RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Miscellaneous.html below:

NCBI C++ ToolKit: Miscellaneous

(sctx, __func__, request, reply)

BEGIN_NCBI_GRPC_REQUEST – Set up AppLog logging for the current (server-side) request handler.

The third argument may be either a reply google::protobuf::Message or a streaming grpc::ServerWriter<>. In the case of a reply message, automatic wrap-up actions will include propagating its byte size to the request context's count of bytes written. In the case of a streaming writer, however, there's no automatic way to determine that count, so callers are responsible for supplying it themselves.

Definition at line 104 of file grpc_integration.hpp.

◆ NCBI_GRPC_RETURN ◆ NCBI_GRPC_RETURN_EX #define NCBI_GRPC_RETURN_EX ( sc, msg ) Value:

GetDiagContext().GetRequestContext().SetRequestStatus(status_code); \

} while (0)

grpc::Status g_AsGRPCStatus(CRequestStatus::ECode status_code)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

NCBI_GRPC_RETURN(_EX) – Provide consistent gRPC request handler status information to AppLog and gRPC.

The _EX variant takes an error message to substitute for a stock status code description. (A 1xx-3xx status code still always yields grpc::OK, with no custom message.)

Definition at line 113 of file grpc_integration.hpp.

◆ NCBI_MACRO ◆ NCBI_MACRO_ANOTHER #define NCBI_MACRO_ANOTHER 2

Brief description of macro – it must be ended with a period.

Optional detailed description of a macro. Continuing with detailed description of macro.

Definition at line 80 of file header_template.hpp.

◆ FHandler typedef char*(* CMyClass::FHandler) (int start, int stop)

Brief description of a function pointer type.

Detailed description of the function pointer type.

Definition at line 123 of file header_template.hpp.

◆ FIdCheck ◆ FModFilter ◆ SDefLineParseInfo ◆ SLineTextAndLoc ◆ TAttrs ◆ TCIGARFlags ◆ TCountToLinkEvidMap ◆ TData ◆ TDelayedRecords ◆ TFastaSeqIds

List of qll sequence ids.

Definition at line 453 of file fasta.hpp.

◆ TFlags [1/3] ◆ TFlags [2/3]

binary OR of EFlags

Definition at line 117 of file fasta.hpp.

◆ TFlags [3/3] ◆ TGapRef ◆ TGaps ◆ TGapTypeObj ◆ TGeneRefs ◆ TGRPCBaseClientContext ◆ TGRPCPropagationOptions ◆ TGRPCServerContext ◆ TIds ◆ TIDTracker ◆ TIgnoredProblems ◆ TLines ◆ TLinkEvidSet ◆ TLoc ◆ TMapVector ◆ TMask ◆ TMasks ◆ TMessage [1/2] ◆ TMessage [2/2] ◆ TMods [1/2] ◆ TMods [2/2] ◆ TModsCI [1/2] ◆ TModsCI [2/2] ◆ TModsRange [1/2] ◆ TModsRange [2/2] ◆ TMyBitMask ◆ TNullableGapType ◆ TNumrow ◆ TParent ◆ TPostponedModMap ◆ TRange ◆ TReadFastaFlags ◆ TRowNum ◆ TSegments ◆ TSeqCache ◆ TSeqNameCache ◆ TSeqTitles ◆ TStartsMap ◆ TStr [1/2] ◆ TStr [2/2] ◆ TStrVec ◆ TSubMap ◆ TWhichMods [1/2] ◆ TWhichMods [2/2] ◆ ECIGARFlags Enumerator fCIGAR_GffForFlybase

Flybase flavour of GFF3.

fCIGAR_Default

Definition at line 56 of file cigar_formatter.hpp.

◆ EConstants ◆ EEigensWanted Enumerator eEigenValues eEigenVectors

Definition at line 48 of file ncbi_lapack.h.

◆ EEOLStyle Enumerator eEOL_unknown

to be detected

eEOL_cr

bare CR (classic Mac)

eEOL_lf

bare LF (Unix et al.)

eEOL_crlf

DOS/Windows.

eEOL_native eEOL_mixed

contains both bare CRs and bare LFs

Definition at line 122 of file line_reader.hpp.

◆ EFlags [1/3] Enumerator fSAM_AlignmentScore

Generate AS tags.

fSAM_ExpectationValue

Generate EV tags.

fSAM_NumNucDiff

Generate NM tags.

fSAM_PercentageIdentity

Generate PI tags.

fSAM_BitScore

Generate BS tags.

fSAM_PlainSeqIds

Drop type prefix in seq-ids.

fSAM_SeqData

Print sequence data.

fSAM_ForceGISeqIds

Force using GI ids.

fSAM_Default

Definition at line 57 of file sam_formatter.hpp.

◆ EFlags [2/3]

Note on fAllSeqIds: some databases (notably nr) have merged identical sequences, joining their deflines together with control-As.

Normally, the reader stops at the first control-A; however, this flag makes it parse all the IDs.

Enumerator fAssumeNuc

Assume nucs unless accns indicate otherwise.

fAssumeProt

Assume prots unless accns indicate otherwise.

fForceType

Force specified type regardless of accession.

fNoParseID

Generate an ID (whole defline -> title)

fParseGaps

Make a delta sequence if gaps found.

fOneSeq

Just read the first sequence found.

fAllSeqIds

Read Seq-ids past the first ^A (see note)

fNoSeqData

Parse the deflines but skip the data.

fRequireID

Reject deflines that lack IDs.

fDLOptional

Don't require a leading defline.

fParseRawID

Try to identify raw accessions.

fSkipCheck

Skip (rudimentary) body content check.

fNoSplit

Don't split out ambiguous sequence regions.

fValidate

Check (alphabetic) residue validity.

fUniqueIDs

Forbid duplicate IDs.

fStrictGuess

Assume no typos when guessing sequence type.

fLaxGuess

Use legacy heuristic for guessing seq. type.

fAddMods

Parse defline mods and add to SeqEntry.

fLetterGaps

Parse runs of Ns when splitting data.

fNoUserObjs

Don't save raw deflines in User-objects.

fBadModThrow fUnknModThrow fLeaveAsText

Don't reencode at all, just parse.

fQuickIDCheck

Just check local IDs' first characters.

fUseIupacaa

If Prot, use iupacaa instead of the default ncbieaa.

fHyphensIgnoreAndWarn

When a hyphen is encountered in seq data, ignore it but warn.

fDisableNoResidues

If no residues found do not raise an error.

fDisableParseRange

No ranges in seq-ids. Ranges part of seq-id instead.

fIgnoreMods

Ignore mods entirely. Incompatible with fAddMods.

Definition at line 86 of file fasta.hpp.

◆ EFlags [3/3] Enumerator fNoGTF

don't honor/recognize GTF conventions

attribute tags are GenBank qualifiers

fGBQuals

merge exons with the same transcript_id

fMergeExons

restrict merging to just CDS and mRNA features

fMergeOnyCdsMrna

move protein_id and transcript_id to products for mRNA and CDS features

fSetProducts

create gene features for mRNAs and CDSs if none exist already

fCreateGeneFeats

numeric identifiers are local IDs

fNumericIdsAsLocal

all identifiers are local IDs

fAllIdsAsLocal

all identifiers are local IDs

fSetVersion3 fDefaults

Definition at line 74 of file gff_reader.hpp.

◆ EFormat

Length-first (ENSEMBL) and operation-first (original) variants both exist; allowing for the possibility of implicit lengths (defaulting to 1), as observed in at least the operation-first variant makes any string that both starts AND ends with a letter ambiguous.

Enumerator eConservativeGuess eLengthFirst eLengthFirstIfAmbiguous eOpFirst eOpFirstIfAmbiguous

Definition at line 78 of file cigar.hpp.

◆ EFormatBy Enumerator eFormatBy_NotSet eFormatBy_ReferenceId eFormatBy_TargetId

Definition at line 120 of file cigar_formatter.hpp.

◆ EGroupOrder Enumerator eGO_Skip

Do not print GO tag.

eGO_None

GO:none.

eGO_Query

GO:query (default)

eGO_Reference

GO:reference.

eGO_User

User-provided string.

Definition at line 124 of file sam_formatter.hpp.

◆ EHandleBadMod [1/2] Enumerator eHandleBadMod_Ignore eHandleBadMod_Throw eHandleBadMod_PrintToCerr eHandleBadMod_ErrorListener eHandleBadMod_Ignore eHandleBadMod_Throw eHandleBadMod_PrintToCerr eHandleBadMod_ErrorListener

Definition at line 89 of file source_mod_parser.hpp.

◆ EHandleBadMod [2/2] Enumerator eHandleBadMod_Ignore eHandleBadMod_Throw eHandleBadMod_PrintToCerr eHandleBadMod_ErrorListener eHandleBadMod_Ignore eHandleBadMod_Throw eHandleBadMod_PrintToCerr eHandleBadMod_ErrorListener

Definition at line 89 of file source_mod_parser.hpp.

◆ EInternalFlags Enumerator fAligning fInSegSet

Definition at line 235 of file fasta.hpp.

◆ EInvocationType

How was BeginRequest or EndRequest called?

Enumerator eImplicit

From {Pre,Post}SynchronousRequest.

eExplicit

Via CGRPCRequestLogger or the like.

Definition at line 134 of file grpc_support.hpp.

◆ EKnownSize Enumerator eKnownSize_No eKnownSize_Yes

Definition at line 340 of file fasta.hpp.

◆ EMatrixTriangle Enumerator eUpperTriangle eLowerTriangle

Definition at line 53 of file ncbi_lapack.h.

◆ EMaybeTransposed Enumerator eTransposed eNotTransposed

Definition at line 58 of file ncbi_lapack.h.

◆ EMyBitEnum

An enumerator used as a bitmask.

Enumerator eValName1

description for value 0x01.

eValName2

description for value 0x02.

eValName3

description for value 0x04.

Definition at line 113 of file header_template.hpp.

◆ EMyEnum

A brief description of an enumerator.

A more detailed enum description here. Note that you can comment as shown over here before the class/function/member description or alternatively follow a member definition with a single line comment preceded by ///<. Use the style that makes the most sense for the code.

Enumerator eVal1

EMyEnum value eVal1 description. Note the use of ///<.

eVal2

EMyEnum value eVal2 description.

eVal3

EMyEnum value eVal3 description.

Definition at line 106 of file header_template.hpp.

◆ EOperation Enumerator eNotSet

for internal use only

eMatch eInsertion eDeletion eIntron

not documented by GFF3

eForwardShift

only documented by GFF3 (same for R)

eReverseShift

Definition at line 56 of file cigar.hpp.

◆ EPosType Enumerator eRawPos ePosWithGaps ePosWithGapsAndSegs

Definition at line 308 of file fasta.hpp.

◆ ESingularVectorDetailsWanted Enumerator eSVD_All

Full orthogonal matrix, in a dedicated arg.

eSVD_Singular

Only the singular vectors, in a dedicated arg.

eSVD_Overwrite

Only the singular vectors, overwriting A.

eSVD_None

None.

Definition at line 63 of file ncbi_lapack.h.

◆ ESortOrder Enumerator eSO_Skip

Do not print SO tag (default)

eSO_Unsorted

SO:unsorted.

eSO_QueryName

SO:queryname.

eSO_Coordinate

SO:coordinate.

eSO_User

User-provided string.

Definition at line 105 of file sam_formatter.hpp.

◆ EState ◆ EType ◆ EWhichMods [1/2] Enumerator fUsedMods fUnusedMods fAllMods fUsedMods fUnusedMods fAllMods

Definition at line 171 of file source_mod_parser.hpp.

◆ EWhichMods [2/2] Enumerator fUsedMods fUnusedMods fAllMods fUsedMods fUnusedMods fAllMods

Definition at line 171 of file source_mod_parser.hpp.

◆ AddData()

Definition at line 97 of file fasta_aln_builder.cpp.

References CFastaAlignmentBuilder::eDoubleGap, CFastaAlignmentBuilder::m_DS, CFastaAlignmentBuilder::m_LastAlignmentPos, CFastaAlignmentBuilder::m_LastNonDGState, CFastaAlignmentBuilder::m_LastOtherPos, CFastaAlignmentBuilder::m_LastReferencePos, CFastaAlignmentBuilder::m_LastState, CDense_seg_Base::SetLens(), CDense_seg_Base::SetStarts(), CFastaAlignmentBuilder::x_EnsurePos(), and CFastaAlignmentBuilder::x_State().

◆ AddMods() ◆ AddRow() virtual void CCIGAR_Formatter::AddRow ( const string & ) inlineprotectedvirtual ◆ AddSegment() void CCIGAR_Formatter::AddSegment ( ostream & cigar, char seg_type, TSeqPos seg_len ) protectedvirtual ◆ AddSequence() ◆ AddStandardNCBIMetadata() void CGRPCClientContext::AddStandardNCBIMetadata ( TParent & cctx ) static

Definition at line 202 of file grpc_integration.cpp.

References buf, NStr::eNocase, CRequestContext_PassThrough::Enumerate(), ERR_POST_X_ONCE, CDiagContext::GetAppName(), GetDiagContext(), CRequestContext::GetDtab(), CRequestContext::GetNextSubHitID(), CDiagContext::GetRequestContext(), CRequestContext::GetSessionID(), CRequestContext_PassThrough::IsSet(), CRequestContext::IsSetClientIP(), CRequestContext::IsSetSessionID(), NcbiGetHostIP(), s_EncodeMetadataName(), s_EncodeMetadataValue(), NStr::StartsWith(), rapidjson::value, and Warning().

Referenced by CGRPCClientContext::CGRPCClientContext(), and CGRPCClientContext::FromServerContext().

◆ AddStringFlags() void CFastaReader::AddStringFlags ( const list< string > & stringFlags, TFlags & baseFlags ) static

Definition at line 222 of file fasta.cpp.

