Search Toolkit Book for CFeatureTableReader
#include "feature_table_reader.hpp"
(Private to src/app/table2asn.)
Definition at line 32 of file feature_table_reader.hpp.
◆ CFeatureTableReader() ◆ ~CFeatureTableReader() ◆ AddProteins() void CFeatureTableReader::AddProteins ( const objects::CSeq_entry & possible_proteins, objects::CSeq_entry & entry )Definition at line 1061 of file feature_table_reader.cpp.
References _ASSERT, CScope::AddTopLevelSeqEntry(), CSeq_inst_Base::eMol_na, CObjectManager::GetInstance(), CSeq_entry_Handle::GetParentEntry(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CBioseq_set_Base::IsSetSeq_set(), and xAddProteinToSeqEntry().
◆ ChangeDeltaProteinToRawProtein() void CFeatureTableReader::ChangeDeltaProteinToRawProtein ( objects::CSeq_entry & entry ) const ◆ ConvertNucSetToSet() void CFeatureTableReader::ConvertNucSetToSet ( CRef< objects::CSeq_entry > & entry ) constDefinition at line 1165 of file feature_table_reader.cpp.
References CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::GetClass(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSet(), CSeq_entry::Parentize(), CRef< C, Locker >::Reset(), CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
◆ FindOpenReadingFrame() void CFeatureTableReader::FindOpenReadingFrame ( objects::CSeq_entry & entry ) const ◆ MakeGap() CRef< CDelta_seq > CFeatureTableReader::MakeGap ( objects::CBioseq & bioseq, const objects::CSeq_feat & feature_gap ) constDefinition at line 1653 of file feature_table_reader.cpp.
References CFastaReader::CanonicalizeString(), CGapsEditor::CreateGap(), eExtreme_Positional, CSeq_gap::eLinkEvid_Forbidden, CSeq_gap::eLinkEvid_Required, CSeq_gap::eLinkEvid_UnspecifiedOnly, map_checker< Container >::end(), ENUM_METHOD_NAME, CSeq_gap_Base::eType_unknown, CLinkage_evidence_Base::eType_unspecified, map_checker< Container >::find(), g_LogGeneralParsingError(), bm::gap_length(), CSeq_feat_Base::GetLocation(), CSeq_feat::GetNamedQual(), CSeq_feat_Base::GetQual(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), set< Key, Compare >::insert(), CSeq_feat_Base::IsSetLocation(), ITERATE, kInvalidSeqPos, m_context, CSeq_gap::SGapTypeInfo::m_eLinkEvid, CSeq_gap::SGapTypeInfo::m_eType, CTable2AsnContext::m_logger, CSeq_gap::NameToGapTypeInfo(), and s_UnknownEstimatedLength().
◆ MakeGapsFromFeatures() [1/3] void CFeatureTableReader::MakeGapsFromFeatures ( objects::CBioseq & bioseq ) const ◆ MakeGapsFromFeatures() [2/3] void CFeatureTableReader::MakeGapsFromFeatures ( objects::CSeq_entry & entry ) const ◆ MakeGapsFromFeatures() [3/3] void CFeatureTableReader::MakeGapsFromFeatures ( objects::CSeq_entry_Handle seh ) const ◆ MergeCDSFeatures() void CFeatureTableReader::MergeCDSFeatures ( objects::CSeq_entry & , TAsyncToken & ) ◆ MoveProteinSpecificFeats() void CFeatureTableReader::MoveProteinSpecificFeats ( objects::CSeq_entry & entry ) ◆ MoveRegionsToProteins() void CFeatureTableReader::MoveRegionsToProteins ( objects::CSeq_entry & entry )Definition at line 1935 of file feature_table_reader.cpp.
References _ASSERT, CSeq_id::e_YES, CBioseq_set_Base::eClass_nuc_prot, map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::erase(), ftable, CBioseq_Base::GetAnnot(), CBioseq_Base::GetId(), CObjectManager::GetInstance(), CCleanup::GetProteinLocationFromNucleotideLocation(), CBioseq::IsNa(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetAnnot(), map_checker< Container >::lower_bound(), Ref(), CBioseq_Base::ResetAnnot(), s_GatherRegionIterators(), s_GetIdFromLocation(), CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), and CSeq_entry_Base::SetSet().
Referenced by MoveProteinSpecificFeats().
◆ ReadProtein()Definition at line 1018 of file feature_table_reader.cpp.
