#include <ncbi_pch.hpp>#include <corelib/ncbistd.hpp>#include <corelib/ncbistr.hpp>#include <objtools/validator/validatorp.hpp>#include <objtools/validator/validerror_feat.hpp>#include <objtools/validator/single_feat_validator.hpp>#include <objtools/validator/utilities.hpp>#include <objtools/format/items/gene_finder.hpp>#include <serial/serialbase.hpp>#include <objmgr/bioseq_handle.hpp>#include <objmgr/seq_entry_handle.hpp>#include <objmgr/feat_ci.hpp>#include <objmgr/seqdesc_ci.hpp>#include <objmgr/seq_vector.hpp>#include <objmgr/scope.hpp>#include <objmgr/util/sequence.hpp>#include <objmgr/util/feature.hpp>#include <objects/seqfeat/Seq_feat.hpp>#include <objects/seqfeat/BioSource.hpp>#include <objects/seqfeat/Cdregion.hpp>#include <objects/seqfeat/Code_break.hpp>#include <objects/seqfeat/Gb_qual.hpp>#include <objects/seqfeat/Genetic_code.hpp>#include <objects/seqfeat/Genetic_code_table.hpp>#include <objects/seqfeat/Imp_feat.hpp>#include <objects/seqfeat/Org_ref.hpp>#include <objects/seqfeat/Prot_ref.hpp>#include <objects/seqfeat/RNA_ref.hpp>#include <objects/seqfeat/SubSource.hpp>#include <objects/seqfeat/Trna_ext.hpp>#include <objects/seqloc/Seq_loc.hpp>#include <objects/seqloc/Seq_interval.hpp>#include <objects/seqloc/Seq_point.hpp>#include <objects/seqloc/Textseq_id.hpp>#include <objects/seqset/Seq_entry.hpp>#include <objects/seqset/Bioseq_set.hpp>#include <objects/seq/MolInfo.hpp>#include <objects/seq/Bioseq.hpp>#include <objects/seq/seqport_util.hpp>#include <objects/pub/Pub.hpp>#include <objects/pub/Pub_set.hpp>#include <objects/general/Dbtag.hpp>#include <objects/misc/sequence_macros.hpp>#include <objtools/edit/cds_fix.hpp>#include <util/static_set.hpp>#include <util/sequtil/sequtil_convert.hpp>#include <util/sgml_entity.hpp>#include <algorithm>#include <string>
Include dependency graph for validerror_feat.cpp:
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Functions | |
| static int | ValidateAccessionFormat (string accession) |
| bool | s_IsSraPrefix (string str) |
| bool | s_IsAllDigitsOrPeriods (string str) |
| bool | FeaturePairIsTwoTypes (const CSeq_feat &feat1, const CSeq_feat &feat2, CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2) |
| bool | GeneXrefConflicts (const CSeq_feat &feat, const CSeq_feat &gene) |
| bool | s_HasId (const CSeq_feat &feat, const CSeqFeatXref::TId::TLocal &id) |
Function Documentation
◆ FeaturePairIsTwoTypes()
| bool FeaturePairIsTwoTypes | ( | const CSeq_feat & | feat1, |
| const CSeq_feat & | feat2, | ||
| CSeqFeatData::ESubtype | subtype1, | ||
| CSeqFeatData::ESubtype | subtype2 | ||
| ) |
Definition at line 611 of file validerror_feat.cpp.
References CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), and CSeq_feat_Base::IsSetData().
Referenced by CValidError_feat::ValidateOneFeatXrefPair().
◆ GeneXrefConflicts()
Definition at line 629 of file validerror_feat.cpp.
References FOR_EACH_SEQFEATXREF_ON_SEQFEAT, CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), label, and CSingleFeatValidator::s_GeneRefsAreEquivalent().
Referenced by CValidError_feat::ValidateOneFeatXrefPair().
◆ s_HasId()
| bool s_HasId | ( | const CSeq_feat & | feat, |
| const CSeqFeatXref::TId::TLocal & | id | ||
| ) |
Definition at line 740 of file validerror_feat.cpp.
References CSerialObject::Equals(), CSeq_feat_Base::GetId(), CFeat_id_Base::GetLocal(), CFeat_id_Base::IsLocal(), and CSeq_feat_Base::IsSetId().
Referenced by CValidError_feat::ValidateSeqFeatXref().
◆ s_IsAllDigitsOrPeriods()
Definition at line 303 of file validerror_feat.cpp.
References NStr::EndsWith(), NStr::IsBlank(), isdigit(), ITERATE, NStr::StartsWith(), and str().
Referenced by CValidError_feat::ValidateInferenceAccession().
◆ s_IsSraPrefix()
Definition at line 287 of file validerror_feat.cpp.
References str().
Referenced by CValidError_feat::ValidateInferenceAccession().
◆ ValidateAccessionFormat()
Definition at line 254 of file validerror_feat.cpp.
References CSeq_id::eAcc_unknown, and CSeq_id::IdentifyAccession().
Referenced by CValidError_feat::ValidateInferenceAccession().