References CFastaReader::fAddMods, CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, CFastaReader::fDisableNoResidues, CFastaReader::fDisableParseRange, CFastaReader::fDLOptional, CFastaReader::fForceType, CFastaReader::fHyphensIgnoreAndWarn, CFastaReader::fIgnoreMods, CFastaReader::fLaxGuess, CFastaReader::fLeaveAsText, CFastaReader::fLetterGaps, CFastaReader::fNoParseID, CFastaReader::fNoSeqData, CFastaReader::fNoSplit, CFastaReader::fNoUserObjs, CFastaReader::fOneSeq, CFastaReader::fParseGaps, CFastaReader::fParseRawID, CFastaReader::fQuickIDCheck, CFastaReader::fRequireID, CFastaReader::fSkipCheck, CFastaReader::fStrictGuess, CFastaReader::fUniqueIDs, CFastaReader::fUseIupacaa, CFastaReader::fValidate, and CReaderBase::xAddStringFlagsWithMap().

Referenced by CMultiReaderApp::xSetFlags().

◆ AdjustSeqIdType() ◆ ApplyAllMods()

Apply previously extracted modifiers to the given object, marking all relevant ones as used.

Definition at line 575 of file source_mod_parser.cpp.

References CSourceModParser::ApplyMods(), CSourceModParser::ApplyPubMods(), set< Key, Compare >::begin(), CSeq_id::BestRank(), CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Source, CBioseq_set_Base::eClass_nuc_prot, CRef< C, Locker >::Empty(), set< Key, Compare >::end(), FIELD_CHAIN_OF_2_IS_SET, FindBestChoice(), ftable, CSourceModParser::fUnusedMods, CBioseq_set_Base::GetClass(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSourceModParser::GetMods(), CBioseq::GetParentSet(), CConstRef< C, Locker >::GetPointerOrNull(), CBioseq::IsAa(), CAutoInitPtr_Base::IsInitialized(), CBioseq::IsNa(), CBioseq_Base::IsSetAnnot(), CBioseq_set_Base::IsSetClass(), CSeq_inst_Base::IsSetHist(), location, NON_CONST_ITERATE, prot, CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetUser(), CSeq_loc::SetWhole(), unused, CSourceModParser::x_ApplyDBLinkMods(), CSourceModParser::x_ApplyGenomeProjectsDBMods(), CSourceModParser::x_ApplyMods(), CSourceModParser::x_ApplyTPAMods(), and CSourceModParser::x_HandleUnkModValue().

◆ ApplyGenomeProjectsDBMods() void CSourceModParser::ApplyGenomeProjectsDBMods ( CUser_object & gpdb ) inline ◆ ApplyMods() [1/7] void CSourceModParser::ApplyMods ( CBioseq & seq )

Definition at line 753 of file source_mod_parser.cpp.

References CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, NStr::EqualNocase(), CSeq_inst_Base::eStrand_ds, CSeq_inst_Base::eStrand_mixed, CSeq_inst_Base::eStrand_ss, CSeq_inst_Base::eTopology_circular, CSeq_inst_Base::eTopology_linear, FIELD_CHAIN_OF_2_IS_SET, CSourceModParser::FindMod(), CBioseq::IsNa(), mod(), CSeqdesc_Base::SetComment(), CBioseq_Base::SetDescr(), CBioseq_Base::SetInst(), and CSourceModParser::x_HandleBadModValue().

◆ ApplyMods() [2/7] ◆ ApplyMods() [3/7] void CSourceModParser::ApplyMods ( CGB_block & gbb ) ◆ ApplyMods() [4/7] void CSourceModParser::ApplyMods ( CGene_ref & gene ) inline ◆ ApplyMods() [5/7] void CSourceModParser::ApplyMods ( CMolInfo & mi ) ◆ ApplyMods() [6/7] void CSourceModParser::ApplyMods ( CProt_ref & prot ) inline ◆ ApplyMods() [7/7] void CSourceModParser::ApplyMods ( CSeq_hist & hist ) inline ◆ ApplyPubMods() void CSourceModParser::ApplyPubMods ( CBioseq & seq ) ◆ ApplyTPAMods() ◆ AssembleSeq()

Reimplemented in CFastaMapper.

Definition at line 1351 of file fasta.cpp.

References _ASSERT, CDelta_ext::AddAndSplit(), CFastaReader::AssignMolType(), CFastaReader::CloseGap(), CFastaReader::CloseMask(), data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbieaa, CFastaReader::SGap::eKnownSize_No, CInt_fuzz_Base::eLim_unk, CSeq_gap_Base::eLinkage_linked, CObjReaderParseException::eNoResidues, CFastaReader::ePosWithGaps, ILineError::eProblem_ModifierFoundButNoneExpected, CFastaReader::eRawPos, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_virtual, CSeq_gap_Base::eType_unknown, CLinkage_evidence_Base::eType_unspecified, FASTA_ERROR, FASTA_WARNING, CFastaReader::fDisableNoResidues, CFastaReader::fInSegSet, CFastaReader::fLeaveAsText, CFastaReader::fNoSeqData, CFastaReader::fNoSplit, format, CFastaReader::fParseGaps, CFastaReader::fUseIupacaa, CFastaReader::fValidate, CDelta_ext_Base::Get(), CFastaReader::GetCurrentPos(), CSeq_inst_Base::GetLength(), i, CSeq_inst::IsAa(), ITERATE, CTempString::length(), CFastaReader::LineNumber(), CFastaReader::m_BestID, CFastaReader::m_CurrentGapChar, CFastaReader::m_CurrentPos, CFastaReader::m_CurrentSeq, CFastaReader::m_CurrentSeqTitles, CFastaReader::m_Gaps, CFastaReader::m_SegmentBase, CFastaReader::m_SeqData, CFastaReader::m_TotalGapLength, n, NCBI_THROW2, CSeqportUtil::Pack(), CFastaReader::ParseTitle(), CSeq_inst_Base::ResetExt(), CDelta_ext_Base::Set(), CSeq_inst_Base::SetExt(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), CSeq_gap_Base::SetLinkage(), CSeq_gap_Base::SetLinkage_evidence(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), CSeq_gap_Base::SetType(), swap(), CFastaReader::TestFlag(), CSeqportUtil::Validate(), and CFastaReader::x_NucOrProt().

Referenced by CFastaMapper::AssembleSeq(), CFastaReaderEx::AssembleSeq(), and CFastaReader::ReadOneSeq().

◆ AssignMolType()

Reimplemented in CCustomizedFastaReader.

Definition at line 1548 of file fasta.cpp.

References _ASSERT, data, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, CFormatGuess::eNucleotide, CFormatGuess::eProtein, CFormatGuess::eST_Default, CFormatGuess::eST_Lax, CFormatGuess::eST_Strict, CFastaReader::fAssumeNuc, CFastaReader::fAssumeProt, CFastaReader::fForceType, CFastaReader::fLaxGuess, CFastaReader::fStrictGuess, CFastaReader::GetFlags(), CFastaReader::LineNumber(), CFastaReader::m_CurrentSeq, CFastaReader::m_SeqData, min(), NCBI_THROW2, NStr::NumericToString(), CFormatGuess::SequenceType(), CBioseq_Base::SetInst(), sRefineNaMol(), and CFastaReader::TestFlag().

Referenced by CFastaReader::AssembleSeq(), CCustomizedFastaReader::AssignMolType(), and CFastaReaderEx::AssignMolType().

◆ AtEOF() [1/5] bool CFastaReader::AtEOF ( void ) const inline ◆ AtEOF() [2/5] bool CStreamLineReader::AtEOF ( void ) const virtual

Indicates (negatively) whether there is any more input.

Implements ILineReader.

Definition at line 100 of file line_reader.cpp.

References CT_EOF, CT_EQ_INT_TYPE, CStreamLineReader::m_Stream, and CStreamLineReader::m_UngetLine.

Referenced by CLoadSecondaryAccessions::apply(), CAliasTest::DoTest(), C5ColObjectLoader::Execute(), CPslObjectLoader::Execute(), GetAlignmentFromStream(), C5ColLineReader::GetNextRecord(), CBedLineReader::GetNextRecord(), CGff3LineReader::GetNextRecord(), CGtfLineReader::GetNextRecord(), CBlastNodeInputReader::GetQueryBatch(), GetSeqLocFromStream(), CMacroParamsPanel::OnPropertyChanged(), CStreamLineReader::operator++(), CDiscrepancyContext::ParseStrings(), CStreamLineReader::PeekChar(), CBioTreeAttrReader::Read(), ReadFastaQueries(), ReadMsa(), CAnalyzeShiftApp::Run(), s_CreateScope(), s_GetTaxIDList(), CStreamLineReader::x_AdvanceEOLCRLF(), x_GetSeqLocFromStream(), CAlnPrinterFixture::x_LoadSequences(), and CUpdateAlign::x_MapNonPresentIDs().

◆ AtEOF() [3/5] bool CMemoryLineReader::AtEOF ( void ) const virtual ◆ AtEOF() [4/5] bool CBufferedLineReader::AtEOF ( void ) const virtual ◆ AtEOF() [5/5] virtual bool ILineReader::AtEOF ( void ) const pure virtual

Indicates (negatively) whether there is any more input.

Implemented in CCompatLineReader, CBufferedLineReader, CMemoryLineReader, and CStreamLineReader.

Referenced by CStructuredCommentsReader::_LoadHeaderLine(), CTabDelimitedValidator::_OperateRows(), CTabDelimitedValidator::_ProcessHeader(), CFastaReader::AtEOF(), CBioTreeAttrReader::CheckLineReader(), CShortReadFastaInputSource::CShortReadFastaInputSource(), CBlastFastaInputSource::End(), CShortReadFastaInputSource::End(), CLinePreBuffer::FillBuffer(), CLinePreBuffer::GetLine(), CFastaBioseqSource::GetNext(), CAuthorNamesContainer::ImportAuthorsFromFile(), CTable2AsnStructuredCommentsReader::IsVertical(), CStructuredCommentsReader::LoadComments(), CStructuredCommentsReader::LoadCommentsByRow(), CForeignContaminationScreenReportReader::LoadFile(), CLoadStructComments::LoadSingle(), CUpdateMultiSeq_Dlg::OnLoadMapClick(), CReaderOfLines::Read(), CMacroEngine::ReadAndParseMacros(), CMacroEngineParallel::ReadAndParseMacros(), CFeatureTableReader_Imp::ReadSequinFeatureTable(), CFeature_table_reader::ReadSequinFeatureTables(), CFastaReader::ReadSet(), CTabDelimitedValidator::RegisterAliases(), CTbl2AsnApp::Run(), IMacroBioDataIter::STableToApply::SetTableToApply(), sRunTest(), CMacroLib::StoreSynonymList(), sUpdateCase(), CMacroEngine::x_AppendToLibrary(), CMacroEngineParallel::x_AppendToLibrary(), IMacroBioDataIter::STableToApply::x_CacheColFromTable(), CFeatureTableReader_Imp::x_FinishFeature(), IMacroBioDataIter::STableToApply::x_InitAndCheck(), CTaxonCache::x_LoadTaxonCache(), CMacroApplySrcTablePanel::x_ProcessFirstLine(), CShortReadFastaInputSource::x_ReadFastaOneSeq(), CShortReadFastaInputSource::x_ReadFastc(), CShortReadFastaInputSource::x_ReadFastqOneSeq(), and CMultiReaderApp::xProcess5ColFeatTable().

◆ BeginRequest() [1/2] ◆ BeginRequest() [2/2]

Definition at line 355 of file grpc_integration.cpp.

References _ASSERT, CRequestContext::AddPassThroughProperty(), CTempString::assign(), CGRPCServerCallbacks::eImplicit, CTempString::empty(), eNoOwnership, env, ERR_POST_X_ONCE, CDiagContext_Extra::Flush(), CRequestContext::GetClientIP(), GetDiagContext(), CNcbiApplicationAPI::GetEnvironment(), CDiagContext::GetRequestContext(), Info(), CNcbiApplication::Instance(), CNcbiLogFields::LogFields(), NPOS, NULL, CDiagContext_Extra::Print(), CDiagContext::PrintRequestStart(), NStr::ReplaceInPlace(), CTempString::rfind(), s_DecodeMetadataName(), s_DecodeMetadataValue(), s_SetClientIP(), CRequestContext::SetClientIP(), CRequestContext::SetRequestID(), NStr::StartsWith(), CTempString::substr(), NStr::ToLower(), rapidjson::value, and CGRPCServerCallbacks::x_IsRealRequest().

◆ CanonicalizeString() ◆ CBadModError() ◆ CBufferedLineReader() [1/4] ◆ CBufferedLineReader() [2/4] ◆ CBufferedLineReader() [3/4] CBufferedLineReader::CBufferedLineReader ( const string & filename ) ◆ CBufferedLineReader() [4/4] ◆ CCIGAR_Formatter() ◆ CFastaAlignmentBuilder() ◆ CFastaReader() [1/4] ◆ CFastaReader() [2/4] ◆ CFastaReader() [3/4] ◆ CFastaReader() [4/4] ◆ CFooClass() CMyClass::CFooClass ( const CFooClass & ) private

This method is declared as private but is not implemented to prevent member-wise copying.

◆ CGFFReader() ◆ CGRPCClientContext() CGRPCClientContext::CGRPCClientContext ( void ) inline ◆ CGRPCRequestLogger() [1/2] ◆ CGRPCRequestLogger() [2/2] ◆ CheckDataLine()

Definition at line 710 of file fasta.cpp.