References CFastaReader::fAddMods, CFastaReader::fAssumeProt, CFastaReader::fForceType, flags, CFastaReader::fNoUserObjs, CRef< C, Locker >::GetPointerOrNull(), CSerialObject::GetThisTypeInfo(), CTypeInfo::IsType(), m_context, CTable2AsnContext::m_logger, m_PrtModMap, CRef< C, Locker >::NotEmpty(), and result.
◆ RemoveEmptyFtable() void CFeatureTableReader::RemoveEmptyFtable ( objects::CBioseq & bioseq ) static ◆ x_AddProteinFeatureToProtein() CRef< CSeq_feat > CFeatureTableReader::x_AddProteinFeatureToProtein ( CRef< objects::CSeq_entry > nuc, CConstRef< objects::CSeq_loc > cds_loc, const list< CRef< objects::CSeq_id >> & pOriginalProtIds, objects::CBioseq & protein, bool partial5, bool partial3 ) privateDefinition at line 1359 of file feature_table_reader.cpp.
References AddEmptyProteinFeatureToProtein(), CSourceModParser::eHandleBadMod_Ignore, CBioseq_Base::GetId(), set< Key, Compare >::insert(), m_context, CTable2AsnContext::m_logger, m_PrtModMap, mod(), nuc, and s_ReportDuplicateMods().
Referenced by xAddProteinToSeqEntry().
◆ xAddProteinToSeqEntry() bool CFeatureTableReader::xAddProteinToSeqEntry ( const objects::CBioseq & protein, objects::CSeq_entry_Handle seh ) privateDefinition at line 1541 of file feature_table_reader.cpp.
References CScope::AddTopLevelSeqEntry(), CSeq_id::Assign(), CSerialObject::Assign(), CSeqdesc_Base::e_Title, CSeq_id::eContent, eExtreme_Biological, g_LogGeneralParsingError(), CSeq_entry_Handle::GetCompleteObject(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetEditHandle(), CBioseq_Base::GetId(), CTable2AsnContext::GetOrgName(), CConstRef< C, Locker >::GetPointerOrNull(), CSeq_entry_Handle::GetScope(), CSeq_entry_Base::GetSeq(), CSeq_entry_Handle::GetTopLevelEntry(), label, m_context, CTable2AsnContext::m_huge_files_mode, CTable2AsnContext::m_logger, CTable2AsnContext::m_use_hypothetic_protein, CTable2AsnContext::prtAlnOptions, CScope::RemoveTopLevelSeqEntry(), CBioseq_Base::ResetId(), s_GetCDSLoc(), s_GetSingleNucSeq(), s_MakeCDSFeat(), s_MatchProteinById(), CAutoAddDesc::Set(), CSeq_entry::SetDescr(), CBioseq_Base::SetId(), SetMolinfoForProtein(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetTitle(), and x_AddProteinFeatureToProtein().
Referenced by AddProteins().
◆ xCheckIfNeedConversion() bool CFeatureTableReader::xCheckIfNeedConversion ( const objects::CSeq_entry & entry ) const private ◆ xConvertSeqIntoSeqSet() void CFeatureTableReader::xConvertSeqIntoSeqSet ( objects::CSeq_entry & entry, bool nuc_prod_set ) const privateDefinition at line 1135 of file feature_table_reader.cpp.
References CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_genomic, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_nuc_prot, CSeq_inst_Base::eMol_dna, CBioseq_Base::GetInst(), CBioseq::IsNa(), CSeq_entry_Base::IsSeq(), CMolInfo_Base::IsSetBiomol(), CBioseq_Base::IsSetInst(), CSeq_inst_Base::IsSetMol(), CSeq_entry::Parentize(), CAutoAddDesc::Set(), CMolInfo_Base::SetBiomol(), CBioseq_set_Base::SetClass(), CBioseq_Base::SetDescr(), CBioseq_Base::SetInst(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
Referenced by xMergeCDSFeatures_impl().
◆ xMergeCDSFeatures_impl() void CFeatureTableReader::xMergeCDSFeatures_impl ( objects::CSeq_entry & , TAsyncToken & ) privateDefinition at line 793 of file feature_table_reader.cpp.
References CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::GetClass(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CBioseq_set_Base::IsSetClass(), CBioseq_Base::IsSetInst(), NON_CONST_ITERATE, s_HasUnprocessedCdregions(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CSeq_entry_Base::Which(), xCheckIfNeedConversion(), xConvertSeqIntoSeqSet(), and xParseCdregions().
