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/classCFlatFileConfig.html below:

NCBI C++ ToolKit: CFlatFileConfig Class Reference

Search Toolkit Book for CFlatFileConfig

#include <objtools/format/flat_file_config.hpp>

enum EFormat {
  eFormat_GenBank , eFormat_EMBL , eFormat_DDBJ , eFormat_GBSeq ,
  eFormat_INSDSeq , eFormat_FTable , eFormat_FeaturesOnly , eFormat_SAM ,
  eFormat_AGP , eFormat_Lite
} enum EMode { eMode_Release = 0 , eMode_Entrez , eMode_GBench , eMode_Dump } enum EStyle { eStyle_Normal , eStyle_Segment , eStyle_Master , eStyle_Contig } enum EFlags {
  fDoHTML = 1 , fShowContigFeatures = 1 << 1 , fShowContigSources = 1 << 2 , fShowFarTranslations = 1 << 3 ,
  fTranslateIfNoProduct = 1 << 4 , fAlwaysTranslateCDS = 1 << 5 , fOnlyNearFeatures = 1 << 6 , fFavorFarFeatures = 1 << 7 ,
  fCopyCDSFromCDNA = 1 << 8 , fCopyGeneToCDNA = 1 << 9 , fShowContigInMaster = 1 << 10 , fHideImpFeatures = 1 << 11 ,
  fHideRemoteImpFeatures = 1 << 12 , fHideSNPFeatures = 1 << 13 , fHideExonFeatures = 1 << 14 , fHideIntronFeatures = 1 << 15 ,
  fHideMiscFeatures = 1 << 16 , fHideCDSProdFeatures = 1 << 17 , fHideCDDFeatures = 1 << 18 , fShowTranscript = 1 << 19 ,
  fShowPeptides = 1 << 20 , fHideGeneRIFs = 1 << 21 , fOnlyGeneRIFs = 1 << 22 , fLatestGeneRIFs = 1 << 23 ,
  fShowContigAndSeq = 1 << 24 , fHideSourceFeatures = 1 << 25 , fShowFtableRefs = 1 << 26 , fOldFeaturesOrder = 1 << 27 ,
  fHideGapFeatures = 1 << 28 , fNeverTranslateCDS = 1 << 29 , fShowSeqSpans = 1 << 30
} enum ECustom {
  fHideProteinID = 1 , fHideGI = 1 << 1 , fLongLocusNames = 1 << 2 , fExpandGaps = 1 << 3 ,
  fShowSNPFeatures = 1 << 6 , fShowCDDFeatures = 1 << 7 , fShowDebugTiming = 1 << 8 , fFasterReleaseSets = 1 << 9 ,
  fDisableAnnotRefs = 1 << 10 , fUseSeqEntryIndexer = 1 << 11 , fUseAutoDef = 1 << 12 , fIgnoreExistingTitle = 1 << 13 ,
  fGeneRNACDSFeatures = 1 << 14 , fShowFtablePeptides = 1 << 15 , fDisableReferenceCache = 1 << 16 , fShowDeflineModifiers = 1 << 17 ,
  fDoNotUseAutoDef = 1 << 18 , fOldTpaDisplay = 1 << 19 , fDisableDefaultIndex = 1 << 20 , fGeoLocNameCountry = 1 << 21 ,
  fLeavePrefixSuffix = 1 << 22
} enum EView { fViewNucleotides = 0x1 , fViewProteins = 0x2 , fViewAll = (fViewNucleotides | fViewProteins) , fViewFirst = 0x4 } enum EPolicy {
  ePolicy_Adaptive = 0 , ePolicy_Internal = 1 , ePolicy_External = 2 , ePolicy_Exhaustive = 3 ,
  ePolicy_Ftp = 4 , ePolicy_Web = 5 , ePolicy_Genomes = 6
} enum FGenbankBlocks {
  fGenbankBlocks_All = (~0u) , fGenbankBlocks_None = 0 , fGenbankBlocks_Head = (1u << 0) , fGenbankBlocks_Locus = (1u << 1) ,
  fGenbankBlocks_Defline = (1u << 2) , fGenbankBlocks_Accession = (1u << 3) , fGenbankBlocks_Version = (1u << 4) , fGenbankBlocks_Project = (1u << 5) ,
  fGenbankBlocks_Dbsource = (1u << 6) , fGenbankBlocks_Keywords = (1u << 7) , fGenbankBlocks_Segment = (1u << 8) , fGenbankBlocks_Source = (1u << 9) ,
  fGenbankBlocks_Reference = (1u << 10) , fGenbankBlocks_Comment = (1u << 11) , fGenbankBlocks_Primary = (1u << 12) , fGenbankBlocks_Featheader = (1u << 13) ,
  fGenbankBlocks_Sourcefeat = (1u << 14) , fGenbankBlocks_FeatAndGap = (1u << 15) , fGenbankBlocks_Basecount = (1u << 16) , fGenbankBlocks_Origin = (1u << 17) ,
  fGenbankBlocks_Sequence = (1u << 18) , fGenbankBlocks_Contig = (1u << 19) , fGenbankBlocks_Wgs = (1u << 20) , fGenbankBlocks_Tsa = (1u << 21) ,
  fGenbankBlocks_Slash = (1u << 22) , fGenbankBlocks_Cache = (1u << 23)
} typedef EFormat TFormat typedef EMode TMode typedef EStyle TStyle typedef EPolicy TPolicy typedef unsigned int TFlags typedef unsigned int TView typedef unsigned int TGenbankBlocks typedef unsigned int TCustom