References CObjReaderParseException::eFormat, ILineError::eProblem_TooManyAmbiguousResidues, CFastaReader::fAssumeNuc, FASTA_ERROR, FASTA_WARNING, CFastaReader::fForceType, CFastaReader::fHyphensIgnoreAndWarn, CFastaReader::fSkipCheck, CBioseq_Base::GetInst(), CBioseq::IsNa(), CBioseq_Base::IsSetInst(), CSeq_inst_Base::IsSetMol(), isspace(), CTempString::length(), CFastaReader::LineNumber(), CFastaReader::m_CurrentSeq, CFastaReader::m_SeqData, min(), s_ASCII_IsAlpha(), s_ASCII_IsAmbigNuc(), and CFastaReader::TestFlag().

Referenced by CFastaReader::ParseDataLine().

◆ CloseGap() ◆ CloseMask() void CFastaReader::CloseMask ( void ) inlineprotected ◆ CMemoryLineReader() [1/3] ◆ CMemoryLineReader() [2/3] CMemoryLineReader::CMemoryLineReader ( const char * start, const char * end ) inline

Open a line reader over the half-open memory range [start, end).

As always with ILineReader, an explicit call to operator++ or ReadLine() will be necessary to fetch the first line.

Definition at line 187 of file line_reader.hpp.

◆ CMemoryLineReader() [3/3] CMemoryLineReader::CMemoryLineReader ( const char * start, SIZE_TYPE length ) inline

Open a line reader over the half-open memory range [start, start+length).

As always with ILineReader, an explicit call to operator++ or ReadLine() will be necessary to fetch the first line.

Definition at line 195 of file line_reader.hpp.

◆ CMyClass() [1/3] ◆ CMyClass() [2/3] CMyClass::CMyClass ( int param1, int param2 )

A brief description of a non-trivial constructor.

A detailed description of the constructor. More details.

Parameters: param1 First parameter description. param2 Second parameter description.

◆ CMyClass() [3/3]

A brief description of another constructor.

parameter description

◆ CompareKeys() ◆ CreateWarningsForSeqDataInTitle() ◆ CSAM_Formatter() ◆ CSAM_Headers() CSAM_Formatter::CSAM_Headers::CSAM_Headers ( void ) inline

Definition at line 175 of file sam_formatter.hpp.

◆ CSourceModParser() [1/2]

Construct object providing old-style error handling directives.

Definition at line 99 of file source_mod_parser.hpp.

◆ CSourceModParser() [2/2] CSourceModParser::CSourceModParser ( ILineErrorListener * pErrorListener, size_t lineNumber = 1 ) inline ◆ CStreamLineReader() [1/2]

Open a line reader over a given stream, with the given EOL-style and ownership settings (if specified).

As always with ILineReader, an explicit call to operator++ or ReadLine() will be necessary to fetch the first line.

Definition at line 77 of file line_reader.cpp.

◆ CStreamLineReader() [2/2]

Open a line reader over a given stream, with the given ownership setting.

As always with ILineReader, an explicit call to operator++ or ReadLine() will be necessary to fetch the first line.

Definition at line 87 of file line_reader.cpp.

◆ CUnkModError() ◆ EndAlignment() virtual void CCIGAR_Formatter::EndAlignment ( void ) inlineprotectedvirtual ◆ EndRequest() [1/2] ◆ EndRequest() [2/2] ◆ EndRow() virtual void CCIGAR_Formatter::EndRow ( void ) inlineprotectedvirtual ◆ EndRows() virtual void CCIGAR_Formatter::EndRows ( void ) inlineprotectedvirtual ◆ EndSubAlignment() virtual void CCIGAR_Formatter::EndSubAlignment ( void ) inlineprotectedvirtual ◆ EntryFound()

Callback function, called after reading the fasta entry.

Referenced by ScanFastaFile().

◆ EqualKeys() ◆ FindAllMods() [1/3] ◆ FindAllMods() [2/3] ◆ FindAllMods() [3/3] ◆ FindAttribute() ◆ FindMod()

If a modifier with either key is present, mark it as used and return it; otherwise, return NULL.

Definition at line 1656 of file source_mod_parser.cpp.

References CTempString::empty(), set< Key, Compare >::end(), CSourceModParser::EqualKeys(), ncbi::grid::netcache::search::fields::key, set< Key, Compare >::lower_bound(), CSourceModParser::m_Mods, CSourceModParser::m_pModFilter, mod(), and CSourceModParser::SMod::used.

Referenced by CSourceModParser::ApplyMods(), CSourceModParser::x_AddPCRPrimers(), CSourceModParser::x_ApplyDBLinkMods(), CSourceModParser::x_ApplyGenomeProjectsDBMods(), CSourceModParser::x_ApplyMods(), and CSourceModParser::x_ApplyTPAMods().

◆ Flush() void CSAM_Formatter::Flush ( void )

Definition at line 405 of file sam_formatter.cpp.

References ITERATE, CSAM_Formatter::m_Body, CSAM_Formatter::SProgramInfo::m_CmdLine, CSAM_Formatter::CSAM_Headers::m_Data, CSAM_Formatter::SProgramInfo::m_Desc, CSAM_Formatter::m_Header, CSAM_Formatter::SProgramInfo::m_Id, CSAM_Formatter::SProgramInfo::m_Name, CSAM_Formatter::m_Out, CSAM_Formatter::m_ProgramInfo, CSAM_Formatter::SProgramInfo::m_Version, CSAM_Formatter::x_PrintGOTag(), and CSAM_Formatter::x_PrintSOTag().

Referenced by CSAM_Formatter::~CSAM_Formatter().

◆ FormatByReferenceId() void CCIGAR_Formatter::FormatByReferenceId ( const CSeq_id & ref_id ) ◆ FormatByReferenceRow() void CCIGAR_Formatter::FormatByReferenceRow ( TNumrow ref_row ) ◆ FormatByTargetId() void CCIGAR_Formatter::FormatByTargetId ( const CSeq_id & target_id ) ◆ FormatByTargetRow() void CCIGAR_Formatter::FormatByTargetRow ( TNumrow target_row ) ◆ FromServerContext() ◆ g_AsGRPCStatus() [1/2] ◆ g_AsGRPCStatus() [2/2] ◆ g_AsGRPCStatusCode() ◆ g_NCBI_GRPC_GetAddress()

Get "hostport" for the likes of "grpc::CreateChannel(hostport, ...)" trying (in order of priority):

Config file entry "[section] variable"
Environment variables: env_var_name (if not empty/NULL); then "NCBI_CONFIG__<section>__<name>"; then "GRPC_PROXY"
The hard-coded NCBI default "linkerd:4142" The value_source (if not null) will get CParamBase::EParamSource value
Config file entry "[section] variable"
Environment variables: env_var_name (if not empty/NULL); then "NCBI_CONFIG__<section>__<name>"; then "GRPC_PROXY"
The hard-coded NCBI default "linkerd:4142"

Definition at line 506 of file grpc_integration.cpp.

References g_GetConfigString().

Referenced by CSnpPtisClient_Impl::CSnpPtisClient_Impl(), and CSnpPtisClient::IsEnabled().

◆ GenerateID() void CFastaReader::GenerateID ( void ) protectedvirtual ◆ GetAllMods() ◆ GetAllowedValues() ◆ GetAlnMap() ◆ GetBadMod() ◆ GetBadMods() const TMods& CSourceModParser::GetBadMods ( void ) const inline ◆ GetBestID() ◆ GetCompletedAlignment() CRef< CSeq_align > CFastaAlignmentBuilder::GetCompletedAlignment ( void ) ◆ GetCurrentLine()

Definition at line 105 of file line_reader.hpp.

Referenced by CStructuredCommentsReader::_LoadHeaderLine(), CTabDelimitedValidator::_OperateRows(), CTabDelimitedValidator::_ProcessHeader(), CAuthorNamesContainer::ImportAuthorsFromFile(), CTable2AsnStructuredCommentsReader::IsVertical(), CStructuredCommentsReader::LoadComments(), CStructuredCommentsReader::LoadCommentsByRow(), CForeignContaminationScreenReportReader::LoadFile(), CLoadStructComments::LoadSingle(), CUpdateMultiSeq_Dlg::OnLoadMapClick(), CMacroEngine::ReadAndParseMacros(), CMacroEngineParallel::ReadAndParseMacros(), CTabDelimitedValidator::RegisterAliases(), CTbl2AsnApp::Run(), s_GetTaxIDList(), IMacroBioDataIter::STableToApply::SetTableToApply(), CMacroLib::StoreSynonymList(), CMacroEngine::x_AppendToLibrary(), CMacroEngineParallel::x_AppendToLibrary(), IMacroBioDataIter::STableToApply::x_CacheColFromTable(), IMacroBioDataIter::STableToApply::x_InitAndCheck(), CTaxonCache::x_LoadTaxonCache(), and CMacroApplySrcTablePanel::x_ProcessFirstLine().

◆ GetCurrentPos()

Definition at line 503 of file fasta.hpp.

References CFastaReader::ePosWithGaps, CFastaReader::ePosWithGapsAndSegs, CFastaReader::eRawPos, kInvalidSeqPos, CFastaReader::m_CurrentPos, CFastaReader::m_SegmentBase, CFastaReader::m_TotalGapLength, and pos_type.

Referenced by CFastaReader::AssembleSeq(), CFastaReader::ParseGapLine(), CFastaReader::x_CloseGap(), CFastaReader::x_CloseMask(), CMaskFromFasta::x_CloseMask(), CFastaReader::x_OpenMask(), CMaskFromFasta::x_OpenMask(), and CFastaReader::x_ReadSeqsToAlign().

◆ GetCurrentSeq_align() ◆ GetDense_seg() ◆ GetFlags() TFlags CFastaReader::GetFlags ( void ) const inline ◆ GetFrame() ◆ GetIDGenerator() ◆ GetIDs() ◆ GetLabel() ◆ GetLastType() char CCIGAR_Formatter::GetLastType ( void ) const inlineprotected

Definition at line 102 of file cigar_formatter.hpp.

◆ GetLineNumber() [1/4] Uint8 CStreamLineReader::GetLineNumber ( void ) const virtual ◆ GetLineNumber() [2/4] Uint8 CMemoryLineReader::GetLineNumber ( void ) const virtual ◆ GetLineNumber() [3/4] Uint8 CBufferedLineReader::GetLineNumber ( void ) const virtual ◆ GetLineNumber() [4/4] virtual Uint8 ILineReader::GetLineNumber ( void ) const pure virtual

Returns the current line number (counting from 1, not 0).

Attention: Right after constructor or after UngetLine() calling this method is illegal. Call operator++() first

Implemented in CCompatLineReader, CBufferedLineReader, CMemoryLineReader, and CStreamLineReader.

Referenced by CTabDelimitedValidator::_OperateRows(), CTabDelimitedValidator::_ProcessHeader(), CBioTreeAttrReader::CheckLineReader(), CFastaReader::LineNumber(), CStructuredCommentsReader::LoadComments(), CFeatureTableReader_Imp::ReadSequinFeatureTable(), IMacroBioDataIter::STableToApply::x_CacheColFromTable(), CFeatureTableReader_Imp::x_GetLineNumber(), CShortReadFastaInputSource::x_ReadFastc(), and CShortReadFastaInputSource::x_ReadFastqOneSeq().

◆ GetLineReader() ◆ GetMaxIDLength() Uint4 CFastaReader::GetMaxIDLength ( void ) const inline

Get the maximum ID allowed, which will be kMax_UI4 unless someone has manually lowered it.

Returns: currently set maximum ID length

Definition at line 199 of file fasta.hpp.

References CFastaReader::m_MaxIDLength.

◆ GetModAllowedValues()

Given a mod name (e.g.

"topology"), it returns the set of acceptable values (e.g. "linear", "circular", etc.). If the mod is unknown or free-form, the returned set will be blank.

Definition at line 1747 of file source_mod_parser.cpp.

References ENUM_METHOD_NAME, SMolTypeInfo::eShown_Yes, set< Key, Compare >::insert(), ITERATE, key_equal(), and mod().

Referenced by CSourceModParser::GetModAllowedValuesAsOneString().

◆ GetModAllowedValuesAsOneString() ◆ GetMods() ◆ GetPosition() [1/4] CT_POS_TYPE CStreamLineReader::GetPosition ( void ) const virtual ◆ GetPosition() [2/4] CT_POS_TYPE CMemoryLineReader::GetPosition ( void ) const virtual ◆ GetPosition() [3/4] CT_POS_TYPE CBufferedLineReader::GetPosition ( void ) const virtual ◆ GetPosition() [4/4] virtual CT_POS_TYPE ILineReader::GetPosition ( void ) const pure virtual ◆ GetPostponedModMap() ◆ GetProgram() ◆ GetRefId() ◆ GetRefRange() const TRange& CCIGAR_Formatter::GetRefRange ( void ) const inlineprotected ◆ GetRefRow() ◆ GetRefSign() int CCIGAR_Formatter::GetRefSign ( void ) const inlineprotected ◆ GetRefWidth() ◆ GetScope() CScope* CCIGAR_Formatter::GetScope ( void ) const inlineprotected ◆ GetSeq_align() ◆ GetTargetId() ◆ GetTargetRange() const TRange& CCIGAR_Formatter::GetTargetRange ( void ) const inlineprotected ◆ GetTargetRow() ◆ GetTargetSign() int CCIGAR_Formatter::GetTargetSign ( void ) const inlineprotected ◆ GetTargetWidth() ◆ GetUnkMod() ◆ GuessFormat() ◆ IgnoreProblem() ◆ IsFirstSubalign() ◆ IsImplemented() bool CGRPCClientContext::IsImplemented ( void ) static ◆ IsSetFlag() ◆ IsTrivial() ◆ IsValidLocalID() [1/2] ◆ IsValidLocalID() [2/2] ◆ LineNumber() Uint8 CFastaReader::LineNumber ( void ) const inlineprotected

Definition at line 295 of file fasta.hpp.

