) |
Definition at line 2055 of file indexer.cpp.
References m_Flags, m_ForceOnlyNearFeats, m_Policy, m_Scope, and x_DefaultSelector().
Referenced by CFlatGatherer::x_GatherFeaturesOnRangeIdx().
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Definition at line 436 of file indexer.hpp.
References m_Idx.
Referenced by GetFeatureForProduct(), HasOperon(), x_DefaultSelector(), x_InitFeats(), and x_InitGaps().
Definition at line 3092 of file indexer.cpp.
References buffer, and GetSequence().
Definition at line 3057 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().
void CBioseqIndex::GetSequence | ( | string & | buffer | ) |
Definition at line 3102 of file indexer.cpp.
References buffer, and GetSequence().
string CBioseqIndex::GetSequence | ( | void | ) |
Definition at line 3108 of file indexer.cpp.
References buffer.
Referenced by CExploreProcess::DoOneBioseq(), and GetSequence().
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Definition at line 433 of file indexer.hpp.
References m_SeqVec.
CTempString CBioseqIndex::GetSpecies | ( | void | ) |
Definition at line 2566 of file indexer.cpp.
References m_SourcesInitialized, m_Species, and x_InitSource().
Referenced by CDeflineGenerator::x_AdjustProteinTitleSuffixIdx(), CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetSpecimenVoucher | ( | void | ) |
Definition at line 2747 of file indexer.cpp.
References m_SourcesInitialized, m_SpecimenVoucher, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetStrain | ( | void | ) |
Definition at line 2768 of file indexer.cpp.
References m_SourcesInitialized, m_Strain, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
CTempString CBioseqIndex::GetSubstrain | ( | void | ) |
Definition at line 2778 of file indexer.cpp.
References m_SourcesInitialized, m_Substrain, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
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().
TTaxId CBioseqIndex::GetTaxid | ( | void | ) |
Definition at line 2536 of file indexer.cpp.
References m_SourcesInitialized, m_Taxid, and x_InitSource().
Definition at line 2496 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().
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().
Definition at line 2366 of file indexer.cpp.
References m_DescsInitialized, m_Title, and x_InitDescs().
Referenced by CExploreProcess::DoOneBioseq(), and CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 473 of file indexer.hpp.
References m_Topology.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
bool CBioseqIndex::HasClone | ( | void | ) |
Definition at line 2686 of file indexer.cpp.
References m_has_clone, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
bool CBioseqIndex::HasGene | ( | void | ) |
Definition at line 3004 of file indexer.cpp.
References m_FeatsInitialized, m_HasGene, and x_InitFeats().
bool CBioseqIndex::HasMultiIntervalGenes | ( | void | ) |
Definition at line 3014 of file indexer.cpp.
References m_FeatsInitialized, m_HasMultiIntervalGenes, and x_InitFeats().
Referenced by CBioseqContext::HasMultiIntervalGenes().
bool CBioseqIndex::HasOperon | ( | void | ) |
Definition at line 2988 of file indexer.cpp.
References GetSeqMasterIndex(), CWeakRef< C, Locker >::Lock(), m_FeatsInitialized, and x_InitFeats().
Referenced by CBioseqContext::HasOperon(), and CFeatureItem::x_AddQualsIdx().
bool CBioseqIndex::HasSource | ( | void | ) |
Definition at line 3024 of file indexer.cpp.
References m_FeatsInitialized, m_HasSource, and x_InitFeats().
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Definition at line 472 of file indexer.hpp.
References m_IsAA.
Referenced by CExploreProcess::DoOneBioseq(), GetSequence(), CExploreProcess::SeqEntryProcess(), x_InitFeats(), and CDeflineGenerator::x_SetFlagsIdx().
bool CBioseqIndex::IsChromosome | ( | void | ) |
Definition at line 2606 of file indexer.cpp.
References m_IsChromosome, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
bool CBioseqIndex::IsCrossKingdom | ( | void | ) |
Definition at line 2646 of file indexer.cpp.
References m_IsCrossKingdom, m_SourcesInitialized, and x_InitSource().
Referenced by CBioseqContext::IsCrossKingdom(), and CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 476 of file indexer.hpp.
References m_IsDelta.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 477 of file indexer.hpp.
References m_IsDeltaLitOnly.
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().
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Definition at line 464 of file indexer.hpp.
