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USING_SCOPE (objects) DEFINE_STATIC_ARRAY_MAP (TNameTypeMap, sm_NameTypeMap, s_NameTypeStrs) static bool s_IsNAA (const string &annot, char div) static bool s_IsExtendedNAA (const string &sAnnotName, char div, bool isStrict) static CSeqUtils::TLocVec s_GetAlnMapplingLocs (const CSeq_align_set &align_set, TGi gi) static const string & GetLinksURL () static const TAssemblySeqIds & s_GetAssemblySeqIds (const string &assm_acc) template<class T1 , class T2 > static void s_ELinkQuery (const string &db_from, const string &db_to, const vector< T1 > &uids_from, vector< T2 > &uids_to, const string &cmd, const string &xpath) template<class T > static void s_ELinkQuery (const string &db_from, const string &db_to, const vector< T > &uids_from, xml::document &linkset, const string &cmd) template<class T > static void s_ESearchQuery (const string &db, const string &term, vector< T > &uids, size_t &count, const int ret_max, const string &xpath) template<class T > static void s_ESearchQuery (const string &db, const string &term, const string &web_env, const string &query_key, vector< T > &uids, size_t &count, int retstart, const string &xpath) static TMappedLocs s_GetRnaMappingLocs (const CSeq_loc &feat_loc, const CMappedFeat &feat, const CBioseq_Handle &handle) static void s_CreateMappingInfo (const CSeq_loc &prod_loc, const CSeq_loc &gen_loc, CSeqUtils::TMappingInfo &info) Helper function to convert two mapped locations into an interval-to-interval mapping structure. More...For CDS and RNA feature mapping information.
Definition at line 1769 of file utils.cpp.
◆ TNameTypeMap ◆ TNameTypeStr ◆ TTopLevels ◆ DEFINE_STATIC_ARRAY_MAP() ◆ GetBioseqForSeqdesc() ◆ GetBioseqForSeqFeat() ◆ GetDefaultTopLevelSeqEntry() ◆ GetLinksURL() ◆ GetSeqEntryForPubdesc() ◆ GetSeqFeatHandleForBadLocFeature() ◆ GetSortedFeatList()Definition at line 2714 of file utils.cpp.
References all, count, set< Key, Compare >::end(), CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_bad, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_Imp_CDS, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_mat_peptide, CSeqFeatData::eSubtype_max, CSeqFeatData::eSubtype_misc_RNA, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_org, CSeqFeatData::eSubtype_otherRNA, CSeqFeatData::eSubtype_precursor_RNA, CSeqFeatData::eSubtype_prot, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_sig_peptide, CSeqFeatData::eSubtype_source, CSeqFeatData::eSubtype_transit_peptide, CSeqFeatData::eSubtype_txinit, f, set< Key, Compare >::find(), CSeq_feat_Handle::GetData(), CSeqFeatData::GetFeatList(), CSeqFeatData::GetSubtype(), set< Key, Compare >::insert(), ITERATE, max(), NULL, s_CompareDescriptions(), ct::sort(), and unused.
◆ s_AdjustToAnnotatedCDS()Definition at line 1916 of file utils.cpp.
References CSeq_loc_Mapper_Base::eLocationToProduct, eNa_strand_minus, eNa_strand_plus, CSeq_loc_Mapper_Base::eProductToLocation, CMappedFeat::GetMappedFeature(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSize(), i, CSeq_loc_Mapper_Base::Map(), MSerial_AsnText, r(), and Ref().
Referenced by CSeqUtils::GetCdsMappingInfoFromRna().
◆ s_CompareDescriptions() ◆ s_CreateMappingInfo()Helper function to convert two mapped locations into an interval-to-interval mapping structure.
Definition at line 1852 of file utils.cpp.
References CSeq_id::Assign(), CSeq_loc::GetId(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetStrand(), info, CSeq_loc_CI::IsEmpty(), CSeq_loc_CI::IsSetStrand(), r1, r2, CRef< C, Locker >::Reset(), CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), and CSeq_interval_Base::SetTo().
Referenced by CSeqUtils::GetRnaMappingInfo().
◆ s_ELinkQuery() [1/2] ◆ s_ELinkQuery() [2/2]template<class T1 , class T2 >
◆ s_ESearchQuery() [1/2] ◆ s_ESearchQuery() [2/2]Definition at line 1653 of file utils.cpp.
References xml::node_set::begin(), count, ctll::empty(), xml::node_set::end(), xml::node::get_content(), xml::document::get_root_node(), CSeqUtils::GetXmlChildNodeValue(), NULL, xml::node::run_xpath_query(), CEutilsClient::Search(), CEutilsClient::SetMaxReturn(), and NStr::StringToSizet().
Referenced by CSeqUtils::ESearchQuery().
◆ s_GetAlnMapplingLocs()Definition at line 1012 of file utils.cpp.
References CSeq_align::CheckNumRows(), CRange_Base::GetFrom(), CSeq_id_Base::GetGi(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align_Base::C_Segs::GetStd(), CRange_Base::GetTo(), CSeq_id_Base::IsGi(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, and swap().
Referenced by CSeqUtils::GetAccessionPlacementsMsec(), and CSeqUtils::GetGiPlacements().
◆ s_GetAssemblySeqIds() ◆ s_GetRnaMappingLocs()Definition at line 1771 of file utils.cpp.
References SAnnotSelector::AddNamedAnnots(), CSeq_align::CheckNumRows(), ConvertSeq_align(), CSeq_align_Base::C_Segs::e_Denseg, CSeq_loc_Mapper_Base::eLocationToProduct, CSeq_loc_Mapper_Base::eProductToLocation, SAnnotSelector::ExcludeNamedAnnots(), CSeq_feat_Handle::GetAnnot(), CRange_Base::GetFrom(), CSeq_loc::GetId(), CMappedFeat::GetMappedFeature(), CSeq_annot_Handle::GetName(), CMappedFeat::GetProduct(), CBioseq_Handle::GetRangeSeq_loc(), CBioseq_Handle::GetScope(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), SAnnotSelector::IncludeNamedAnnotAccession(), CSeq_annot_Handle::IsNamed(), CSeq_feat_Handle::IsSetProduct(), CSeq_align_Base::C_Segs::IsSpliced(), CSeq_loc_Mapper_Base::Map(), CSeq_id::Match(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), row, SAnnotSelector::SetAdaptiveDepth(), SAnnotSelector::SetExactDepth(), SAnnotSelector::SetResolveAll(), SAnnotSelector::SetResolveDepth(), and NStr::StartsWith().
Referenced by CSeqUtils::GetRnaMappingInfo().
◆ s_IsExtendedNAA() ◆ s_IsNAA() ◆ USING_SCOPE() ◆ kAssmDb ◆ kLinksUrlDefault const char* kLinksUrlDefault static Initial value:=
"https://www.ncbi.nlm.nih.gov/sviewer/links.fcgi?link_name=gi_placement&report=asn"
Definition at line 1056 of file utils.cpp.
Referenced by GetLinksURL().
◆ kNucDb ◆ kRetMax ◆ kTaxDb ◆ m_AssemblySeqIdLock ◆ m_TopLevels ◆ m_TopLevelsLock ◆ s_AssemblySeqIdCache ◆ s_NameTypeStrs Initial value:= {
}
@ eAnnot_Unnamed
unnamed annotation
@ eAnnot_All
all annotations
@ eAnnot_Named
all named annotations
Definition at line 130 of file utils.cpp.
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