References ILineReader::GetLineNumber(), and CFastaReader::m_LineReader.

Referenced by CFastaReader::AssembleSeq(), CFastaReader::AssignMolType(), CFastaReader::CheckDataLine(), CFastaReader::ParseDataLine(), CFastaReader::ParseDefLine(), CFastaReader::ParseGapLine(), CFastaReader::ReadAlignedSet(), CFastaReader::ReadOneSeq(), CFastaReader::x_CloseGap(), CFastaReader::x_ReadSeqsToAlign(), and CFastaReader::x_SetDeflineParseInfo().

◆ NCBI_Erf() double NCBI_Erf ( double x )

The error function of x: the integral from 0 to x of e(-t*t) dt, scaled by 2/sqrt(pi) to fall within the range (-1,1).

◆ NCBI_ErfC() double NCBI_ErfC ( double x )

The complementary error function of x: 1 - erf(x), but calculated more accurately for large x (where erf(x) approaches unity).

◆ NCBI_LinearSolution()

Find the least-squares solution of an overdetermined linear system, or the minimum-norm solution of an undetermined linear system.

(Wraps the LAPACK routine DGELS.)

Parameters: trans Whether to work with matrix A or its transpose. r The number of rows in matrix A. c The number of columns in matrix A. nrhs The number of right-hand sides (columns in matrix B). a On entry, the matrix A, stored in COLUMN-MAJOR order (Fortran-style); expected to have full rank. On successful exit, details of the QR or LQ factorization of A. lda The leading dimension of A (the spacing between the start of A's columns, which need not be contiguous, just uniformly spaced and non-overlapping). b On entry, the matrix B of right-hand side vectors, stored in COLUMN-MAJOR order (Fortran-style). On successful exit, the corresponding solution vectors. ldb The leading dimension of B (the spacing between the start of B's columns, which need not be contiguous, just uniformly spaced and non-overlapping).

Returns: 0 on success, -N if the Nth argument had a bad value, kNcbiLapackMemoryError if unable to allocate temporary memory, +N if the Nth diagonal element of the triangular factor of A is zero.

See also: http://www.netlib.org/lapack/explore-html/d7/d3b/group__double_g_esolve.html#ga225c8efde208eaf246882df48e590eac

Definition at line 130 of file ncbi_lapack.c.

References a, b, dgels_(), free(), info, kNcbiLapackMemoryError, malloc(), n, NULL, and r().

◆ NCBI_SingularValueDecomposition() int NCBI_SingularValueDecomposition ( enum ESingularVectorDetailsWanted jobu, enum ESingularVectorDetailsWanted jobvt, unsigned int r, unsigned int c, double * a, unsigned int lda, double * s, double * u, unsigned int ldu, double * vt, unsigned int ldvt, double * superb )

Compute the singular value decomposition of a matrix.

(Wraps the LAPACK routine DGESVD.)

Parameters: jobu How much of the left orthogonal matrix to return. jobvt How much of the right orthogonal matrix to return. r The number of rows in matrix A. c The number of columns in matrix A. a On entry, the matrix A, stored in COLUMN-MAJOR order (Fortran-style). On successful exit when either jobu or jobvt is eSVD_Overwrite, either the left singular vectors in column-major order or the right singular vectors in row-major order, respectively. On exit in all other cases, undefined. lda The leading dimension of A (the spacing between the start of A's columns, which need not be contiguous, just uniformly spaced and non-overlapping). s On success, receives the singular values of A, in descending order. u Depending on jobu, may receive the left singular vectors in column-major order or the full left orthogonal matrix, or be left alone altogether. ldu The leading dimension of U. Must be positive even if no output to U is requested. vt Depending on jobu, may receive the right singular vectors in row-major order or the full right orthogonal matrix, or be left alone altogether. ldvt The leading dimension of VT. Must be positive even if no output to VT is requested. superb If the algorithm didn't converge, receives (unless NULL!) the unconverged superdiagonal elements of an upper bidiagonal matrix B whose diagonal is in S (not necessarily sorted).

Note: jobu and jobvt cannot both be eSVD_Overwrite!

Returns: 0 on success, -N if the Nth argument had an illegal value, kNcbiLapackMemoryError if unable to allocate temporary memory, +N if N superdiagonals of an intermediate bidiagonal form didn't converge to 0.

See also: http://www.netlib.org/lapack/explore-html/d1/d7e/group__double_g_esing.html#ga84fdf22a62b12ff364621e4713ce02f2

Definition at line 153 of file ncbi_lapack.c.

References a, dgesvd_(), free(), info, kNcbiLapackMemoryError, malloc(), n, NULL, r(), and s_Min().

◆ NCBI_SymmetricEigens()

Compute the eigenvalues, and optionally also the eigenvectors, of a symmetric matrix.

(Wraps the LAPACK routine DSYEV.)

Parameters: jobz Whether to compute eigenvectors, or just eigenvalues. uplo Which triangle of the matrix to consult. n The order of the matrix. a On entry, the matrix A to analyze, stored in COLUMN-MAJOR order (Fortran-style). On successful exit in eEigenVectors mode, contains the orthonormal eigenvectors of the original matrix. On exit in all other cases, undefined. lda The leading dimension of A (the spacing between the start of A's columns, which need not be contiguous, just uniformly spaced and non-overlapping). w On successful exit, contains the eigenvalues in ascending order.

Returns: 0 on success, -N if the Nth argument had a bad value, kNcbiLapackMemoryError if unable to allocate temporary memory, +N if N off-diagonal elements of an intermediate tridiagonal form did not converge to zero.

See also: http://www.netlib.org/lapack/explore-html/d2/d8a/group__double_s_yeigen.html#ga442c43fca5493590f8f26cf42fed4044

Definition at line 109 of file ncbi_lapack.c.

References a, dsyev_(), free(), info, kNcbiLapackMemoryError, malloc(), n, and NULL.

◆ New() [1/2]

Return a new ILineReader object corresponding to the given input stream, optionally taking ownership thereof.

As always with ILineReader, an explicit call to operator++ or ReadLine() will be necessary to fetch the first line.

Definition at line 69 of file line_reader.cpp.

References lr().

◆ New() [2/2]

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "./-") to mean standard input.

As always with ILineReader, an explicit call to operator++ or ReadLine() will be necessary to fetch the first line.

Definition at line 49 of file line_reader.cpp.

References ERR_POST_X, eTakeOwnership, Info(), and lr().

Referenced by CFindITSParser::CFindITSParser(), CAgpObjectLoader::Execute(), CAuthorNamesContainer::ImportAuthorsFromFile(), CFastaObjectLoader::LoadAlignsFromStream(), CFastaObjectLoader::LoadFromStream(), CTbl2AsnApp::LoadPEPFile(), CTbl2AsnApp::LoadPRTFile(), CLoadStructComments::LoadSingle(), CLoadStructComments::LoadWithAccessions(), CUpdateMultiSeq_Dlg::OnLoadMapClick(), CWholeFileAnnotation::Open(), CBiosampleChkApp::ProcessFileList(), CBiosampleChkApp::ProcessList(), CTAbleValApp::ProcessOneFile(), CMacroEngine::ReadAndParseMacros(), CMacroEngineParallel::ReadAndParseMacros(), ReadFastaFileMap(), CTabDelimitedValidator::RegisterAliases(), CTbl2AsnApp::Run(), s_AddOneDataFile(), s_InitializeInstitutionCollectionCodeMaps(), s_InitializeOrgRefMap(), s_LoadECNumberTable(), s_ReadMultipleTablesFromString(), s_ReadOneTableFromString(), ScanFastaFile(), IMacroBioDataIter::STableToApply::SetTableToApply(), sReadInputAndGenerateAsn(), sRunTest(), CMacroLib::StoreSynonymList(), sUpdateCase(), CMacroEngine::x_AppendToLibrary(), CMacroEngineParallel::x_AppendToLibrary(), IMacroBioDataIter::STableToApply::x_CacheColFromTable(), IMacroBioDataIter::STableToApply::x_InitAndCheck(), CLatLonMap_Base::x_InitFromFile(), SAccGuide::x_Load(), CTable2AsnStructuredCommentsReader::x_LoadComments(), CTaxonCache::x_LoadTaxonCache(), CMacroApplySrcTablePanel::x_ProcessFirstLine(), CMultiReaderApp::xProcess5ColFeatTable(), and CMultiReaderApp::xProcessRmo().

◆ OpenMask() void CFastaReader::OpenMask ( void ) inlineprotected ◆ operator()() [1/4]

Definition at line 164 of file cigar.cpp.

References CSeq_id::Assign(), count, CSeq_align::CreateDensegFromStdseg(), SCigarAlignment::eDeletion, SCigarAlignment::eForwardShift, SCigarAlignment::eInsertion, SCigarAlignment::eIntron, SCigarAlignment::eMatch, SCigarAlignment::eNotSet, SCigarAlignment::eReverseShift, CSeq_align_Base::eType_partial, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_interval::GetLength(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), IsReverse(), CSeq_interval_Base::IsSetStrand(), ITERATE, CRef< C, Locker >::Reset(), SCigarAlignment::segments, CSeq_align_Base::SetDim(), CSeq_loc::SetEmpty(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), and SCigarAlignment::x_NextChunk().

◆ operator()() [2/4] ◆ operator()() [3/4] ◆ operator()() [4/4] ◆ operator*() [1/4] CTempString CStreamLineReader::operator* ( void ) const virtual ◆ operator*() [2/4] CTempString CMemoryLineReader::operator* ( void ) const virtual ◆ operator*() [3/4] CTempString CBufferedLineReader::operator* ( void ) const virtual ◆ operator*() [4/4] virtual CTempString ILineReader::operator* ( void ) const pure virtual ◆ operator++() [1/4]

Make a line available.

MUST be called even for the first line; MAY trigger EOF conditions even when also retrieving data. When beyond the last string, becomes a no-op.

Implements ILineReader.

Reimplemented in CTranslatingLineReader, and CStreamLineReaderConverter.

Definition at line 154 of file line_reader.cpp.

References CStreamLineReader::AtEOF(), CStreamLineReader::eEOL_cr, CStreamLineReader::eEOL_crlf, CStreamLineReader::eEOL_lf, CStreamLineReader::eEOL_mixed, CStreamLineReader::eEOL_unknown, CStreamLineReader::m_EOLStyle, CStreamLineReader::m_Line, CStreamLineReader::m_LineNumber, CStreamLineReader::m_Stream, CStreamLineReader::m_UngetLine, NcbiGetline(), string, CStreamLineReader::x_AdvanceEOLCRLF(), CStreamLineReader::x_AdvanceEOLSimple(), and CStreamLineReader::x_AdvanceEOLUnknown().

Referenced by CStreamLineReaderConverter::operator++(), and CTranslatingLineReader::operator++().

◆ operator++() [2/4] ◆ operator++() [3/4]

Make a line available.

MUST be called even for the first line; MAY trigger EOF conditions even when also retrieving data. When beyond the last string, becomes a no-op.

Implements ILineReader.

Definition at line 509 of file line_reader.cpp.

References _ASSERT, CBufferedLineReader::AtEOF(), CTempString::begin(), CBufferedLineReader::m_End, CBufferedLineReader::m_LastReadSize, CBufferedLineReader::m_Line, CBufferedLineReader::m_LineNumber, CBufferedLineReader::m_Pos, CBufferedLineReader::m_String, CBufferedLineReader::m_UngetLine, NULL, CBufferedLineReader::x_LoadLong(), and CBufferedLineReader::x_ReadBuffer().

◆ operator++() [4/4] ◆ operator<() bool CSourceModParser::SMod::operator< ( const SMod & rhs ) const inline ◆ operator=() [1/3] ◆ operator=() [2/3]

This method is declared as private but is not implemented to prevent member-wise copying.

◆ operator=() [3/3] ◆ ParseDataLine()

Reimplemented in CMaskFromFasta.

Definition at line 774 of file fasta.cpp.

References _ASSERT, _TROUBLE, CFastaReader::CheckDataLine(), CFastaReader::CloseGap(), CFastaReader::CloseMask(), CBadResiduesException::SBadResiduePositions::ConvertBadIndexesToString(), CRef< C, Locker >::Empty(), ILineError::eProblem_IgnoredResidue, ILineError::eProblem_InvalidResidue, CFastaReader::fAssumeNuc, FASTA_WARNING, FASTA_WARNING_EX, CFastaReader::fForceType, CFastaReader::fHyphensIgnoreAndWarn, FIELD_CHAIN_OF_2_IS_SET, CFastaReader::fLetterGaps, CFastaReader::fParseGaps, CFastaReader::fSkipCheck, CFastaReader::fValidate, CFastaReader::GetFlags(), CBioseq::IsNa(), kEmptyStr, CTempString::length(), CFastaReader::LineNumber(), CFastaReader::m_BestID, CFastaReader::m_CurrentGapChar, CFastaReader::m_CurrentGapLength, CFastaReader::m_CurrentMask, CFastaReader::m_CurrentPos, CFastaReader::m_CurrentSeq, CFastaReader::m_SeqData, max(), NCBI_THROW2, CFastaReader::OpenMask(), CFastaReader::ParseGapLine(), s_ASCII_MustBeLowerToUpper(), NStr::StartsWith(), CFastaReader::TestFlag(), toupper(), and CFastaReader::x_NucOrProt().

Referenced by CMaskFromFasta::ParseDataLine(), and CFastaReader::ReadOneSeq().

◆ ParseDefLine() [1/2] ◆ ParseDefLine() [2/2]

Reimplemented in CFastaMapper.

Definition at line 566 of file fasta.cpp.