References m_FetchFailure.
bool CBioseqIndex::IsForceOnlyNearFeats | ( | void | ) |
Definition at line 2878 of file indexer.cpp.
References m_DescsInitialized, m_ForceOnlyNearFeats, and x_InitDescs().
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().
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().
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().
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().
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().
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Definition at line 479 of file indexer.hpp.
References m_IsMap.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
bool CBioseqIndex::IsMultispecies | ( | void | ) |
Definition at line 2576 of file indexer.cpp.
References m_Multispecies, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 471 of file indexer.hpp.
References m_IsNA.
Referenced by CExploreProcess::DoOneBioseq(), CExploreProcess::SeqEntryProcess(), x_InitFeats(), and CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 485 of file indexer.hpp.
References m_IsNC.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 486 of file indexer.hpp.
References m_IsNM.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 487 of file indexer.hpp.
References m_IsNR.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 488 of file indexer.hpp.
References m_IsNZ.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 489 of file indexer.hpp.
References m_IsPatent.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 490 of file indexer.hpp.
References m_IsPDB.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
bool CBioseqIndex::IsPlasmid | ( | void | ) |
Definition at line 2596 of file indexer.cpp.
References m_IsPlasmid, m_SourcesInitialized, and x_InitSource().
Referenced by CDeflineGenerator::x_SetBioSrcIdx(), and CDeflineGenerator::x_SetFlagsIdx().
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().
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Definition at line 484 of file indexer.hpp.
References m_IsRefSeq.
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Definition at line 492 of file indexer.hpp.
References m_ThirdParty.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
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Definition at line 495 of file indexer.hpp.
References m_TLSMaster.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
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().
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().
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().
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Definition at line 494 of file indexer.hpp.
References m_TSAMaster.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
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().
bool CBioseqIndex::IsUnreviewedUnannotated | ( | void | ) |
Definition at line 2948 of file indexer.cpp.
References m_DescsInitialized, m_IsUnreviewedUnannotated, and x_InitDescs().
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
bool CBioseqIndex::IsUnverifiedContaminant | ( | void | ) |
Definition at line 2928 of file indexer.cpp.
References m_DescsInitialized, m_IsUnverifiedContaminant, and x_InitDescs().
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
bool CBioseqIndex::IsUnverifiedMisassembled | ( | void | ) |
Definition at line 2918 of file indexer.cpp.
References m_DescsInitialized, m_IsUnverifiedMisassembled, and x_InitDescs().
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
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().
bool CBioseqIndex::IsUsingAnamorph | ( | void | ) |
Definition at line 2546 of file indexer.cpp.
References m_SourcesInitialized, m_UsingAnamorph, and x_InitSource().
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Definition at line 478 of file indexer.hpp.
References m_IsVirtual.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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().
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Definition at line 493 of file indexer.hpp.
References m_WGSMaster.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 491 of file indexer.hpp.
References m_IsWP.
Referenced by CDeflineGenerator::x_SetFlagsIdx().
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Definition at line 1058 of file indexer.hpp.
References count, ERR_POST, Error(), m_DescsInitialized, m_SdxList, CException::what(), and x_InitDescs().
Referenced by CFlatGatherer::x_GatherReferencesIdx().
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Definition at line 1105 of file indexer.hpp.
References count, ERR_POST, Error(), m_SfxList, CException::what(), and x_InitFeats().
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Definition at line 1082 of file indexer.hpp.
References count, ERR_POST, Error(), m_FeatsInitialized, m_SfxList, CException::what(), and x_InitFeats().
Referenced by CExploreProcess::DoOneBioseq(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), and CValidError_bioseq::x_ValidateCDSVDJCmatch().
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Definition at line 1034 of file indexer.hpp.
References count, ERR_POST, Error(), m_GapList, m_GapsInitialized, CException::what(), and x_InitGaps().
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Definition at line 466 of file indexer.hpp.
References m_FetchFailure.
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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().
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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().
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Definition at line 2292 of file indexer.cpp.
References x_InitFeats().
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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().
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Definition at line 2286 of file indexer.cpp.
Referenced by GetBestProteinFeature(), GetFeatureForProduct(), GetFeatureIndices(), HasGene(), HasMultiIntervalGenes(), HasOperon(), HasSource(), IterateFeatures(), and x_InitFeats().
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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().
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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().
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Definition at line 667 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetAccession().
