NCBI C++ ToolKit
Functions | Variables
AltValidator.cpp File Reference
#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:

Go to the source code of this file.

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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< CObjectManagerm_ObjectManager
 
static CRef< CScopem_Scope
 

Function Documentation

◆ ExtractAccession()

string ExtractAccession ( const string long_acc)

Definition at line 499 of file AltValidator.cpp.

References NPOS, and CSeq_id::ParseFastaIds().

Referenced by CAgpValidateApplication::x_LoadLenFa().

◆ OverrideLenIfAccession()

void OverrideLenIfAccession ( const string acc,
int in_out_len 
)

◆ s_WriteLine()

static void s_WriteLine ( const string accession,
const CTempString line,
bool  inDatabase,
int  currentVersion,
bool  versionSpecifiedInFile,
CNcbiOstream ostr 
)
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

CRef<CObjectManager> m_ObjectManager
static

Definition at line 72 of file AltValidator.cpp.

Referenced by CAltValidator::Init().

◆ m_Scope

CRef<CScope> m_Scope
static

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().

Modified on Mon Apr 22 04:05:42 2024 by modify_doxy.py rev. 669887