References CUser_object::AddField(), CSeq_id::AsFastaString(), CSeq_id_Handle::AsString(), CSeq_id::BestRank(), CFastaIdHandler::CacheIdHandle(), data, CObjReaderParseException::eDuplicateID, CObjReaderParseException::eNoIDs, FASTA_ERROR, FASTA_PROGRESS, CFastaReader::fForceType, FindBestChoice(), CFastaReader::fNoUserObjs, CFastaReader::fRequireID, CFastaReader::fUniqueIDs, CSeq_id_Handle::GetHandle(), CFastaReader::GetIDs(), ITERATE, CFastaReader::LineNumber(), CFastaReader::m_BestID, CFastaReader::m_CurrentSeq, CFastaReader::m_CurrentSeqTitles, CFastaReader::m_fIdCheck, CFastaReader::m_IDHandler, CFastaDeflineReader::ParseDefline(), CFastaReader::PostProcessIDs(), NStr::PrintableString(), CBioseq_Base::SetDescr(), CBioseq_Base::SetInst(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), CFastaReader::TestFlag(), CFastaReader::x_SetDeflineParseInfo(), and CFastaReader::xSetSeqMol().

◆ ParseGapLine()

Definition at line 1094 of file fasta.cpp.

References _ASSERT, map_checker< Container >::begin(), set< Key, Compare >::begin(), CFastaReader::CanonicalizeString(), set< Key, Compare >::clear(), CFastaReader::CloseGap(), CFastaReader::SGap::eKnownSize_No, CFastaReader::SGap::eKnownSize_Yes, CSeq_gap::eLinkEvid_Forbidden, CSeq_gap::eLinkEvid_Required, CSeq_gap::eLinkEvid_UnspecifiedOnly, map_checker< Container >::empty(), set< Key, Compare >::empty(), CTempString::empty(), map_checker< Container >::end(), ENUM_METHOD_NAME, ILineError::eProblem_ContradictoryModifiers, ILineError::eProblem_ExpectedModifierMissing, ILineError::eProblem_ExtraModifierFound, ILineError::eProblem_ModifierFoundButNoneExpected, ILineError::eProblem_NonPositiveLength, ILineError::eProblem_ParsingModifiers, ILineError::eProblem_UnrecognizedQualifierName, CFastaReader::eRawPos, NStr::eTrunc_Begin, CSeq_gap_Base::eType_unknown, CLinkage_evidence_Base::eType_unspecified, FASTA_WARNING, FASTA_WARNING_EX, NStr::fConvErr_NoThrow, CTempString::find(), map_checker< Container >::find(), NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, CFastaReader::GetCurrentPos(), CSeq_gap::GetNameToGapTypeInfoMap(), set< Key, Compare >::insert(), isdigit(), ITERATE, kEmptyStr, CTempString::length(), CFastaReader::LineNumber(), CSeq_gap::SGapTypeInfo::m_eLinkEvid, CSeq_gap::SGapTypeInfo::m_eType, CFastaReader::m_gap_type, CFastaReader::m_Gaps, CFastaReader::m_GapsizeToLinkageEvidence, CFastaReader::m_TotalGapLength, CSeq_gap::NameToGapTypeInfo(), CTempString::npos, CConstRef< C, Locker >::Reset(), set< Key, Compare >::size(), CTempString::size(), NStr::Split(), NStr::StartsWith(), NStr::StringToUInt(), CTempString::substr(), NStr::TruncateSpaces_Unsafe(), and NStr::TruncateSpacesInPlace().

Referenced by CFastaReader::ParseDataLine().

◆ ParseRange() ◆ ParseTitle() [1/2] ◆ ParseTitle() [2/2] ◆ PeekChar() [1/4] char CStreamLineReader::PeekChar ( void ) const virtual ◆ PeekChar() [2/4] char CMemoryLineReader::PeekChar ( void ) const virtual ◆ PeekChar() [3/4] char CBufferedLineReader::PeekChar ( void ) const virtual ◆ PeekChar() [4/4] virtual char ILineReader::PeekChar ( void ) const pure virtual ◆ PostProcessIDs() ◆ PostSynchronousRequest() void CGRPCServerCallbacks::PostSynchronousRequest ( grpc::ServerContext * sctx ) inlineoverride ◆ PostWarning() ◆ PreSynchronousRequest() void CGRPCServerCallbacks::PreSynchronousRequest ( grpc::ServerContext * sctx ) inlineoverride ◆ Print() [1/4] ◆ Print() [2/4] ◆ Print() [3/4] ◆ Print() [4/4] ◆ ProtectedFunc() static int CMyClass::ProtectedFunc ( char ch ) staticprotected

Brief function description here.

Detailed description here. More description.

Returns: Return value description here. parameter description

◆ Read() [1/2] ◆ Read() [2/2]

Definition at line 118 of file gff_reader.cpp.

References _ASSERT, _TRACE, CSeq_annot_Base::C_Data::e_Ftable, CTempString::empty(), map_checker< Container >::end(), set< Key, Compare >::end(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CGFFReader::fCreateGeneFeats, map_checker< Container >::find(), flags, CGFFReader::fSetProducts, CGFFReader::fSetVersion3, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_feat::GetGeneXref(), CSeq_loc::GetId(), CGene_ref::GetLabel(), COpenRange< Position >::GetLength(), CSeq_feat_Base::GetLocation(), CGene_ref_Base::GetLocus(), CSeq_feat::GetNamedQual(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), in(), set< Key, Compare >::insert(), CGene_ref_Base::IsSetLocus(), ITERATE, CGFFReader::SRecord::key, CGFFReader::SRecord::loc, CGFFReader::m_DelayedRecords, CGFFReader::m_Flags, CGFFReader::m_GeneRefs, CGFFReader::m_LineNumber, CGFFReader::m_LineReader, CGFFReader::m_TSE, CGFFReader::m_Version, match(), NON_CONST_ITERATE, NULL, r(), r2, CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), map_checker< Container >::size(), CTempString::size(), CSeq_annot_Base::C_Data::Which(), CGFFReader::x_Error(), CGFFReader::x_IsLineUcscMetaInformation(), CGFFReader::x_MergeRecords(), CGFFReader::x_ParseAndPlace(), CGFFReader::x_ParseFeatureInterval(), CGFFReader::x_ParseStructuredComment(), CGFFReader::x_ReadFastaSequences(), CGFFReader::x_Reset(), and CGFFReader::x_ResolveSeqName().

◆ ReadAlignedSet()

Read as many sequences as are available, and interpret them as an alignment, with hyphens marking relative deletions.

Parameters: reference_row 0-based; the special value -1 yields a full (pseudo-?)N-way alignment.

Definition at line 1683 of file fasta.cpp.

References CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSet(), CFastaReader::LineNumber(), max(), NCBI_THROW2, CSeq_entry::Parentize(), CBioseq_set_Base::SetAnnot(), CSeq_entry_Base::SetSet(), CFastaReader::x_AddMultiwayAlignment(), CFastaReader::x_AddPairwiseAlignments(), and CFastaReader::x_ReadSeqsToAlign().

Referenced by ReadMsa(), and CMSAToolJob::x_CreateProjectItems().

◆ ReadFasta() ◆ ReadFastaFileMap() ◆ ReadLine() void ILineReader::ReadLine ( void ) inline

Definition at line 88 of file line_reader.hpp.

◆ ReadObject() ◆ ReadOneSeq()

Read a single effective sequence, which may turn out to be a segmented set.

Reimplemented in CBlastInputReader.

Definition at line 312 of file fasta.cpp.

References CBadResiduesException::SBadResiduePositions::AddBadIndexMap(), CFastaReader::AssembleSeq(), CFastaReader::AtEOF(), CObjReaderParseException::eEOF, map_checker< Container >::empty(), CTempString::empty(), FASTA_ERROR, FASTA_PROGRESS, CFastaReader::fDLOptional, CFastaReader::fInSegSet, CFastaReader::fNoSeqData, CBadResiduesException::GetBadResiduePositions(), CFastaReader::GetLineReader(), CRef< C, Locker >::IsNull(), kInvalidSeqPos, CFastaReader::LineNumber(), CBadResiduesException::SBadResiduePositions::m_BadIndexMap, CFastaReader::m_BestID, CFastaReader::m_CurrentGapChar, CFastaReader::m_CurrentGapLength, CFastaReader::m_CurrentMask, CFastaReader::m_CurrentPos, CFastaReader::m_CurrentSeq, CFastaReader::m_CurrentSeqTitles, CFastaReader::m_Gaps, CFastaReader::m_MaskRangeStart, CFastaReader::m_MaskVec, CFastaReader::m_NextMask, CFastaReader::m_Offset, CFastaReader::m_SegmentBase, CFastaReader::m_SeqData, CBadResiduesException::SBadResiduePositions::m_SeqId, CFastaReader::m_TotalGapLength, NCBI_THROW2, NStr::NumericToString(), CSeq_entry::Parentize(), CFastaReader::ParseDataLine(), CFastaReader::ParseDefLine(), ILineReader::PeekChar(), CRef< C, Locker >::Reset(), CFastaReader::SaveMask(), CSeq_loc::SetNull(), CSeq_entry_Base::SetSeq(), NStr::StartsWith(), CTempString::substr(), CFastaReader::TestFlag(), tmp, NStr::TruncateSpaces_Unsafe(), ILineReader::UngetLine(), and CFastaReader::x_NucOrProt().

Referenced by AddFastaToScope(), BOOST_AUTO_TEST_CASE(), CFastaBioseqSource::GetNext(), CMaskFromFasta::GetNextSequence(), GetSeqLocFromStream(), CFastaReaderEx::ReadDeltaFasta(), ReadFastaQueries(), CBlastInputReader::ReadOneSeq(), CFastaReader::ReadSet(), CLocalFinderApp::Run(), s_CreateScope(), s_FastaStringToBioseq(), s_ReadAndTestQueryFromString_CFastaReader(), ScanFastaFile(), sReadInputAndGenerateAsn(), CBlastFastaInputSource::x_FastaToSeqLoc(), x_GetSeqLocFromStream(), CNgAlignApp::x_LoadExternalSequences(), CLDS2_DataLoader::x_LoadFastaTSE(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAlnPrinterFixture::x_LoadSequences(), CLDS2_Manager::x_ParseFile(), CPrimeCacheApplication::x_Process_Fasta(), CSplignApp::x_ReadFastaSetId(), CFastaReader::x_ReadSeqsToAlign(), and CMacroFunction_UpdateProteinSeqs::x_ReadUpdateSeqs().

◆ ReadSeqEntry() ◆ ReadSet()

Read multiple sequences (by default, as many as are available.)

Definition at line 442 of file fasta.cpp.

References ILineReader::AtEOF(), CObjReaderParseException::eEOF, CFastaReader::fOneSeq, CParseTemplException< TBase >::GetErrCode(), CFastaReader::GetLineReader(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), i, CSeq_entry_Base::IsSet(), CRef< C, Locker >::NotEmpty(), CSeq_entry::Parentize(), CFastaReader::ReadOneSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CFastaReader::TestFlag().

Referenced by BOOST_AUTO_TEST_CASE(), CAgpObjectLoader::Execute(), CAlnMrgApp::LoadFasta(), CConversionApp::Read(), ReadFasta(), ReadFastaFileMap(), ReadFastaSeqsFromFile(), CBasicFastaWrapper::ReadFile(), CFastaReader::ReadSeqEntry(), CSeqFastaReader::ReadSequences(), UpdateViewer::ReadSequencesFromFile(), CNmer_repeatsApplication::Run(), sReadInputAndGenerateAsn(), CGFFReader::x_ReadFastaSequences(), CGapStatsApplication::x_ReadFileOrAccn(), CUpdateSeq_Input::x_ReadUpdateSeq_Fasta(), and CUpdateMultipleSeq_Input::x_ReadUpdateSeqs_Fasta().

◆ ResetIDTracker() void CFastaReader::ResetIDTracker ( void ) inline ◆ SaveMask() ◆ SaveMasks() void CFastaReader::SaveMasks ( TMasks * masks ) inline ◆ ScanFastaFile() ◆ SCigarAlignment() ◆ SetAllUnused() void CSourceModParser::SetAllUnused ( ) ◆ SetCurrentSeq() CBioseq& CFastaReader::SetCurrentSeq ( void ) inlineprotected ◆ SetExcludedMods() void CFastaReader::SetExcludedMods ( const vector< string > & excluded_mods ) ◆ SetFlag() void CSAM_Formatter::SetFlag ( EFlags flag ) inline ◆ SetFlags() void CSAM_Formatter::SetFlags ( TFlags flags ) inline ◆ SetGapLinkageEvidence() ◆ SetGapLinkageEvidences() ◆ SetGroupOrder() ◆ SetIDGenerator() [1/2] ◆ SetIDGenerator() [2/2] ◆ SetIDs() ◆ SetIgnoredMods() void CFastaReader::SetIgnoredMods ( const list< string > & ignored_mods ) ◆ SetMaxIDLength() void CFastaReader::SetMaxIDLength ( Uint4 max_len ) ◆ SetMinGaps() void CFastaReader::SetMinGaps ( TSeqPos gapNmin, TSeqPos gap_Unknown_length ) ◆ SetModFilter()

The filter indicates whether certain mods are okay or not.

Parameters: pModFilter If this is an unset CRef, it turns off filtering.

Definition at line 256 of file source_mod_parser.hpp.

◆ SetOutputStream() ◆ SetPostponedMods() void CFastaReader::SetPostponedMods ( const list< string > & postponed_mods ) ◆ SetProgram() [1/2] ◆ SetProgram() [2/2] ◆ SetScope() void CSAM_Formatter::SetScope ( CScope & scope ) inline ◆ SetSortOrder() ◆ SFastaEntry() SFastaFileMap::SFastaEntry::SFastaEntry ( ) inline

Definition at line 451 of file fasta.hpp.