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Definition at line 641 of file indexer.hpp.
Referenced by GetBestProteinFeature(), and x_InitFeats().
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Definition at line 640 of file indexer.hpp.
Referenced by CBioseqIndex(), GetBestProteinFeature(), and x_InitFeats().
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Definition at line 697 of file indexer.hpp.
Referenced by CBioseqIndex(), GetBiomol(), and x_InitDescs().
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Definition at line 714 of file indexer.hpp.
Referenced by CBioseqIndex(), GetBioSource(), x_InitDescs(), x_InitFeats(), and x_InitSource().
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Definition at line 745 of file indexer.hpp.
Referenced by CBioseqIndex(), GetBreed(), and x_InitSource().
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Definition at line 617 of file indexer.hpp.
Referenced by CBioseqIndex(), GetBioseqHandle(), GetFeatureForProduct(), GetSequence(), and x_InitFeats().
Definition at line 618 of file indexer.hpp.
Referenced by GetBioseq().
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Definition at line 736 of file indexer.hpp.
Referenced by CBioseqIndex(), GetChromosome(), and x_InitSource().
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Definition at line 738 of file indexer.hpp.
Referenced by CBioseqIndex(), GetClone(), and x_InitSource().
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Definition at line 781 of file indexer.hpp.
Referenced by CBioseqIndex(), GetComment(), and x_InitDescs().
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Definition at line 717 of file indexer.hpp.
Referenced by CBioseqIndex(), GetCommon(), and x_InitSource().
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Definition at line 699 of file indexer.hpp.
Referenced by CBioseqIndex(), GetCompleteness(), and x_InitDescs().
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Definition at line 746 of file indexer.hpp.
Referenced by CBioseqIndex(), GetCultivar(), and x_InitSource().
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Definition at line 711 of file indexer.hpp.
Referenced by CBioseqIndex(), x_InitDescs(), and x_InitSource().
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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().
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Definition at line 712 of file indexer.hpp.
Referenced by CBioseqIndex(), GetDescTaxname(), and x_InitSource().
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Definition at line 637 of file indexer.hpp.
Referenced by CBioseqIndex(), GetFeatureForProduct(), and x_InitFeats().
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Definition at line 645 of file indexer.hpp.
Referenced by GetFeatIndex(), and x_InitFeats().
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Definition at line 632 of file indexer.hpp.
Referenced by CBioseqIndex(), GetBestProteinFeature(), GetFeatureForProduct(), GetFeatureIndices(), HasGene(), HasMultiIntervalGenes(), HasOperon(), HasSource(), IterateFeatures(), and x_InitFeats().
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Definition at line 638 of file indexer.hpp.
Referenced by GetFeatureForProduct(), and x_InitFeats().
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Definition at line 652 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSequence(), IsFetchFailure(), SetFetchFailure(), and x_InitFeats().
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Definition at line 731 of file indexer.hpp.
Referenced by CBioseqIndex(), GetFirstSuperKingdom(), and x_InitDescs().
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Definition at line 650 of file indexer.hpp.
Referenced by GetSelector(), and x_InitFeats().
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Definition at line 766 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSelector(), IsForceOnlyNearFeats(), x_InitDescs(), and x_InitFeats().
Definition at line 627 of file indexer.hpp.
Referenced by GetGapIndices(), IterateGaps(), and x_InitGaps().
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Definition at line 626 of file indexer.hpp.
Referenced by CBioseqIndex(), GetGapIndices(), IterateGaps(), and x_InitGaps().
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Definition at line 683 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetGeneralId().
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Definition at line 682 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetGeneralStr().
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Definition at line 725 of file indexer.hpp.
Referenced by CBioseqIndex(), GetGenome(), and x_InitSource().
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Definition at line 722 of file indexer.hpp.
Referenced by CBioseqIndex(), GetGenus(), and x_InitSource().
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Definition at line 739 of file indexer.hpp.
Referenced by CBioseqIndex(), HasClone(), and x_InitSource().
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Definition at line 785 of file indexer.hpp.
Referenced by CBioseqIndex(), HasGene(), and x_InitFeats().
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Definition at line 786 of file indexer.hpp.
Referenced by CBioseqIndex(), HasMultiIntervalGenes(), and x_InitFeats().
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Definition at line 787 of file indexer.hpp.