Definition at line 116 of file flat_file_config.hpp.

◆ TCustom ◆ TFlags ◆ TFormat ◆ TGenbankBlocks ◆ TMode ◆ TPolicy ◆ TStyle ◆ TView ◆ ECustom Enumerator fHideProteinID fHideGI fLongLocusNames fExpandGaps fShowSNPFeatures fShowCDDFeatures fShowDebugTiming fFasterReleaseSets fDisableAnnotRefs fUseSeqEntryIndexer fUseAutoDef fIgnoreExistingTitle fGeneRNACDSFeatures fShowFtablePeptides fDisableReferenceCache fShowDeflineModifiers fDoNotUseAutoDef fOldTpaDisplay fDisableDefaultIndex fGeoLocNameCountry fLeavePrefixSuffix

Definition at line 186 of file flat_file_config.hpp.

◆ EFlags Enumerator fDoHTML fShowContigFeatures fShowContigSources fShowFarTranslations fTranslateIfNoProduct fAlwaysTranslateCDS fOnlyNearFeatures fFavorFarFeatures fCopyCDSFromCDNA fCopyGeneToCDNA fShowContigInMaster fHideImpFeatures fHideRemoteImpFeatures fHideSNPFeatures fHideExonFeatures fHideIntronFeatures fHideMiscFeatures fHideCDSProdFeatures fHideCDDFeatures fShowTranscript fShowPeptides fHideGeneRIFs fOnlyGeneRIFs fLatestGeneRIFs fShowContigAndSeq fHideSourceFeatures fShowFtableRefs fOldFeaturesOrder fHideGapFeatures fNeverTranslateCDS fShowSeqSpans

Definition at line 151 of file flat_file_config.hpp.

◆ EFormat Enumerator eFormat_GenBank eFormat_EMBL eFormat_DDBJ eFormat_GBSeq eFormat_INSDSeq eFormat_FTable eFormat_FeaturesOnly eFormat_SAM eFormat_AGP eFormat_Lite

Definition at line 120 of file flat_file_config.hpp.

◆ EMode ◆ EPolicy Enumerator ePolicy_Adaptive ePolicy_Internal ePolicy_External ePolicy_Exhaustive ePolicy_Ftp ePolicy_Web ePolicy_Genomes

Definition at line 219 of file flat_file_config.hpp.

◆ EStyle Enumerator eStyle_Normal eStyle_Segment eStyle_Master eStyle_Contig

Definition at line 143 of file flat_file_config.hpp.

◆ EView ◆ FGenbankBlocks Enumerator fGenbankBlocks_All fGenbankBlocks_None fGenbankBlocks_Head fGenbankBlocks_Locus fGenbankBlocks_Defline fGenbankBlocks_Accession fGenbankBlocks_Version fGenbankBlocks_Project fGenbankBlocks_Dbsource fGenbankBlocks_Keywords fGenbankBlocks_Segment fGenbankBlocks_Source fGenbankBlocks_Reference fGenbankBlocks_Comment fGenbankBlocks_Primary fGenbankBlocks_Featheader fGenbankBlocks_Sourcefeat fGenbankBlocks_FeatAndGap fGenbankBlocks_Basecount fGenbankBlocks_Origin fGenbankBlocks_Sequence fGenbankBlocks_Contig fGenbankBlocks_Wgs fGenbankBlocks_Tsa fGenbankBlocks_Slash fGenbankBlocks_Cache

Definition at line 231 of file flat_file_config.hpp.