◆ SGap() [1/2] CFastaReader::SGap::SGap ( const SGap & rhs ) private ◆ SGap() [2/2] ◆ SMod() [1/2] ◆ SMod() [2/2] CSourceModParser::SMod::SMod ( void ) default ◆ SProgramInfo() ◆ StartAlignment() virtual void CCIGAR_Formatter::StartAlignment ( void ) inlineprotectedvirtual ◆ StartRow() virtual void CCIGAR_Formatter::StartRow ( void ) inlineprotectedvirtual ◆ StartRows() virtual void CCIGAR_Formatter::StartRows ( void ) inlineprotectedvirtual ◆ StartSubAlignment() virtual void CCIGAR_Formatter::StartSubAlignment ( void ) inlineprotectedvirtual ◆ StreamPosition() Int8 CFastaReader::StreamPosition ( void ) const inlineprotected ◆ TestFlag() [1/2]

Definition at line 299 of file fasta.hpp.

References CFastaReader::GetFlags().

Referenced by CFastaReader::AssembleSeq(), CFastaReader::AssignMolType(), CFastaReader::CheckDataLine(), CFastaReader::CreateWarningsForSeqDataInTitle(), CFastaReader::GenerateID(), CFastaReader::ParseDataLine(), CFastaReader::ParseDefLine(), CFastaReader::ReadOneSeq(), CFastaReader::ReadSet(), CFastaReader::x_ApplyMods(), CFastaReader::x_CloseGap(), and CFastaReader::x_ReadSeqsToAlign().

◆ TestFlag() [2/2] ◆ TestMe()

A brief description of TestMe.

A detailed description of TestMe. Use the following when parameter descriptions are going to be long, and you are describing a complex method:

Parameters: foo An int value meaning something. bar A constant character pointer meaning something.

Returns: The TestMe() results.

See also: CMyClass(), ~CMyClass() and TestMeToo() - see also.

◆ TestMeToo() virtual void CMyClass::TestMeToo ( char par1, const string & par2 ) pure virtual

A brief description of TestMeToo.

Details for TestMeToo. Use this style if the parameter descriptions are going to be on one line each:

See also: TestMe()

Parameters: par1 short description for par1 par2 short description for par2

◆ ToString() string CSourceModParser::SMod::ToString ( void ) const inline ◆ UngetLine() [1/4] void CStreamLineReader::UngetLine ( void ) virtual ◆ UngetLine() [2/4] void CMemoryLineReader::UngetLine ( void ) virtual ◆ UngetLine() [3/4] void CBufferedLineReader::UngetLine ( void ) virtual ◆ UngetLine() [4/4] virtual void ILineReader::UngetLine ( void ) pure virtual

Unget current line, which must be valid.

After calling this method: 1. AtEOF() returns false, 2. PeekChar() returns first char of the current line, 3. Calling operator*() or UngetLine() is illegal, 4. Calling operator++() will make the line current again

Implemented in CCompatLineReader, CBufferedLineReader, CMemoryLineReader, and CStreamLineReader.

Referenced by CTable2AsnStructuredCommentsReader::IsVertical(), CBlastInputReader::ReadOneSeq(), CFastaReader::ReadOneSeq(), and CFeatureTableReader_Imp::ReadSequinFeatureTable().

◆ UnsetFlag() ◆ x_AddAndClear() void SCigarAlignment::x_AddAndClear ( SSegment & seg ) inlineprivate ◆ x_AddAttribute() void CGFFReader::x_AddAttribute ( SRecord & record, vector< string > & attr ) protectedvirtual ◆ x_AddMods()

Definition at line 2047 of file fasta.cpp.

References _ASSERT, CModHandler::AddMods(), CModAdder::Apply(), CTitleParser::Apply(), CModHandler::Clear(), eDiag_Info, CModHandler::eReplace, CBioseq::GetFirstId(), CFastaReader::m_ModHandler, s_AppendMods(), IObjtoolsListener::SevEnabled(), and CFastaReader::x_CheckForPostponedMods().

Referenced by CFastaReader::x_ApplyMods().

◆ x_AddMultiwayAlignment()

Definition at line 1805 of file fasta.cpp.

References _ASSERT, map_checker< Container >::begin(), map_checker< Container >::end(), CSeq_align_Base::eType_not_set, CDense_seg_Base::GetLens(), CFastaAlignmentBuilder::kNoPos, len, CFastaReader::m_Row, CFastaReader::m_Starts, next(), r(), CSeq_annot_Base::SetData(), CDense_seg_Base::SetDim(), CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CSeq_align_Base::SetType(), and map_checker< Container >::size().

Referenced by CFastaReaderEx::ReadAlignedSet(), and CFastaReader::ReadAlignedSet().

◆ x_AddPairwiseAlignments() ◆ x_AddPCRPrimers() ◆ x_AdvanceEOLCRLF()

Definition at line 271 of file line_reader.cpp.

References CStreamLineReader::AtEOF(), CStreamLineReader::eEOL_cr, CStreamLineReader::eEOL_crlf, CStreamLineReader::eEOL_lf, CStreamLineReader::eEOL_mixed, NStr::EndsWith(), CStreamLineReader::m_AutoEOL, CStreamLineReader::m_EOLStyle, CStreamLineReader::m_LastReadSize, CStreamLineReader::m_Line, CStreamLineReader::m_Stream, NcbiGetline(), and CStreamLineReader::x_AdvanceEOLSimple().

Referenced by CStreamLineReader::operator++().

◆ x_AdvanceEOLSimple()

Definition at line 245 of file line_reader.cpp.

References CT_EQ_INT_TYPE, CT_TO_INT_TYPE, CStreamLineReader::eEOL_cr, CStreamLineReader::eEOL_crlf, CStreamLineReader::eEOL_lf, CStreamLineReader::eEOL_mixed, AutoPtr< X, Del >::get(), CStreamLineReader::m_AutoEOL, CStreamLineReader::m_EOLStyle, CStreamLineReader::m_LastReadSize, CStreamLineReader::m_Line, CStreamLineReader::m_Stream, NcbiGetline(), NPOS, and CStreamUtils::Pushback().

Referenced by CStreamLineReader::operator++(), and CStreamLineReader::x_AdvanceEOLCRLF().

◆ x_AdvanceEOLUnknown()

Definition at line 219 of file line_reader.cpp.

References _ASSERT, CT_EQ_INT_TYPE, CT_INT_TYPE, CT_TO_INT_TYPE, CStreamLineReader::eEOL_cr, CStreamLineReader::eEOL_crlf, AutoPtr< X, Del >::get(), CStreamLineReader::m_AutoEOL, CStreamLineReader::m_EOLStyle, CStreamLineReader::m_LastReadSize, CStreamLineReader::m_Line, CStreamLineReader::m_Stream, and NcbiGetline().

Referenced by CStreamLineReader::operator++().

◆ x_ApplyDBLinkMods() void CSourceModParser::x_ApplyDBLinkMods ( CBioseq & bioseq ) private ◆ x_ApplyGenomeProjectsDBMods()

Definition at line 1544 of file source_mod_parser.cpp.

References data, NStr::fConvErr_NoThrow, CSourceModParser::FindMod(), NStr::fSplit_MergeDelimiters, ITERATE, mod(), CRef< C, Locker >::Reset(), s_PopulateUserObject(), CUser_field_Base::SetData(), CUser_field_Base::SetLabel(), NStr::Split(), and NStr::StringToUInt().

Referenced by CSourceModParser::ApplyAllMods(), and CSourceModParser::ApplyGenomeProjectsDBMods().

◆ x_ApplyMods() [1/7]

Definition at line 953 of file source_mod_parser.cpp.

References CTempString::Copy(), CBioSource_Base::eGenome_extrachrom, CBioSource_Base::eGenome_insertion_seq, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_proviral, CTempString::empty(), ENUM_METHOD_NAME, CBioSource_Base::eOrigin_mut, CBioSource_Base::eOrigin_natmut, NStr::EqualNocase(), CSubSource_Base::eSubtype_other, NStr::fConvErr_NoThrow, CTempString::find(), CSourceModParser::FindAllMods(), CSourceModParser::FindMod(), first(), i, CAutoInitPtr_Base::IsInitialized(), CSubSource::IsMultipleValuesAllowed(), kEmptyStr, CSourceModParser::SMod::key, mod(), CSubSource::NeedsNoText(), CTempString::npos, remove_if(), CAutoAddDesc::Set(), CAutoInitRef< T >::Set(), CDbtag_Base::SetDb(), CSubSource_Base::SetName(), CObject_id_Base::SetStr(), COrgMod_Base::SetSubname(), COrgMod_Base::SetSubtype(), CSubSource_Base::SetSubtype(), CDbtag_Base::SetTag(), NStr::StringToInt(), CSourceModParser::x_AddPCRPrimers(), CSourceModParser::x_HandleBadModValue(), and ZERO_TAX_ID.

Referenced by CSourceModParser::ApplyAllMods(), and CSourceModParser::ApplyMods().

◆ x_ApplyMods() [2/7] ◆ x_ApplyMods() [3/7] ◆ x_ApplyMods() [4/7] ◆ x_ApplyMods() [5/7] ◆ x_ApplyMods() [6/7] ◆ x_ApplyMods() [7/7] ◆ x_ApplyTPAMods()

Definition at line 1416 of file source_mod_parser.cpp.

References CUtf8::AsUTF8(), data, eEncoding_UTF8, CSourceModParser::FindMod(), NStr::fSplit_MergeDelimiters, ITERATE, mod(), s_PopulateUserObject(), CUser_field_Base::SetData(), CUser_field_Base::SetLabel(), and NStr::Split().

Referenced by CSourceModParser::ApplyAllMods(), and CSourceModParser::ApplyTPAMods().

◆ x_CalculateErrorString() [1/2] ◆ x_CalculateErrorString() [2/2] string CSourceModParser::CUnkModError::x_CalculateErrorString ( const SMod & unkMod ) private ◆ x_CheckForPostponedMods() ◆ x_CloseGap()

Reimplemented in CCustomizedFastaReader.

Definition at line 1018 of file fasta.cpp.

References _ASSERT, CFastaReader::SGap::eKnownSize_No, CFastaReader::SGap::eKnownSize_Yes, map_checker< Container >::end(), CFastaReader::ePosWithGapsAndSegs, CFastaReader::eRawPos, CFastaReader::fAligning, map_checker< Container >::find(), CFastaReader::fParseGaps, CFastaReader::GetCurrentPos(), CFastaReader::GetLineReader(), CFastaAlignmentBuilder::kNoPos, l(), len, CFastaReader::LineNumber(), CFastaReader::m_CurrentGapChar, CFastaReader::m_CurrentGapLength, CFastaReader::m_CurrentPos, CFastaReader::m_DefaultLinkageEvidence, CFastaReader::m_gap_type, CFastaReader::m_gap_Unknown_length, CFastaReader::m_gapNmin, CFastaReader::m_Gaps, CFastaReader::m_GapsizeToLinkageEvidence, CFastaReader::m_Offset, CFastaReader::m_Row, CFastaReader::m_SeqData, CFastaReader::m_Starts, CFastaReader::m_TotalGapLength, and CFastaReader::TestFlag().

Referenced by CFastaReader::CloseGap().

◆ x_CloseMask() void CFastaReader::x_CloseMask ( void ) protectedvirtual ◆ x_CreateGeneFeatures()

Definition at line 1362 of file gff_reader.cpp.

References _ASSERT, CSeq_annot_Base::C_Data::e_Ftable, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_feat::GetGeneXref(), CSeq_loc::GetId(), CGene_ref::GetLabel(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeq_loc::GetTotalRange(), ITERATE, r2, CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_annot_Base::C_Data::Which(), and CGFFReader::x_Error().

◆ x_EnsurePos() ◆ x_Error() void CGFFReader::x_Error ( const string & message, unsigned int line = 0 ) protectedvirtual ◆ x_FeatureID()

Returning the empty string indicates that record constitutes an entire feature.

Returning anything else requests merging with other records that yield the same ID.

Definition at line 978 of file gff_reader.cpp.

References CGFFReader::SRecord::attrs, CGFFReader::SRecord::eFeat, ctll::empty(), set< Key, Compare >::end(), CGFFReader::SRecord::FindAttribute(), NStr::FindNoCase(), CGFFReader::fMergeExons, CGFFReader::fMergeOnyCdsMrna, CGFFReader::fNoGTF, CGFFReader::SRecord::id, kEmptyStr, CGFFReader::SRecord::key, CGFFReader::m_Version, NPOS, CGFFReader::SRecord::parent, CGFFReader::SRecord::source, CGFFReader::SRecord::type, and CGFFReader::x_GetFlags().

Referenced by CGFFReader::x_ParseFeatureInterval().

◆ x_FormatAlignmentRows() [1/2]

Definition at line 84 of file cigar_formatter.cpp.

◆ x_FormatAlignmentRows() [2/2] void CCIGAR_Formatter::x_FormatAlignmentRows ( void ) private ◆ x_FormatDensegRows()

Definition at line 355 of file cigar_formatter.cpp.

Referenced by CCIGAR_Formatter::x_FormatAlignmentRows().

◆ x_FormatLine() void CCIGAR_Formatter::x_FormatLine ( bool width_inverted ) private

Definition at line 157 of file cigar_formatter.cpp.

Referenced by CCIGAR_Formatter::x_FormatDensegRows().

◆ x_GetFlags() TFlags CGFFReader::x_GetFlags ( void ) const inlineprotected ◆ x_GetLineNumber() unsigned int CGFFReader::x_GetLineNumber ( void ) inlineprotected ◆ x_GetRowById() ◆ x_HandleBadModValue() void CSourceModParser::x_HandleBadModValue ( const SMod & mod ) private

Definition at line 1845 of file source_mod_parser.cpp.

