#include <ncbi_pch.hpp>#include "discrepancy_core.hpp"#include <objects/biblio/Cit_sub.hpp>#include <objects/general/Date.hpp>#include <objects/general/Dbtag.hpp>#include <objects/general/Object_id.hpp>#include <objects/general/User_object.hpp>#include <objects/misc/sequence_util_macros.hpp>#include <objects/pub/Pub.hpp>#include <objects/pub/Pub_equiv.hpp>#include <objects/seq/Pubdesc.hpp>#include <objects/seq/Seqdesc.hpp>#include <objects/seqfeat/Org_ref.hpp>#include <objects/seqloc/Packed_seqpnt.hpp>#include <objects/seqloc/Seq_bond.hpp>#include <objects/seqloc/Seq_loc_equiv.hpp>#include <objects/seqloc/Seq_interval.hpp>#include <objects/seqloc/Seq_loc_mix.hpp>#include <objects/seqloc/Seq_point.hpp>#include <objmgr/seq_vector.hpp>#include <objmgr/util/feature.hpp>#include <objmgr/util/sequence.hpp>#include <objtools/edit/apply_object.hpp>#include <objtools/cleanup/cleanup.hpp>
Include dependency graph for report_object.cpp:
Go to the source code of this file.
Go to the SVN repository for this file.
Functions | |
| USING_SCOPE (objects) | |
| CConstRef< CSeq_id > | GetBestId (const CBioseq &bioseq) |
| string | GetLocusTagForFeature (const CSeq_feat &seq_feat, CScope &scope) |
| string | GetProduct (const CProt_ref &prot_ref) |
| string | GetProductForCDS (const CSeq_feat &cds, CScope &scope) |
| void | GetSeqFeatLabel (const CSeq_feat &seq_feat, string &label) |
| static bool | IsAccession (const CSeq_id &id) |
| void | UpgradeSeqLocId (CSeq_point &pnt, CScope &scope) |
| void | UpgradeSeqLocId (CSeq_interval &interval, CScope &scope) |
| void | UpgradeSeqLocId (CSeq_loc &loc, CScope &scope) |
| string | GetSeqLocDescription (const CSeq_loc &loc, CScope &scope) |
Variables | |
| USING_NCBI_SCOPE | |
Function Documentation
◆ GetBestId()
Definition at line 153 of file report_object.cpp.
References CBioseq_Base::GetId(), IsAccession(), and CSeq_id::kMaxScore.
Referenced by CGffIdGenerator::GetGffSourceId(), CDiscrepancyObject::GetTextObjectDescription(), CBedFeatureRecord::SetLocation(), UpgradeSeqLocId(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xAssignFeatureAttributeTranscriptId(), CGff2Writer::xAssignFeatureSeqId(), CGff3Writer::xAssignSourceSeqId(), CGffIdGenerator::xExtractFeatureLocation(), CGff3Writer::xWriteRecord(), and CGff3Writer::xWriteSequenceHeader().
◆ GetLocusTagForFeature()
Definition at line 68 of file report_object.cpp.
References CGene_ref_Base::CanGetLocus_tag(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), GetGeneForFeature(), CGene_ref_Base::GetLocus_tag(), kEmptyStr, CConstRef< C, Locker >::NotEmpty(), and tag.
Referenced by CDiscrepancyObject::GetTextObjectDescription().
◆ GetProduct()
Definition at line 90 of file report_object.cpp.
References CProt_ref_Base::CanGetName(), and CProt_ref_Base::GetName().
Referenced by GetProductForCDS(), CCreateFeat::GetProductId(), CDiscrepancyObject::GetTextObjectDescription(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), and CFeatGlyph::x_DrawRNAProductSequence().
◆ GetProductForCDS()
Definition at line 100 of file report_object.cpp.
References CSeqFeatData_Base::e_Prot, eOverlap_Contains, GetBestOverlappingFeat(), CSeq_feat_Base::GetData(), GetProduct(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::GetProt(), CSeq_feat::GetProtXref(), CSeqFeatData_Base::IsProt(), CSeq_feat_Base::IsSetProduct(), kEmptyStr, and prot.
Referenced by CDiscrepancyObject::GetTextObjectDescription().
◆ GetSeqFeatLabel()
Definition at line 122 of file report_object.cpp.
References CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_intron, fFGL_Content, CSeq_feat_Base::GetData(), GetLabel(), CSeqFeatData::GetSubtype(), CSeqFeatData_Base::IsRna(), label, and number.
Referenced by CDiscrepancyObject::GetTextObjectDescription().
◆ GetSeqLocDescription()
Definition at line 266 of file report_object.cpp.
References CSeq_loc::Assign(), CSeq_loc::GetLabel(), location, and UpgradeSeqLocId().
Referenced by CDiscrepancyObject::GetTextObjectDescription().
◆ IsAccession()
Definition at line 144 of file report_object.cpp.
References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, and CSeq_id_Base::e_Other.
Referenced by GetBestId().
◆ UpgradeSeqLocId() [1/3]
| void UpgradeSeqLocId | ( | CSeq_interval & | interval, |
| CScope & | scope | ||
| ) |
Definition at line 188 of file report_object.cpp.
References GetBestId(), CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_interval_Base::GetId(), CSeq_interval_Base::IsSetId(), and CSeq_interval_Base::SetId().
◆ UpgradeSeqLocId() [2/3]
Definition at line 202 of file report_object.cpp.
References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, GetBestId(), CScope::GetBioseqHandle(), CSeq_loc_Base::GetBond(), CBioseq_Handle::GetCompleteBioseq(), CPacked_seqpnt_Base::GetId(), CSeq_loc_Base::GetPacked_pnt(), CSeq_bond_Base::IsSetA(), CSeq_bond_Base::IsSetB(), CPacked_seqpnt_Base::IsSetId(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_int(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CSeq_loc::SetWhole(), UpgradeSeqLocId(), and CSeq_loc_Base::Which().
◆ UpgradeSeqLocId() [3/3]
| void UpgradeSeqLocId | ( | CSeq_point & | pnt, |
| CScope & | scope | ||
| ) |
Definition at line 174 of file report_object.cpp.
References GetBestId(), CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_point_Base::GetId(), CSeq_point_Base::IsSetId(), and CSeq_point_Base::SetId().
Referenced by GetSeqLocDescription(), and UpgradeSeqLocId().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 63 of file report_object.cpp.