◆ CFlatFileConfig()

Definition at line 311 of file flat_file_config.cpp.

References BasicCleanup(), eFormat_FTable, eStyle_Master, fGenbankBlocks_All, m_FeatDepth, m_Format, m_GapDepth, m_html_formatter, m_RefSeqConventions, m_Style, CRef< C, Locker >::Reset(), SetCanceledCallback(), SetGenbankBlockCallback(), and SetGenbankBlocks().

◆ ~CFlatFileConfig() ◆ AddArgumentDescriptions()

Definition at line 506 of file flat_file_config.cpp.

References CArgDescriptions::AddDefaultKey(), CArgDescriptions::AddFlag(), CArgDescriptions::AddOptionalKey(), DENT, CArgDescriptions::eDouble, CArgDescriptions::eExcludes, CArgDescriptions::eInteger, CArgDescriptions::eString, GetAllGenbankStrings(), NStr::Join(), CArgDescriptions::SetConstraint(), CArgDescriptions::SetCurrentGroup(), and CArgDescriptions::SetDependency().

Referenced by CAsn2FlatApp::Init().

◆ AlwaysTranslateCDS() bool CFlatFileConfig::AlwaysTranslateCDS ( void ) const inline ◆ AvoidLocusColl() ◆ BasicCleanup() [1/2] void CFlatFileConfig::BasicCleanup ( bool clean ) inline ◆ BasicCleanup() [2/2] bool CFlatFileConfig::BasicCleanup ( void ) const inline ◆ CheckCDSProductId() ◆ CheckQualSyntax() ◆ CitArtIsoJta() ◆ CodonRecognizedToNote() bool CFlatFileConfig::CodonRecognizedToNote ( void ) const ◆ CopyCDSFromCDNA() ◆ CopyGeneToCDNA() bool CFlatFileConfig::CopyGeneToCDNA ( void ) const inline ◆ DisableAnnotRefs() bool CFlatFileConfig::DisableAnnotRefs ( void ) const inline ◆ DisableDefaultIndex() bool CFlatFileConfig::DisableDefaultIndex ( void ) const inline ◆ DisableReferenceCache() bool CFlatFileConfig::DisableReferenceCache ( void ) const inline ◆ DoHTML() bool CFlatFileConfig::DoHTML ( void ) const inline

Definition at line 798 of file flat_file_config.hpp.

◆ DoNotUseAutoDef() ◆ DropBadCitGens() bool CFlatFileConfig::DropBadCitGens ( void ) const ◆ DropBadDbxref() ◆ DropIllegalQuals() bool CFlatFileConfig::DropIllegalQuals ( void ) const ◆ DropShortAA() ◆ ExpandGaps() bool CFlatFileConfig::ExpandGaps ( void ) const inline ◆ FasterReleaseSets() bool CFlatFileConfig::FasterReleaseSets ( void ) const inline ◆ FavorFarFeatures() ◆ ForGBRelease() bool CFlatFileConfig::ForGBRelease ( void ) const ◆ FrequencyToNote() ◆ FromArguments() void CFlatFileConfig::FromArguments ( const CArgs & args )

Definition at line 1057 of file flat_file_config.cpp.

References fHideCDDFeatures, fHideSNPFeatures, flags, format, fShowCDDFeatures, fShowSNPFeatures, m_BasicCleanup, m_fGenbankBlocks, SetCustom(), SetFeatDepth(), SetFlags(), SetFormat(), SetGapDepth(), SetMode(), SetPolicy(), SetSingleAccession(), SetStyle(), and SetView().