Referenced by CBioseqIndex(), HasSource(), and x_InitFeats().
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Definition at line 754 of file indexer.hpp.
Referenced by CBioseqIndex(), IsHTGSCancelled(), and x_InitDescs().
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Definition at line 755 of file indexer.hpp.
Referenced by CBioseqIndex(), IsHTGSDraft(), and x_InitDescs().
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Definition at line 756 of file indexer.hpp.
Referenced by CBioseqIndex(), IsHTGSPooled(), and x_InitDescs().
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Definition at line 702 of file indexer.hpp.
Referenced by CBioseqIndex(), IsHTGSUnfinished(), and x_InitDescs().
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Definition at line 701 of file indexer.hpp.
Referenced by CBioseqIndex(), IsHTGTech(), and x_InitDescs().
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Definition at line 624 of file indexer.hpp.
Referenced by GetSeqMasterIndex().
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Definition at line 657 of file indexer.hpp.
Referenced by CBioseqIndex(), IsAA(), and x_InitSource().
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Definition at line 727 of file indexer.hpp.
Referenced by CBioseqIndex(), IsChromosome(), and x_InitSource().
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Definition at line 733 of file indexer.hpp.
Referenced by CBioseqIndex(), IsCrossKingdom(), and x_InitDescs().
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Definition at line 661 of file indexer.hpp.
Referenced by CBioseqIndex(), IsDelta(), and x_InitGaps().
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Definition at line 662 of file indexer.hpp.
Referenced by CBioseqIndex(), IsDeltaLitOnly(), and x_DefaultSelector().
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Definition at line 706 of file indexer.hpp.
Referenced by CBioseqIndex(), IsEST_STS_GSS(), and x_InitDescs().
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Definition at line 664 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsMap().
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Definition at line 656 of file indexer.hpp.
Referenced by CBioseqIndex(), IsNA(), and x_InitDescs().
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Definition at line 670 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsNC().
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Definition at line 671 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsNM().
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Definition at line 672 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsNR().
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Definition at line 673 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsNZ().
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Definition at line 748 of file indexer.hpp.
Referenced by CBioseqIndex(), GetIsolate(), and x_InitSource().
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Definition at line 674 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsPatent().
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Definition at line 675 of file indexer.hpp.
Referenced by CBioseqIndex(), IsPDB(), and x_InitDescs().
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Definition at line 726 of file indexer.hpp.
Referenced by CBioseqIndex(), IsPlasmid(), and x_InitSource().
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Definition at line 782 of file indexer.hpp.
Referenced by CBioseqIndex(), IsPseudogene(), and x_InitDescs().
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Definition at line 669 of file indexer.hpp.
Referenced by CBioseqIndex(), IsRefSeq(), and x_DefaultSelector().
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Definition at line 703 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTLS(), and x_InitDescs().
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Definition at line 704 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTSA(), and x_InitDescs().
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Definition at line 775 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnreviewed(), and x_InitDescs().
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Definition at line 776 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnreviewedUnannotated(), and x_InitDescs().
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Definition at line 768 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnverified(), and x_InitDescs().
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Definition at line 772 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnverifiedContaminant(), and x_InitDescs().
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Definition at line 769 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnverifiedFeature(), and x_InitDescs().
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Definition at line 771 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnverifiedMisassembled(), and x_InitDescs().
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Definition at line 770 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnverifiedOrganism(), and x_InitDescs().
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Definition at line 663 of file indexer.hpp.
Referenced by CBioseqIndex(), IsVirtual(), and x_InitDescs().
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Definition at line 705 of file indexer.hpp.
Referenced by CBioseqIndex(), IsWGS(), x_InitDescs(), and x_InitSource().
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Definition at line 676 of file indexer.hpp.
Referenced by CBioseqIndex(), IsWP(), and x_InitDescs().
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Definition at line 659 of file indexer.hpp.
Referenced by CBioseqIndex(), GetLength(), and x_InitFeats().
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Definition at line 718 of file indexer.hpp.
Referenced by CBioseqIndex(), GetLineage(), and x_InitSource().
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Definition at line 737 of file indexer.hpp.
Referenced by CBioseqIndex(), GetLinkageGroup(), and x_InitSource().
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Definition at line 740 of file indexer.hpp.
Referenced by CBioseqIndex(), GetMap(), and x_InitSource().
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Definition at line 751 of file indexer.hpp.
