NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/Prot_ref.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_bond.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/seqfeat_macros.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objtools/edit/field_handler.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <gui/objutils/convert_feat.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/util_cmds.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>
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Functions | |
USING_SCOPE (objects) | |
CProt_ref::EProcessed | GetProtProcessedFromFeatureSubtype (CSeqFeatData::ESubtype subtype) |
CRNA_ref::EType | GetRnaTypeFromFeatureSubtype (CSeqFeatData::ESubtype subtype) |
static void | AdjustMappedStop (CRef< CSeq_loc > loc, const CSeq_loc &product, CScope &scope) |
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static |
Definition at line 340 of file convert_feat.cpp.
References CSeq_id::Assign(), CSeq_loc::Assign(), eExtreme_Positional, CSeq_loc::fMerge_All, CSeq_loc::fSort, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_loc::GetId(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStop(), Seq_loc_Subtract(), and CSeq_loc::SetPartialStop().
Referenced by CConvertFeatureBase::x_MoveFeatureToProtein().
CProt_ref::EProcessed GetProtProcessedFromFeatureSubtype | ( | CSeqFeatData::ESubtype | subtype | ) |
Definition at line 120 of file convert_feat.cpp.
References CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_not_set, CProt_ref_Base::eProcessed_preprotein, CProt_ref_Base::eProcessed_signal_peptide, CProt_ref_Base::eProcessed_transit_peptide, CSeqFeatData::eSubtype_mat_peptide, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_sig_peptide, CSeqFeatData::eSubtype_sig_peptide_aa, CSeqFeatData::eSubtype_transit_peptide, and CSeqFeatData::eSubtype_transit_peptide_aa.
Referenced by CConvertImpToProt::Convert(), and CConvertFeatureBase::x_SimpleConversion().
CRNA_ref::EType GetRnaTypeFromFeatureSubtype | ( | CSeqFeatData::ESubtype | subtype | ) |
Definition at line 146 of file convert_feat.cpp.
References CSeqFeatData::eSubtype_misc_RNA, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_otherRNA, CSeqFeatData::eSubtype_precursor_RNA, CSeqFeatData::eSubtype_preRNA, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_scRNA, CSeqFeatData::eSubtype_snoRNA, CSeqFeatData::eSubtype_snRNA, CSeqFeatData::eSubtype_tmRNA, CSeqFeatData::eSubtype_tRNA, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_mRNA, CRNA_ref_Base::eType_ncRNA, CRNA_ref_Base::eType_other, CRNA_ref_Base::eType_premsg, CRNA_ref_Base::eType_rRNA, CRNA_ref_Base::eType_scRNA, CRNA_ref_Base::eType_snoRNA, CRNA_ref_Base::eType_snRNA, CRNA_ref_Base::eType_tmRNA, CRNA_ref_Base::eType_tRNA, and CRNA_ref_Base::eType_unknown.
Referenced by CConvertCDSToRNA::Convert(), CConvertGeneToRNA::Convert(), CConvertImpToRNA::Convert(), CConvertRegionToRna::Convert(), CConvertRNAToRNA::Convert(), and CConvertFeatureBase::x_SimpleConversion().
USING_SCOPE | ( | objects | ) |