Referenced by CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ GeneRNACDSFeatures() bool CFlatFileConfig::GeneRNACDSFeatures ( void ) const inline ◆ GeoLocNameCountry() ◆ GetAllGenbankStrings() const vector< string > & CFlatFileConfig::GetAllGenbankStrings ( void ) static ◆ GetCanceledCallback() ◆ GetCustom() ◆ GetFeatDepth() int CFlatFileConfig::GetFeatDepth ( void ) const inline ◆ GetFlags() ◆ GetFormat() ◆ GetGapDepth() int CFlatFileConfig::GetGapDepth ( void ) const inline ◆ GetGenbankBlockCallback() ◆ GetHTMLFormatter() ◆ GetMode() const TMode& CFlatFileConfig::GetMode ( void ) const inline ◆ GetPolicy() ◆ GetSingleAccession() const string& CFlatFileConfig::GetSingleAccession ( void ) const inline ◆ GetStyle() ◆ GetView() const TView& CFlatFileConfig::GetView ( void ) const inline ◆ GoQualsEachMerge() bool CFlatFileConfig::GoQualsEachMerge ( void ) const ◆ GoQualsToNote() bool CFlatFileConfig::GoQualsToNote ( void ) const ◆ HideBankItComment() ◆ HideCDDFeatures() bool CFlatFileConfig::HideCDDFeatures ( void ) const inline ◆ HideCDSProdFeatures() bool CFlatFileConfig::HideCDSProdFeatures ( void ) const inline ◆ HideEmptySource() bool CFlatFileConfig::HideEmptySource ( void ) const ◆ HideExonFeatures() bool CFlatFileConfig::HideExonFeatures ( void ) const inline ◆ HideGapFeatures() bool CFlatFileConfig::HideGapFeatures ( void ) const inline ◆ HideGeneRIFs() bool CFlatFileConfig::HideGeneRIFs ( void ) const inline ◆ HideGI() bool CFlatFileConfig::HideGI ( void ) const inline ◆ HideImpFeatures() bool CFlatFileConfig::HideImpFeatures ( void ) const inline ◆ HideIntronFeatures() bool CFlatFileConfig::HideIntronFeatures ( void ) const inline ◆ HideMiscFeatures() bool CFlatFileConfig::HideMiscFeatures ( void ) const inline ◆ HideProteinID() bool CFlatFileConfig::HideProteinID ( void ) const inline ◆ HideRemoteImpFeatures() bool CFlatFileConfig::HideRemoteImpFeatures ( void ) const inline ◆ HideSNPFeatures() bool CFlatFileConfig::HideSNPFeatures ( void ) const inline ◆ HideSourceFeatures() bool CFlatFileConfig::HideSourceFeatures ( void ) const inline ◆ HideSpecificGeneMaps() ◆ HideUnclassPartial() ◆ IgnoreExistingTitle() ◆ IgnorePatPubs() ◆ IsFormatAGP() bool CFlatFileConfig::IsFormatAGP ( void ) const inline ◆ IsFormatDDBJ() bool CFlatFileConfig::IsFormatDDBJ ( void ) const inline ◆ IsFormatEMBL() bool CFlatFileConfig::IsFormatEMBL ( void ) const inline ◆ IsFormatFTable() bool CFlatFileConfig::IsFormatFTable ( void ) const inline ◆ IsFormatGBSeq() bool CFlatFileConfig::IsFormatGBSeq ( void ) const inline ◆ IsFormatGenbank() bool CFlatFileConfig::IsFormatGenbank ( void ) const inline ◆ IsFormatINSDSeq() bool CFlatFileConfig::IsFormatINSDSeq ( void ) const inline ◆ IsFormatLite() bool CFlatFileConfig::IsFormatLite ( void ) const inline ◆ IsModeDump() bool CFlatFileConfig::IsModeDump ( void ) const inline ◆ IsModeEntrez() bool CFlatFileConfig::IsModeEntrez ( void ) const inline ◆ IsModeGBench() bool CFlatFileConfig::IsModeGBench ( void ) const inline ◆ IsModeRelease() bool CFlatFileConfig::IsModeRelease ( void ) const inline ◆ IsPolicyAdaptive() bool CFlatFileConfig::IsPolicyAdaptive ( void ) const inline ◆ IsPolicyExhaustive() bool CFlatFileConfig::IsPolicyExhaustive ( void ) const inline ◆ IsPolicyExternal() bool CFlatFileConfig::IsPolicyExternal ( void ) const inline ◆ IsPolicyFtp() bool CFlatFileConfig::IsPolicyFtp ( void ) const inline

Definition at line 504 of file flat_file_config.hpp.

References ePolicy_Ftp, and m_Policy.

