#include <ncbi_pch.hpp>#include "AltValidator.hpp"#include <objects/seq/Bioseq.hpp>#include <objects/seqfeat/Org_ref.hpp>#include <objects/seqloc/Seq_id.hpp>#include <objects/seqloc/Seq_loc.hpp>#include <objects/seqloc/Seq_interval.hpp>#include <objects/seq/Seq_inst.hpp>#include <objects/seq/seq_id_handle.hpp>#include <objects/entrez2/entrez2_client.hpp>#include <objects/entrez2/Entrez2_docsum.hpp>#include <objects/entrez2/Entrez2_docsum_data.hpp>#include <objects/taxon1/taxon1.hpp>#include <objmgr/object_manager.hpp>#include <objmgr/scope.hpp>#include <objmgr/util/sequence.hpp>#include <objmgr/seq_vector.hpp>#include <objmgr/seqdesc_ci.hpp>#include <objmgr/feat_ci.hpp>#include <objmgr/align_ci.hpp>#include <objtools/data_loaders/genbank/gbloader.hpp>
Include dependency graph for AltValidator.cpp:
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Functions | |
| static void | s_WriteLine (const string &accession, const CTempString &line, bool inDatabase, int currentVersion, bool versionSpecifiedInFile, CNcbiOstream &ostr) |
| string | ExtractAccession (const string &long_acc) |
| void | OverrideLenIfAccession (const string &acc, int &in_out_len) |
Variables | |
| static CRef< CObjectManager > | m_ObjectManager |
| static CRef< CScope > | m_Scope |
Function Documentation
◆ ExtractAccession()
Definition at line 499 of file AltValidator.cpp.
References NPOS, and CSeq_id::ParseFastaIds().
Referenced by CAgpValidateApplication::x_LoadLenFa().
◆ OverrideLenIfAccession()
Definition at line 530 of file AltValidator.cpp.
References CSeq_id::fAcc_nuc, CSeq_id::fAcc_prot, CScope::GetBioseqHandle(), CBioseq_Handle::GetInst_Length(), CSeq_id::IdentifyAccession(), CSeq_id_Base::IsLocal(), and m_Scope.
Referenced by CAgpValidateApplication::x_LoadLenFa().
◆ s_WriteLine()
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static |
Definition at line 371 of file AltValidator.cpp.
References i, NPOS, CTempString::size(), and CTempString::substr().
Referenced by CAltValidator::ProcessQueue().
Variable Documentation
◆ m_ObjectManager
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static |
Definition at line 72 of file AltValidator.cpp.
Referenced by CAltValidator::Init().
◆ m_Scope
Definition at line 73 of file AltValidator.cpp.
Referenced by CValidError_imp::AddBioseqWithNoPub(), BEGIN_NAMED_CLASS_INFO(), BioseqHandleFromLocation(), BOOST_AUTO_TEST_CASE(), CValidError_feat::DoesCDSHaveShortIntrons(), CDefaultSynonymMapper::GetBestSynonym(), CTableDataSeq_table::GetScope(), CMultiAligner::GetScope(), CDeclare_Base::C_Attlist::GetScope(), CCIGAR_Formatter::GetScope(), CAlnBuildApp::GetScope(), CAlnTestApp::GetScope(), CPairwiseAlnApp::GetScope(), CValidError_feat::GetTSACDSOnMinusStrandErrors(), CFlatFileField::GetVal(), CBankITCommentField::GetVals(), CGeneralCommentField::GetVals(), CAltValidator::Init(), CValidError_feat::IsIntronShort(), CValidError_feat::IsOverlappingGenePseudo(), CWinMaskUtil::CInputBioseq_CI::operator++(), OverrideLenIfAccession(), CAlnPrinterFixture::PrintAlignment(), CGeneFinder::CGeneSearchPlugin::processMainLoop(), CValidError_imp::ReportMissingPubs(), CDeclare_Base::C_Attlist::ResetScope(), CIdMapperTestApp::Run(), CNetScheduleServerListener::Scope(), CHeapScope::Set(), CDeclare_Base::C_Attlist::SetScope(), CSAM_Formatter::SetScope(), CValidError_feat::SetScope(), CTreeAlignMerger::SetScope(), CMacroFunction_SetBothPartials::TheFunction(), CMacroFunction_RemoveBothPartials::TheFunction(), CMacroFunction_Set5Partial::TheFunction(), CMacroFunction_Set3Partial::TheFunction(), CMacroFunction_Clear5Partial::TheFunction(), CMacroFunction_Clear3Partial::TheFunction(), CMacroFunction_ConvertLocStrand::TheFunction(), CMacroFunction_ConvertLocType::TheFunction(), CMacroFunction_Extend5Feature::TheFunction(), CMacroFunction_Extend3Feature::TheFunction(), CGeneValidator::Validate(), CValidError_feat::ValidateOneFeatXrefPair(), CMultiAligner::x_AddNewSegment(), CValidError_imp::x_DowngradeForMissingAffil(), CValidError_feat::x_GetCachedBsh(), CDeltaBlastTestFixture::x_InitScope(), CAlnPrinterFixture::x_InitScope(), CAlnPrinterFixture::x_LoadSequences(), CAltValidator::x_QueryAccessions(), CPsiBl2SeqTestFixture::x_SetupSubject(), CGeneValidator::x_ValidateMultiIntervalGene(), CGeneValidator::x_ValidateOperon(), CValidError_feat::x_ValidateSeqFeatExceptXref(), CAlnPrinterFixture::~CAlnPrinterFixture(), CDeltaBlastTestFixture::~CDeltaBlastTestFixture(), and CPsiBl2SeqTestFixture::~CPsiBl2SeqTestFixture().