References _TROUBLE, CObjReaderLineException::Create(), eDiag_Warning, CSourceModParser::eHandleBadMod_ErrorListener, CSourceModParser::eHandleBadMod_Ignore, CSourceModParser::eHandleBadMod_PrintToCerr, CSourceModParser::eHandleBadMod_Throw, ILineError::eProblem_GeneralParsingError, CSourceModParser::GetModAllowedValuesAsOneString(), set< Key, Compare >::insert(), CSourceModParser::m_BadMods, CSourceModParser::m_HandleBadMod, CSourceModParser::m_LineNumber, mod(), and CSourceModParser::x_ProcessError().

Referenced by CSourceModParser::ApplyMods(), and CSourceModParser::x_ApplyMods().

◆ x_HandleUnkModValue() void CSourceModParser::x_HandleUnkModValue ( const SMod & mod ) private

Definition at line 1879 of file source_mod_parser.cpp.

References _TROUBLE, CObjReaderLineException::Create(), eDiag_Warning, CSourceModParser::eHandleBadMod_ErrorListener, CSourceModParser::eHandleBadMod_Ignore, CSourceModParser::eHandleBadMod_PrintToCerr, CSourceModParser::eHandleBadMod_Throw, ILineError::eProblem_GeneralParsingError, CSourceModParser::m_HandleBadMod, CSourceModParser::m_LineNumber, CSourceModParser::m_pModFilter, mod(), and CSourceModParser::x_ProcessError().

Referenced by CSourceModParser::ApplyAllMods().

◆ x_Info() void CGFFReader::x_Info ( const string & message, unsigned int line = 0 ) protectedvirtual ◆ x_Init()

Definition at line 212 of file grpc_support.hpp.

References CGRPCServerCallbacks::BeginRequest(), eDiagAppState_RequestBegin, CGRPCServerCallbacks::eExplicit, CDiagContext::Extra(), CDiagContext::GetAppState(), CGRPCRequestLogger::m_DiagContext, CGRPCRequestLogger::m_ManagingRequest, CGRPCRequestLogger::m_RequestContext, NCBI_GRPC_GET_BYTE_SIZE, CDiagContext_Extra::Print(), and CRequestContext::SetBytesRd().

Referenced by CGRPCRequestLogger::CGRPCRequestLogger().

◆ x_IsLineUcscMetaInformation() bool CGFFReader::x_IsLineUcscMetaInformation ( const TStr & line ) protectedvirtual ◆ x_IsRealRequest() ◆ x_LoadLong() void CBufferedLineReader::x_LoadLong ( void ) private ◆ x_MergeAttributes()

Definition at line 1140 of file gff_reader.cpp.

References CGFFReader::SRecord::attrs, set< Key, Compare >::begin(), set< Key, Compare >::end(), set< Key, Compare >::erase(), CGFFReader::fNoGTF, set< Key, Compare >::insert(), ITERATE, tag, and CGFFReader::x_GetFlags().

Referenced by CGFFReader::x_MergeRecords().

◆ x_MergeRecords()

Definition at line 1056 of file gff_reader.cpp.

References eNa_strand_plus, NStr::EndsWith(), CGFFReader::fNoGTF, CGFFReader::SRecord::frame, ITERATE, CGFFReader::SRecord::key, CGFFReader::SRecord::line_no, CGFFReader::SRecord::loc, NON_CONST_ITERATE, CGFFReader::x_GetFlags(), CGFFReader::x_MergeAttributes(), and CGFFReader::x_Warn().

Referenced by CGFFReader::Read().

◆ x_NewRecord() ◆ x_NextChunk() ◆ x_NucOrProt() ◆ x_OpenMask() void CFastaReader::x_OpenMask ( void ) protectedvirtual ◆ x_ParseAlignRecord()

Definition at line 713 of file gff_reader.cpp.

References CGFFReader::SRecord::attrs, eNa_strand_plus, set< Key, Compare >::end(), SCigarAlignment::eOpFirstIfAmbiguous, CSeq_align_Base::eType_partial, CGFFReader::SRecord::FindAttribute(), NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_interval_Base::GetStrand(), CSeq_loc_Base::IsInt(), CSeq_interval_Base::IsSetStrand(), CGFFReader::SRecord::line_no, CGFFReader::SRecord::loc, CGFFReader::SRecord::score, CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CSeq_loc::SetInt(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetScore(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CSeq_align_Base::SetType(), NStr::Split(), NStr::StringToDouble(), NStr::StringToUInt(), CGFFReader::x_ResolveLoc(), CGFFReader::x_ResolveSeqName(), and CGFFReader::x_Warn().

Referenced by CGFFReader::x_ParseAndPlace().

◆ x_ParseAndPlace() ◆ x_ParseDateComment() void CGFFReader::x_ParseDateComment ( const TStr & date ) protectedvirtual ◆ x_ParseFeatRecord()

Definition at line 589 of file gff_reader.cpp.

References CFeature_table_reader::AddFeatQual(), CGFFReader::SRecord::attrs, CFeature_table_reader::CreateSeqFeat(), ERR_POST_X, CGFFReader::fGBQuals, CFeature_table_reader::fKeepBadKey, CGFFReader::SRecord::frame, CFeature_table_reader::fTranslateBadKey, CSeq_feat_Base::GetData(), map_checker< Container >::insert(), CSeqFeatData_Base::IsCdregion(), ITERATE, kEmptyStr, CGFFReader::SRecord::key, CGFFReader::SRecord::line_no, CGFFReader::SRecord::loc, CGFFReader::m_GeneRefs, CGFFReader::m_Version, NPOS, s_StringToFeatId(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetId(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CGb_qual_Base::SetVal(), CSeq_feat_Base::SetXref(), rapidjson::source, CGFFReader::SRecord::source, NStr::StartsWith(), tag, val, rapidjson::value, Warning(), CGFFReader::x_GetFlags(), CGFFReader::x_ResolveLoc(), and CGFFReader::x_Warn().

Referenced by CGFFReader::x_ParseAndPlace().

◆ x_ParseFeatureInterval()

Definition at line 474 of file gff_reader.cpp.

References CGFFReader::SRecord::SSubLoc::accession, CGFFReader::SRecord::eAlign, CGFFReader::SRecord::eFeat, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, NStr::fSplit_Tokenize, i, CGFFReader::m_LineNumber, CGFFReader::m_Version, max(), CGFFReader::SRecord::SSubLoc::ranges, s_URLDecode(), NStr::Split(), NStr::StartsWith(), CGFFReader::SRecord::SSubLoc::strand, NStr::StringToUInt(), CGFFReader::x_Error(), CGFFReader::x_FeatureID(), CGFFReader::x_GetLineNumber(), CGFFReader::x_Info(), CGFFReader::x_NewRecord(), CGFFReader::x_ParseV2Attributes(), CGFFReader::x_ParseV3Attributes(), and CGFFReader::x_Warn().

Referenced by CGFFReader::Read().

◆ x_ParseStructuredComment() ◆ x_ParseTypeComment() ◆ x_ParseV2Attributes() ◆ x_ParseV3Attributes()

Definition at line 926 of file gff_reader.cpp.

References NStr::fSplit_Tokenize, i, ITERATE, ncbi::grid::netcache::search::fields::key, NStr::MatchesMask(), s_URLDecode(), NStr::Split(), v2, rapidjson::value, CGFFReader::x_AddAttribute(), CGFFReader::x_GetLineNumber(), CGFFReader::x_SplitKeyValuePair(), and CGFFReader::x_Warn().

Referenced by CGFFReader::x_ParseFeatureInterval().

◆ x_PlaceAlignment() ◆ x_PlaceFeature()

Definition at line 1176 of file gff_reader.cpp.

References BREAK, CSeq_feat_Base::GetLocation(), CSeq_feat_Base::IsSetProduct(), kEmptyStr, CGFFReader::m_TSE, NON_CONST_ITERATE, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CBioseq_Base::SetAnnot(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_entry_Base::SetSet(), and CGFFReader::x_ResolveID().

Referenced by CGFFReader::x_ParseAndPlace().

◆ x_PlaceSeq() void CGFFReader::x_PlaceSeq ( CBioseq & seq ) protectedvirtual ◆ x_PrintGOTag() void CSAM_Formatter::x_PrintGOTag ( void ) const private ◆ x_PrintSOTag() void CSAM_Formatter::x_PrintSOTag ( void ) const private ◆ x_PrivateFunc() double CMyClass::x_PrivateFunc ( int some_int = 1 ) private

Brief function description here.

Detailed description here. More description.

Returns: Return value description here. describe parameter here

◆ x_ProcessError() ◆ x_ReadBuffer() bool CBufferedLineReader::x_ReadBuffer ( ) private

Definition at line 619 of file line_reader.cpp.

References _ASSERT, CT_OFF_TYPE, eRead, eRW_Eof, eRW_Error, eRW_NotImplemented, eRW_Success, eRW_Timeout, AutoArray< X, Del >::get(), CBufferedLineReader::m_Buffer, CBufferedLineReader::m_BufferSize, CBufferedLineReader::m_End, CBufferedLineReader::m_Eof, CBufferedLineReader::m_InputPos, CBufferedLineReader::m_Pos, CBufferedLineReader::m_Reader, NCBI_THROW, IReader::Read(), result, and ncbi::grid::netcache::search::fields::size.

Referenced by CBufferedLineReader::CBufferedLineReader(), CBufferedLineReader::operator++(), and CBufferedLineReader::x_LoadLong().

◆ x_ReadFastaSequences() void CGFFReader::x_ReadFastaSequences ( ILineReader & in ) protectedvirtual

Definition at line 450 of file gff_reader.cpp.

References CFastaReader::fAssumeNuc, in(), kEmptyStr, CGFFReader::m_TSE, CFastaReader::ReadSet(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CGFFReader::x_ResolveID().

Referenced by CGFFReader::Read(), and CGFFReader::x_ParseStructuredComment().

◆ x_ReadSeqsToAlign()

Definition at line 1708 of file fasta.cpp.

References _ASSERT, CFastaReader::AtEOF(), map_checker< Container >::clear(), CObjReaderParseException::eFormat, CFastaReader::ePosWithGapsAndSegs, CFastaReader::fAligning, FASTA_ERROR, CFastaReader::fParseGaps, CFastaReader::fValidate, CFastaReader::GetBestID(), CFastaReader::GetCurrentPos(), CFastaReader::GetFlags(), CFastaReader::GetLineReader(), CFastaAlignmentBuilder::kNoPos, len, CFastaReader::LineNumber(), CFastaReader::m_Flags, CFastaReader::m_Offset, CFastaReader::m_Row, CFastaReader::m_Starts, CFastaReader::ReadOneSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CFastaReader::TestFlag().

Referenced by CFastaReaderEx::ReadAlignedSet(), and CFastaReader::ReadAlignedSet().

◆ x_RemapGeneRefs() ◆ x_Reset() void CGFFReader::x_Reset ( void ) protectedvirtual

Reset all state, since we're between streams.

Definition at line 389 of file gff_reader.cpp.

References map_checker< Container >::clear(), CGFFReader::m_DefMol, CGFFReader::m_DelayedRecords, CGFFReader::m_GeneRefs, CGFFReader::m_LineNumber, CGFFReader::m_SeqCache, CGFFReader::m_SeqNameCache, CGFFReader::m_TSE, CGFFReader::m_Version, and CRef< C, Locker >::Reset().

Referenced by CGFFReader::Read().

◆ x_ResolveID()

Falls back to x_ResolveNewID on cache misses.

Definition at line 1291 of file gff_reader.cpp.

References CBioseq_Base::GetId(), map_checker< Container >::insert(), ITERATE, CGFFReader::m_SeqCache, CRef< C, Locker >::Reset(), CGFFReader::x_PlaceSeq(), and CGFFReader::x_ResolveNewID().

Referenced by CGFFReader::x_ParseTypeComment(), CGFFReader::x_PlaceAlignment(), CGFFReader::x_PlaceFeature(), and CGFFReader::x_ReadFastaSequences().

◆ x_ResolveLoc()

Definition at line 786 of file gff_reader.cpp.

References eNa_strand_unknown, CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), IsReverse(), ITERATE, CSeq_point_Base::SetId(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPnt(), CSeq_point_Base::SetPoint(), CSeq_point_Base::SetStrand(), si, and CGFFReader::x_ResolveSeqName().

Referenced by CGFFReader::x_ParseAlignRecord(), and CGFFReader::x_ParseFeatRecord().

◆ x_ResolveNewID() ◆ x_ResolveNewSeqName() ◆ x_ResolveSeqName()

Falls back to x_ResolveNewSeqName on cache misses.

Definition at line 1242 of file gff_reader.cpp.

References CSeq_id_Base::e_Local, CSeq_id_Base::e_MaxChoice, CSeq_id_Base::e_not_set, CGFFReader::m_SeqNameCache, CSeq_id_Base::Which(), CGFFReader::x_ResolveNewSeqName(), and CGFFReader::x_Warn().

Referenced by CGFFReader::Read(), CGFFReader::x_ParseAlignRecord(), CGFFReader::x_ParseTypeComment(), CGFFReader::x_ResolveLoc(), and CGFFReader::x_SetProducts().

◆ x_SetDeflineParseInfo() ◆ x_SetProducts() ◆ x_SplitKeyValuePair() ◆ x_State() ◆ x_Warn() void CGFFReader::x_Warn ( const string & message, unsigned int line = 0 ) protectedvirtual

Definition at line 359 of file gff_reader.cpp.

References ERR_POST_X, and Warning().