Referenced by MergeCDSFeatures().
◆ xMoveCdRegions() void CFeatureTableReader::xMoveCdRegions ( objects::CSeq_entry_Handle entry_h, objects::CSeq_annot::TData::TFtable & seq_ftable, objects::CSeq_annot::TData::TFtable & set_ftable, TAsyncToken & ) privateDefinition at line 860 of file feature_table_reader.cpp.
References CBioseq_set_EditHandle::AttachEntry(), TAsyncToken::bioseq, data, CCdregion_Base::eFrame_one, NStr::Find(), CSeqTranslator::FindBestFrame(), CSeq_entry_Handle::GetBioseqHandle(), CBioseq_set_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CSeq_feat_Base::GetExcept_text(), CSeq_loc::GetId(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetProduct(), CRef< C, Locker >::NotEmpty(), NPOS, CCleanup::ParseCodeBreaks(), s_TranslateCds(), TAsyncToken::scope, CSeq_feat_Base::SetData(), CSeq_entry_EditHandle::SetSet(), and xTranslateProtein().
Referenced by xParseCdregions().
◆ xParseCdregions() void CFeatureTableReader::xParseCdregions ( objects::CSeq_entry & entry, TAsyncToken & ) privateDefinition at line 924 of file feature_table_reader.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), TAsyncToken::bioseq, TAsyncToken::Clear(), CBioseq_set_Base::eClass_nuc_prot, CBioseq_Base::GetAnnot(), CBioseq_set_Base::GetClass(), CObjectManager::GetInstance(), CSeq_entry_Base::GetSet(), TAsyncToken::InitFeatures(), CSeq_annot::IsFtable(), CSeq_entry_Base::IsSet(), MSerial_AsnText, MSerial_VerifyNo(), CScope::RemoveTopLevelSeqEntry(), CRef< C, Locker >::Reset(), CBioseq_Base::Reset(), CBioseq_Base::ResetAnnot(), TAsyncToken::scope, CBioseq_Base::SetAnnot(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and xMoveCdRegions().
Referenced by xMergeCDSFeatures_impl().
◆ xTranslateProtein()Definition at line 547 of file feature_table_reader.cpp.
References CSeq_feat::AddSeqFeatXref(), AdjustProteinMolInfoToMatchCDS(), AssignLocalIdIfEmpty(), CopyFeaturePartials(), CSeqdesc_Base::e_Molinfo, CRNA_ref_Base::C_Ext::e_not_set, CMolInfo_Base::eBiomol_peptide, CSeq_id::eContent, CRef< C, Locker >::Empty(), CMolInfo_Base::eTech_concept_trans, CCleanup::ExtendStopPosition(), CCleanup::ExtendToStopIfShortAndNotPartial(), CSeq_id::fParse_PartialOK, CSeq_id::fParse_ValidLocal, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CBioseq_Base::GetId(), CSeq_feat_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::GetLocation(), CGene_ref_Base::GetLocus_tag(), CProt_ref_Base::GetName(), CSeq_feat::GetNamedQual(), CSeq_feat_Base::GetProduct(), CSeq_loc_Base::GetWhole(), CSeqFeatData_Base::IsGene(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CGene_ref_Base::IsSetLocus_tag(), CProt_ref_Base::IsSetName(), CSeq_feat_Base::IsSetProduct(), CSeq_loc_Base::IsWhole(), CCleanup::LocationMayBeExtendedToMatch(), m_context, m_local_id_counter, m_replacement_protein, CTable2AsnContext::m_use_hypothetic_protein, TAsyncToken::ParentGene(), TAsyncToken::ParentMrna(), CSeq_id::ParseIDs(), Ref(), CSeq_feat::RemoveQualifier(), s_SetProtRef(), TAsyncToken::scope, CAutoAddDesc::Set(), CMolInfo_Base::SetBiomol(), CSeq_feat_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetMolinfo(), CProt_ref_Base::SetName(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CMolInfo_Base::SetTech(), CSeq_feat_Base::SetXref(), CSeqTranslator::TranslateToProtein(), and whole.
Referenced by xMoveCdRegions().
◆ m_context ◆ m_local_id_counter int CFeatureTableReader::m_local_id_counter = 0 ◆ m_PrtModMap objects::CFastaReader::TPostponedModMap CFeatureTableReader::m_PrtModMap private ◆ m_replacement_protein CRef<objects::CSeq_entry> CFeatureTableReader::m_replacement_proteinThe documentation for this class was generated from the following files:
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