#include <ncbi_pch.hpp>#include <corelib/ncbistd.hpp>#include <serial/serialbase.hpp>#include <objects/submit/Seq_submit.hpp>#include <objects/general/Dbtag.hpp>#include <objects/pub/Pub_equiv.hpp>#include <objects/seq/Bioseq.hpp>#include <objects/seq/Pubdesc.hpp>#include <objects/seq/Seqdesc.hpp>#include <objects/seqfeat/Feat_id.hpp>#include <objects/seqfeat/Imp_feat.hpp>#include <objects/seqfeat/Org_ref.hpp>#include <objects/seqfeat/OrgName.hpp>#include <objects/seqfeat/OrgMod.hpp>#include <objects/general/User_object.hpp>#include <objmgr/object_manager.hpp>#include <objmgr/util/sequence.hpp>#include <objtools/validator/validerror_format.hpp>#include <objtools/validator/validerror_suppress.hpp>#include <objtools/validator/utilities.hpp>#include <util/static_map.hpp>
Include dependency graph for validerror_format.cpp:
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Functions | |
| USING_SCOPE (sequence) | |
| void | RemovePrefix (string &str, const string &prefix) |
| void | RemoveSuffix (string &str, const string &suffix) |
| string | s_GetSpecificHostFromBioSource (const CBioSource &biosrc) |
| string | s_GetInstCodeFromBioSource (const CBioSource &biosrc) |
| static string | s_GetFeatureIdLabel (const CObject_id &object_id) |
| static void | s_FixBioseqLabelProblems (string &str) |
| static string | s_GetOrgRefContentLabel (const COrg_ref &org) |
| static string | s_GetBioSourceContentLabel (const CBioSource &bsrc) |
| static string | s_GetFeatureContentLabelExtras (const CSeq_feat &feat) |
| static string | s_GetCdregionContentLabel (const CSeq_feat &feat, CRef< CScope > scope) |
| static bool | s_IsSuppressField (const CUser_field &field) |
Variables | |
| static const string | kSuppressFieldLabel = "Suppress" |
Function Documentation
◆ RemovePrefix()
Definition at line 266 of file validerror_format.cpp.
References NStr::Find(), prefix, and str().
Referenced by CValidErrorFormat::x_FormatGenericForSubmitterReport().
◆ RemoveSuffix()
Definition at line 274 of file validerror_format.cpp.
References NStr::Find(), str(), and suffix.
Referenced by CValidErrorFormat::x_FormatGenericForSubmitterReport().
◆ s_FixBioseqLabelProblems()
Definition at line 623 of file validerror_format.cpp.
References NStr::Find(), and str().
Referenced by CValidErrorFormat::GetBioseqLabel(), and CValidErrorFormat::GetBioseqSetLabel().
◆ s_GetBioSourceContentLabel()
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static |
Definition at line 651 of file validerror_format.cpp.
References CBioSource_Base::GetOrg(), CBioSource_Base::IsSetOrg(), and s_GetOrgRefContentLabel().
Referenced by CValidErrorFormat::GetDescriptorContent(), and CValidErrorFormat::GetFeatureContentLabel().
◆ s_GetCdregionContentLabel()
Definition at line 689 of file validerror_format.cpp.
References ConstBegin(), CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Prot, CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_feat_Base::GetData(), CSeqFeatXref_Base::GetData(), CSeqFeatData_Base::GetGene(), GetId(), CGene_ref::GetLabel(), CProt_ref::GetLabel(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::GetProt(), CSeq_feat_Base::GetXref(), NStr::IsBlank(), CSeqFeatData_Base::IsCdregion(), CSeqFeatXref_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Base::IsSetXref(), ITERATE, s_GetFeatureContentLabelExtras(), and CSeqFeatData_Base::Which().
Referenced by CValidErrorFormat::GetFeatureContentLabel().
◆ s_GetFeatureContentLabelExtras()
Definition at line 661 of file validerror_format.cpp.
References CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Base::IsSetQual(), ITERATE, and prefix.
Referenced by s_GetCdregionContentLabel().
◆ s_GetFeatureIdLabel()
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static |
Definition at line 576 of file validerror_format.cpp.
References CObject_id_Base::GetId(), CObject_id_Base::GetStr(), NStr::IntToString(), CObject_id_Base::IsId(), and CObject_id_Base::IsStr().
Referenced by CValidErrorFormat::GetFeatureIdLabel().
◆ s_GetInstCodeFromBioSource()
| string s_GetInstCodeFromBioSource | ( | const CBioSource & | biosrc | ) |
Definition at line 434 of file validerror_format.cpp.
References COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_specimen_voucher, NStr::Find(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), NStr::IsBlank(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), and ITERATE.
Referenced by CValidErrorFormat::x_FormatBadInstCodeForSubmitterReport().
◆ s_GetOrgRefContentLabel()
Definition at line 637 of file validerror_format.cpp.
References COrg_ref_Base::GetCommon(), COrg_ref_Base::GetDb(), COrg_ref_Base::GetTaxname(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), and COrg_ref_Base::IsSetTaxname().
Referenced by s_GetBioSourceContentLabel().
◆ s_GetSpecificHostFromBioSource()
| string s_GetSpecificHostFromBioSource | ( | const CBioSource & | biosrc | ) |
Definition at line 384 of file validerror_format.cpp.
References COrgMod_Base::eSubtype_nat_host, COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), NStr::IsBlank(), COrgName_Base::IsSetMod(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), and ITERATE.
Referenced by CValidErrorFormat::x_FormatBadSpecificHostForSubmitterReport().
◆ s_IsSuppressField()
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static |
Definition at line 1115 of file validerror_format.cpp.
References NStr::EqualNocase(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::IsSetLabel(), CObject_id_Base::IsStr(), and kSuppressFieldLabel.
◆ USING_SCOPE()
| USING_SCOPE | ( | sequence | ) |
Variable Documentation
◆ kSuppressFieldLabel
Definition at line 1113 of file validerror_format.cpp.
Referenced by s_IsSuppressField().