Referenced by CGFFReader::x_MergeRecords(), CGFFReader::x_ParseAlignRecord(), CGFFReader::x_ParseAndPlace(), CGFFReader::x_ParseFeatRecord(), CGFFReader::x_ParseFeatureInterval(), CGFFReader::x_ParseV2Attributes(), CGFFReader::x_ParseV3Attributes(), CGFFReader::x_ResolveNewID(), CGFFReader::x_ResolveSeqName(), and CGFFReader::x_SplitKeyValuePair().

◆ xCreateAlignment()

Definition at line 521 of file fasta.cpp.

References eNa_strand_minus, eNa_strand_plus, CSeq_align_Base::eType_partial, CDense_seg_Base::SetDim(), CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and CSeq_align_Base::SetType().

Referenced by CFastaReader::PostProcessIDs().

◆ xSetSeqMol() ◆ ~CBadModError() ◆ ~CBufferedLineReader() CBufferedLineReader::~CBufferedLineReader ( ) virtual

Definition at line 464 of file line_reader.cpp.

◆ ~CCIGAR_Formatter() ◆ ~CFastaReader() CFastaReader::~CFastaReader ( void ) virtual ◆ ~CGFFReader() virtual CGFFReader::~CGFFReader ( ) inlinevirtual

Definition at line 108 of file gff_reader.hpp.

◆ ~CGRPCRequestLogger() CGRPCRequestLogger::~CGRPCRequestLogger ( ) inline ◆ ~CModFilter() virtual CSourceModParser::CModFilter::~CModFilter ( void ) inlinevirtual

Definition at line 249 of file source_mod_parser.hpp.

◆ ~CMyClass() ◆ ~CSAM_Formatter() CSAM_Formatter::~CSAM_Formatter ( void ) ◆ ~CStreamLineReader() CStreamLineReader::~CStreamLineReader ( )

Definition at line 95 of file line_reader.cpp.

◆ ~CUnkModError() ◆ ~IFastaEntryScan() IFastaEntryScan::~IFastaEntryScan ( ) virtual

Definition at line 1871 of file fasta.cpp.

◆ accession string CGFFReader::SRecord::SSubLoc::accession ◆ all_seq_ids ◆ attrs TAttrs CGFFReader::SRecord::attrs ◆ description string SFastaFileMap::SFastaEntry::description ◆ file_map ◆ format ◆ frame int CGFFReader::SRecord::frame ◆ id string CGFFReader::SRecord::id ◆ kEmptyMod

Used for passing an empty mod to some funcs without having to constantly recreate an empty one.

Definition at line 213 of file source_mod_parser.hpp.

◆ key [1/2] string CSourceModParser::SMod::key ◆ key [2/2] string CGFFReader::SRecord::key ◆ kKeyCanonicalizationTable static const unsigned char CSourceModParser::kKeyCanonicalizationTable staticprivate Initial value:

"\x00\x01\x02\x03\x04\x05\x06\x07\x08\x09\x0A\x0B\x0C\x0D\x0E\x0F"

"\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1A\x1B\x1C\x1D\x1E\x1F"

"-!\"#$%&'()*+,-./0123456789:;<=>?"

"@abcdefghijklmnopqrstuvwxyz[\\]^-"

"`abcdefghijklmnopqrstuvwxyz{|}~\x7F"

"\x80\x81\x82\x83\x84\x85\x86\x87\x88\x89\x8A\x8B\x8C\x8D\x8E\x8F"

"\x90\x91\x92\x93\x94\x95\x96\x97\x98\x99\x9A\x9B\x9C\x9D\x9E\x9F"

"\xA0\xA1\xA2\xA3\xA4\xA5\xA6\xA7\xA8\xA9\xAA\xAB\xAC\xAD\xAE\xAF"

"\xB0\xB1\xB2\xB3\xB4\xB5\xB6\xB7\xB8\xB9\xBA\xBB\xBC\xBD\xBE\xBF"

"\xC0\xC1\xC2\xC3\xC4\xC5\xC6\xC7\xC8\xC9\xCA\xCB\xCC\xCD\xCE\xCF"

"\xD0\xD1\xD2\xD3\xD4\xD5\xD6\xD7\xD8\xD9\xDA\xDB\xDC\xDD\xDE\xDF"

"\xE0\xE1\xE2\xE3\xE4\xE5\xE6\xE7\xE8\xE9\xEA\xEB\xEC\xED\xEE\xEF"

"\xF0\xF1\xF2\xF3\xF4\xF5\xF6\xF7\xF8\xF9\xFA\xFB\xFC\xFD\xFE\xFF"

Definition at line 269 of file source_mod_parser.hpp.

Referenced by CSourceModParser::CompareKeys().

◆ kNcbiLapackMemoryError ◆ len TSeqPos SCigarAlignment::SSegment::len ◆ line_no unsigned int CGFFReader::SRecord::line_no ◆ loc TLoc CGFFReader::SRecord::loc ◆ m_Align ◆ m_AlnMap ◆ m_AutoEOL bool CStreamLineReader::m_AutoEOL private ◆ m_BadMod SMod CSourceModParser::CBadModError::m_BadMod private ◆ m_BadMods [1/2] ◆ m_BadMods [2/2] TMods CSourceModParser::m_BadMods private ◆ m_BestID ◆ m_bModifiedMaxIdLength bool CFastaReader::m_bModifiedMaxIdLength =false private ◆ m_Body ◆ m_Buffer AutoArray<char> CBufferedLineReader::m_Buffer private ◆ m_BufferSize size_t CBufferedLineReader::m_BufferSize private ◆ m_CmdLine string CSAM_Formatter::SProgramInfo::m_CmdLine ◆ m_CurAlign ◆ m_CurrentGapChar char CFastaReader::m_CurrentGapChar protected ◆ m_CurrentGapLength TSeqPos CFastaReader::m_CurrentGapLength protected ◆ m_CurrentMask TMask CFastaReader::m_CurrentMask protected ◆ m_CurrentPos ◆ m_CurrentSeq

Definition at line 391 of file fasta.hpp.

Referenced by CFastaReader::AssembleSeq(), CFastaReader::AssignMolType(), CFastaReader::CheckDataLine(), CFastaReader::GetIDs(), CFastaReader::ParseDataLine(), CFastaReader::ParseDefLine(), CFastaReader::ParseTitle(), CFastaReader::PostProcessIDs(), CFastaReader::ReadOneSeq(), CFastaReader::SetCurrentSeq(), CFastaReader::SetIDs(), and CFastaReader::x_NucOrProt().

◆ m_CurrentSeqTitles ◆ m_Data TData CSAM_Formatter::CSAM_Headers::m_Data ◆ m_DefaultLinkageEvidence ◆ m_DefMol ◆ m_DelayedRecords ◆ m_DenseSeg ◆ m_Desc string CSAM_Formatter::SProgramInfo::m_Desc ◆ m_DiagContext ◆ m_DS ◆ m_eKnownSize ◆ m_End [1/2] const char* CMemoryLineReader::m_End private ◆ m_End [2/2] const char* CBufferedLineReader::m_End private ◆ m_Eof bool CBufferedLineReader::m_Eof private ◆ m_EOLStyle ◆ m_fIdCheck ◆ m_Flags [1/4] ◆ m_Flags [2/4] TFlags CSAM_Formatter::m_Flags private ◆ m_Flags [3/4] stack<TFlags> CFastaReader::m_Flags protected ◆ m_Flags [4/4] ◆ m_fModFilter ◆ m_FooBar double CMyClass::m_FooBar protected

Brief description of a data member – notice no details are here since brief description is adequate.

Definition at line 177 of file header_template.hpp.

◆ m_FormatBy ◆ m_Frame int CCIGAR_Formatter::m_Frame private ◆ m_gap_type ◆ m_gap_Unknown_length TSeqPos CFastaReader::m_gap_Unknown_length protected ◆ m_gapNmin ◆ m_Gaps TGaps CFastaReader::m_Gaps protected ◆ m_GapsizeToLinkageEvidence ◆ m_GeneRefs ◆ m_GO ◆ m_GO_Value string CSAM_Formatter::m_GO_Value private ◆ m_HandleBadMod ◆ m_Header ◆ m_Id string CSAM_Formatter::SProgramInfo::m_Id ◆ m_IDHandler ◆ m_IDTracker ◆ m_ignorable ◆ m_InputPos ◆ m_IsFirstSubalign bool CCIGAR_Formatter::m_IsFirstSubalign private ◆ m_IsTrivial bool CCIGAR_Formatter::m_IsTrivial private ◆ m_LastAlignmentPos TSeqPos CFastaAlignmentBuilder::m_LastAlignmentPos private ◆ m_LastNonDGState EState CFastaAlignmentBuilder::m_LastNonDGState private ◆ m_LastOtherPos ◆ m_LastReadSize [1/2] ◆ m_LastReadSize [2/2] SIZE_TYPE CBufferedLineReader::m_LastReadSize private ◆ m_LastReferencePos ◆ m_LastState EState CFastaAlignmentBuilder::m_LastState private ◆ m_LastType char CCIGAR_Formatter::m_LastType private ◆ m_Line [1/3] string CStreamLineReader::m_Line private ◆ m_Line [2/3] ◆ m_Line [3/3] ◆ m_LineNumber [1/5] size_t CSourceModParser::m_LineNumber private ◆ m_LineNumber [2/5] Uint8 CStreamLineReader::m_LineNumber private ◆ m_LineNumber [3/5] Uint8 CMemoryLineReader::m_LineNumber private ◆ m_LineNumber [4/5] Uint8 CBufferedLineReader::m_LineNumber private ◆ m_LineNumber [5/5] unsigned int CGFFReader::m_LineNumber protected ◆ m_LineReader [1/2] ◆ m_LineReader [2/2] ◆ m_ManagingRequest bool CGRPCRequestLogger::m_ManagingRequest private ◆ m_MaskRangeStart TSeqPos CFastaReader::m_MaskRangeStart protected ◆ m_MaskVec TMasks* CFastaReader::m_MaskVec protected ◆ m_MaxIDLength Uint4 CFastaReader::m_MaxIDLength protected ◆ m_MemFile ◆ m_ModHandler ◆ m_Mods TMods CSourceModParser::m_Mods private ◆ m_Name string CSAM_Formatter::SProgramInfo::m_Name ◆ m_NextMask TMask CFastaReader::m_NextMask protected ◆ m_Offset ◆ m_Out ◆ m_pErrorListener ◆ m_pGapType ◆ m_pModFilter ◆ m_Pos [1/2] const char* CMemoryLineReader::m_Pos private ◆ m_Pos [2/2] const char* CBufferedLineReader::m_Pos private ◆ m_PostponedModMap ◆ m_PostponedMods unordered_set<string> CFastaReader::m_PostponedMods protected ◆ m_PrivateData int CMyClass::m_PrivateData private ◆ m_ProgramInfo ◆ m_PublicData int CMyClass::m_PublicData ◆ m_Reader ◆ m_RefId ◆ m_RefRange TRange CCIGAR_Formatter::m_RefRange private ◆ m_RefRow ◆ m_RefSign int CCIGAR_Formatter::m_RefSign private ◆ m_RefWidth TSeqPos CCIGAR_Formatter::m_RefWidth private ◆ m_Reply [1/2] ◆ m_Reply [2/2] ◆ m_RequestContext ◆ m_Row ◆ m_sAllowedValues std::string CSourceModParser::CBadModError::m_sAllowedValues private ◆ m_Scope [1/2] ◆ m_Scope [2/2] ◆ m_SegmentBase TSeqPos CFastaReader::m_SegmentBase protected ◆ m_SeqCache ◆ m_SeqData string CFastaReader::m_SeqData protected ◆ m_SeqNameCache ◆ m_setOfLinkageEvidence ◆ m_SO ◆ m_SO_Value string CSAM_Formatter::m_SO_Value private ◆ m_Start const char* CMemoryLineReader::m_Start private ◆ m_Starts ◆ m_Stream ◆ m_String string CBufferedLineReader::m_String private ◆ m_TargetId ◆ m_TargetRange TRange CCIGAR_Formatter::m_TargetRange private ◆ m_TargetRow TNumrow CCIGAR_Formatter::m_TargetRow private ◆ m_TargetSign int CCIGAR_Formatter::m_TargetSign private ◆ m_TargetWidth TSeqPos CCIGAR_Formatter::m_TargetWidth private ◆ m_TotalGapLength TSeqPos CFastaReader::m_TotalGapLength protected ◆ m_TSE ◆ m_uLen ◆ m_uLineNumber ◆ m_UngetLine [1/2] bool CStreamLineReader::m_UngetLine private ◆ m_UngetLine [2/2] bool CBufferedLineReader::m_UngetLine private ◆ m_UnkMod SMod CSourceModParser::CUnkModError::m_UnkMod private ◆ m_UnusedMods ◆ m_uPos ◆ m_Version [1/2] string CSAM_Formatter::SProgramInfo::m_Version ◆ m_Version [2/2] int CGFFReader::m_Version protected ◆ merge_ranges

a subsidiary set of ranges that is merged into ranges after parsing.

this is used to account for things like start/stop codons, that are CDS intervals and should be merged into CDS intervals

Definition at line 129 of file gff_reader.hpp.

◆ name ◆ op ◆ parent string CGFFReader::SRecord::parent ◆ pos size_t CSourceModParser::SMod::pos = 0 ◆ ranges ◆ score string CGFFReader::SRecord::score ◆ segments ◆ seq_id string SFastaFileMap::SFastaEntry::seq_id ◆ seqid ◆ sm_PrivateStaticData int CMyClass::sm_PrivateStaticData staticprivate ◆ source string CGFFReader::SRecord::source ◆ strand ◆ stream_offset ◆ type EType CGFFReader::SRecord::type ◆ used ◆ value string CSourceModParser::SMod::value ◆ CSAM_CIGAR_Formatter ◆ CSomeFriendClass ◆ SomeFriendFunc bool SomeFriendFunc ( void ) friend

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4