Referenced by CBioseqIndex(), GetMetaGenomeSource(), and x_InitSource().
Definition at line 696 of file indexer.hpp.
Referenced by CBioseqIndex(), GetMolInfo(), and x_InitDescs().
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Definition at line 724 of file indexer.hpp.
Referenced by CBioseqIndex(), IsMultispecies(), and x_InitSource().
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Definition at line 729 of file indexer.hpp.
Referenced by CBioseqIndex(), GetOrganelle(), and x_InitSource().
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Definition at line 619 of file indexer.hpp.
Referenced by GetOrigBioseqHandle(), x_InitDescs(), and x_InitGaps().
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Definition at line 685 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetPatentCountry().
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Definition at line 686 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetPatentNumber().
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Definition at line 687 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetPatentSequence().
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Definition at line 689 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetPDBChain().
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Definition at line 690 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetPDBChainID().
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Definition at line 763 of file indexer.hpp.
Referenced by CBioseqIndex(), GetPDBCompound(), and x_InitDescs().
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Definition at line 741 of file indexer.hpp.
Referenced by CBioseqIndex(), GetPlasmid(), and x_InitSource().
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Definition at line 649 of file indexer.hpp.
Referenced by GetSelector(), and x_InitFeats().
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Definition at line 620 of file indexer.hpp.
Referenced by GetParent().
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Definition at line 790 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetrEnzyme().
Definition at line 622 of file indexer.hpp.
Referenced by GetFeatureForProduct(), GetScope(), GetSelector(), and x_InitFeats().
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Definition at line 630 of file indexer.hpp.
Referenced by GetDescriptorIndices(), IterateDescriptors(), and x_InitDescs().
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Definition at line 732 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSecondSuperKingdom(), and x_InitDescs().
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Definition at line 742 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSegment(), and x_InitSource().
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Definition at line 647 of file indexer.hpp.
Referenced by GetSequence(), and GetSeqVector().
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Definition at line 633 of file indexer.hpp.
Referenced by GetFeatureIndices(), IterateFeatures(), and x_InitFeats().
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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().
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Definition at line 723 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSpecies(), and x_InitSource().
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Definition at line 747 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSpecimenVoucher(), and x_InitSource().
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Definition at line 749 of file indexer.hpp.
Referenced by CBioseqIndex(), GetStrain(), and x_InitSource().
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Definition at line 750 of file indexer.hpp.
Referenced by CBioseqIndex(), GetSubstrain(), and x_InitSource().
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Definition at line 778 of file indexer.hpp.
Referenced by CBioseqIndex(), GetTargetedLocus(), and x_InitDescs().
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Definition at line 719 of file indexer.hpp.
Referenced by CBioseqIndex(), GetTaxid(), and x_InitSource().
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Definition at line 715 of file indexer.hpp.
Referenced by CBioseqIndex(), GetTaxname(), and x_InitSource().
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Definition at line 698 of file indexer.hpp.
Referenced by CBioseqIndex(), GetTech(), and x_InitDescs().
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Definition at line 677 of file indexer.hpp.
Referenced by CBioseqIndex(), IsThirdParty(), and x_InitDescs().
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Definition at line 693 of file indexer.hpp.
Referenced by CBioseqIndex(), GetTitle(), and x_InitDescs().
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Definition at line 680 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTLSMaster(), and x_InitDescs().
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Definition at line 658 of file indexer.hpp.
Referenced by CBioseqIndex(), and GetTopology().
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Definition at line 757 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTPAExp(), and x_InitDescs().
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Definition at line 758 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTPAInf(), and x_InitDescs().
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Definition at line 759 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTPAReasm(), and x_InitDescs().
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Definition at line 679 of file indexer.hpp.
Referenced by CBioseqIndex(), IsTSAMaster(), and x_InitDescs().
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Definition at line 621 of file indexer.hpp.
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Definition at line 760 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUnordered(), and x_InitDescs().
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Definition at line 777 of file indexer.hpp.
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Definition at line 773 of file indexer.hpp.
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Definition at line 708 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUseBiosrc(), and x_InitDescs().
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Definition at line 720 of file indexer.hpp.
Referenced by CBioseqIndex(), IsUsingAnamorph(), and x_InitSource().
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Definition at line 678 of file indexer.hpp.
Referenced by CBioseqIndex(), and IsWGSMaster().