Referenced by CGenbankFormatter::FormatVersion(), CFlatFileGenerator::Generate(), s_SetSelection(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualProteinId(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), CGenbankGatherer::x_DoSingleSection(), CFeatureItem::x_GetAssociatedProtInfo(), CFeatureItem::x_GetAssociatedProtInfoIdx(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), and CGenbankFormatter::x_LocusHtmlPrefix().

◆ IsPolicyGenomes() bool CFlatFileConfig::IsPolicyGenomes ( void ) const inline

Definition at line 506 of file flat_file_config.hpp.

References ePolicy_Genomes, and m_Policy.

Referenced by CGenbankFormatter::FormatVersion(), CFlatFileGenerator::Generate(), s_SetSelection(), s_SkipFeature(), CFeatureItem::x_AddProductIdQuals(), CFeatureItem::x_AddQualProteinId(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), CGenbankGatherer::x_DoSingleSection(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFeatureItem::x_GetAssociatedProtInfo(), CFeatureItem::x_GetAssociatedProtInfoIdx(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), and CGenbankFormatter::x_LocusHtmlPrefix().

◆ IsPolicyInternal() bool CFlatFileConfig::IsPolicyInternal ( void ) const inline ◆ IsPolicyWeb() bool CFlatFileConfig::IsPolicyWeb ( void ) const inline ◆ IsShownGenbankBlock() ◆ IsStyleContig() bool CFlatFileConfig::IsStyleContig ( void ) const inline ◆ IsStyleMaster() bool CFlatFileConfig::IsStyleMaster ( void ) const inline ◆ IsStyleNormal() bool CFlatFileConfig::IsStyleNormal ( void ) const inline ◆ IsStyleSegment() bool CFlatFileConfig::IsStyleSegment ( void ) const inline ◆ IsViewAll() bool CFlatFileConfig::IsViewAll ( void ) const inline ◆ IsViewFirst() bool CFlatFileConfig::IsViewFirst ( void ) const inline ◆ IsViewNuc() bool CFlatFileConfig::IsViewNuc ( void ) const inline ◆ IsViewProt() bool CFlatFileConfig::IsViewProt ( void ) const inline ◆ IupacaaOnly() bool CFlatFileConfig::IupacaaOnly ( void ) const ◆ LatestGeneRIFs() bool CFlatFileConfig::LatestGeneRIFs ( void ) const inline ◆ LeavePrefixSuffix() ◆ LongLocusNames() bool CFlatFileConfig::LongLocusNames ( void ) const inline ◆ NeedAtLeastOneRef() ◆ NeedOrganismQual() ◆ NeedRequiredQuals() bool CFlatFileConfig::NeedRequiredQuals ( void ) const ◆ NeverTranslateCDS() bool CFlatFileConfig::NeverTranslateCDS ( void ) const inline ◆ NoAffilOnUnpub() bool CFlatFileConfig::NoAffilOnUnpub ( void ) const ◆ OldFeaturesOrder() ◆ OldTpaDisplay() ◆ OnlyGeneRIFs() bool CFlatFileConfig::OnlyGeneRIFs ( void ) const inline ◆ OnlyNearFeatures() bool CFlatFileConfig::OnlyNearFeatures ( void ) const inline ◆ SelenocysteineToNote() bool CFlatFileConfig::SelenocysteineToNote ( void ) const ◆ SetAlwaysTranslateCDS() ◆ SetCanceledCallback() void CFlatFileConfig::SetCanceledCallback ( ICanceled * pCallback ) inline ◆ SetCopyCDSFromCDNA() ◆ SetCopyGeneToCDNA() ◆ SetCustom() ◆ SetDisableAnnotRefs() ◆ SetDisableDefaultIndex() ◆ SetDisableReferenceCache() ◆ SetDoHTML() ◆ SetDoNotUseAutoDef() ◆ SetExpandGaps() ◆ SetFasterReleaseSets() ◆ SetFavorFarFeatures() ◆ SetFeatDepth() void CFlatFileConfig::SetFeatDepth ( const int featDepth ) inline ◆ SetFlags() void CFlatFileConfig::SetFlags ( const TFlags & flags ) inline ◆ SetFormat() ◆ SetFormatAGP() void CFlatFileConfig::SetFormatAGP ( void ) inline ◆ SetFormatDDBJ() void CFlatFileConfig::SetFormatDDBJ ( void ) inline ◆ SetFormatEMBL() void CFlatFileConfig::SetFormatEMBL ( void ) inline ◆ SetFormatFTable() void CFlatFileConfig::SetFormatFTable ( void ) inline ◆ SetFormatGBSeq() void CFlatFileConfig::SetFormatGBSeq ( void ) inline ◆ SetFormatGenbank() void CFlatFileConfig::SetFormatGenbank ( void ) inline ◆ SetFormatINSDSeq() void CFlatFileConfig::SetFormatINSDSeq ( void ) inline ◆ SetFormatLite() void CFlatFileConfig::SetFormatLite ( void ) inline ◆ SetGapDepth() void CFlatFileConfig::SetGapDepth ( const int gapDepth ) inline ◆ SetGenbankBlockCallback() ◆ SetGenbankBlocks() ◆ SetGeneRNACDSFeatures() ◆ SetGeoLocNameCountry() ◆ SetHideCDDFeatures() ◆ SetHideCDSProdFeatures() ◆ SetHideExonFeatures() ◆ SetHideGapFeatures() ◆ SetHideGeneRIFs() ◆ SetHideGI() ◆ SetHideImpFeatures() ◆ SetHideIntronFeatures() ◆ SetHideMiscFeatures() ◆ SetHideProteinID() ◆ SetHideRemoteImpFeatures() ◆ SetHideSNPFeatures() ◆ SetHideSourceFeatures() ◆ SetHTMLFormatter() ◆ SetIgnoreExistingTitle() ◆ SetLatestGeneRIFs() ◆ SetLeavePrefixSuffix() ◆ SetLongLocusNames() ◆ SetMode() void CFlatFileConfig::SetMode ( const TMode & mode ) inline ◆ SetModeDump() void CFlatFileConfig::SetModeDump ( void ) inline ◆ SetModeEntrez() void CFlatFileConfig::SetModeEntrez ( void ) inline ◆ SetModeGBench() void CFlatFileConfig::SetModeGBench ( void ) inline ◆ SetModeRelease() void CFlatFileConfig::SetModeRelease ( void ) inline ◆ SetNeverTranslateCDS() ◆ SetOldFeaturesOrder() ◆ SetOldTpaDisplay() ◆ SetOnlyGeneRIFs() ◆ SetOnlyNearFeatures() ◆ SetPolicy() ◆ SetPolicyAdaptive() void CFlatFileConfig::SetPolicyAdaptive ( void ) inline ◆ SetPolicyExhaustive() void CFlatFileConfig::SetPolicyExhaustive ( void ) inline ◆ SetPolicyExternal() void CFlatFileConfig::SetPolicyExternal ( void ) inline ◆ SetPolicyFtp() void CFlatFileConfig::SetPolicyFtp ( void ) inline ◆ SetPolicyGenomes() void CFlatFileConfig::SetPolicyGenomes ( void ) inline ◆ SetPolicyInternal() void CFlatFileConfig::SetPolicyInternal ( void ) inline ◆ SetPolicyWeb() void CFlatFileConfig::SetPolicyWeb ( void ) inline ◆ SetRefSeqConventions() void CFlatFileConfig::SetRefSeqConventions ( void ) inline ◆ SetShowCDDFeatures() ◆ SetShowContigAndSeq() ◆ SetShowContigFeatures() ◆ SetShowContigInMaster() ◆ SetShowContigSources() ◆ SetShowDebugTiming() ◆ SetShowDeflineModifiers() ◆ SetShowFarTranslations() ◆ SetShowFtablePeptides() ◆ SetShowFtableRefs() ◆ SetShowPeptides() ◆ SetShowSeqSpans() ◆ SetShowSNPFeatures() ◆ SetShowTranscript() ◆ SetSingleAccession() void CFlatFileConfig::SetSingleAccession ( const string & accn ) inline ◆ SetStyle() void CFlatFileConfig::SetStyle ( const TStyle & style ) inline ◆ SetStyleContig() void CFlatFileConfig::SetStyleContig ( void ) inline ◆ SetStyleMaster() void CFlatFileConfig::SetStyleMaster ( void ) inline ◆ SetStyleNormal() void CFlatFileConfig::SetStyleNormal ( void ) inline ◆ SetStyleSegment() void CFlatFileConfig::SetStyleSegment ( void ) inline ◆ SetTranslateIfNoProduct() ◆ SetUseAutoDef() ◆ SetUseSeqEntryIndexer() ◆ SetView() void CFlatFileConfig::SetView ( const TView & view ) inline ◆ SetViewAll() void CFlatFileConfig::SetViewAll ( void ) inline ◆ SetViewFirst() void CFlatFileConfig::SetViewFirst ( bool enabled ) inline ◆ SetViewNuc() void CFlatFileConfig::SetViewNuc ( void ) inline ◆ SetViewProt() void CFlatFileConfig::SetViewProt ( void ) inline ◆ ShowCDDFeatures() bool CFlatFileConfig::ShowCDDFeatures ( void ) const inline ◆ ShowContigAndSeq() bool CFlatFileConfig::ShowContigAndSeq ( void ) const inline ◆ ShowContigFeatures() bool CFlatFileConfig::ShowContigFeatures ( void ) const inline ◆ ShowContigInMaster() ◆ ShowContigSources() bool CFlatFileConfig::ShowContigSources ( void ) const inline ◆ ShowDebugTiming() bool CFlatFileConfig::ShowDebugTiming ( void ) const inline ◆ ShowDeflineModifiers() ◆ ShowFarTranslations() bool CFlatFileConfig::ShowFarTranslations ( void ) const inline ◆ ShowFtablePeptides() bool CFlatFileConfig::ShowFtablePeptides ( void ) const inline ◆ ShowFtableRefs() ◆ ShowGenbankBlock() void CFlatFileConfig::ShowGenbankBlock ( FGenbankBlocks fTGenbankBlocksMask ) inline ◆ ShowOutOfBoundsFeats() ◆ ShowPeptides() ◆ ShowSeqSpans() bool CFlatFileConfig::ShowSeqSpans ( void ) const inline ◆ ShowSNPFeatures() bool CFlatFileConfig::ShowSNPFeatures ( void ) const inline ◆ ShowTranscript() bool CFlatFileConfig::ShowTranscript ( void ) const inline ◆ SkipGenbankBlock() void CFlatFileConfig::SkipGenbankBlock ( FGenbankBlocks fTGenbankBlocksMask ) inline ◆ SrcQualsToNote() bool CFlatFileConfig::SrcQualsToNote ( void ) const ◆ StringToGenbankBlock() ◆ SuppressLocalId() bool CFlatFileConfig::SuppressLocalId ( void ) const ◆ ThrowIfCanceled() void CFlatFileConfig::ThrowIfCanceled ( void ) const inline ◆ TranslateIfNoProduct() bool CFlatFileConfig::TranslateIfNoProduct ( void ) const inline ◆ UseAutoDef() ◆ UseEmblMolType() ◆ UseSeqEntryIndexer() bool CFlatFileConfig::UseSeqEntryIndexer ( void ) const inline ◆ ValidateFeatures() bool CFlatFileConfig::ValidateFeatures ( void ) const ◆ x_ThrowHaltNow() void CFlatFileConfig::x_ThrowHaltNow ( void ) const private ◆ m_BasicCleanup bool CFlatFileConfig::m_BasicCleanup private ◆ m_Custom ◆ m_FeatDepth int CFlatFileConfig::m_FeatDepth private ◆ m_fGenbankBlocks ◆ m_Flags TFlags CFlatFileConfig::m_Flags private ◆ m_Format

Definition at line 753 of file flat_file_config.hpp.

Referenced by CFlatFileConfig(), GetFormat(), IsFormatAGP(), IsFormatDDBJ(), IsFormatEMBL(), IsFormatFTable(), IsFormatGBSeq(), IsFormatGenbank(), IsFormatINSDSeq(), IsFormatLite(), SetFormat(), SetFormatAGP(), SetFormatDDBJ(), SetFormatEMBL(), SetFormatFTable(), SetFormatGBSeq(), SetFormatGenbank(), SetFormatINSDSeq(), and SetFormatLite().

◆ m_GapDepth int CFlatFileConfig::m_GapDepth private ◆ m_GenbankBlockCallback ◆ m_html_formatter ◆ m_Mode TMode CFlatFileConfig::m_Mode private

Definition at line 754 of file flat_file_config.hpp.

Referenced by CodonRecognizedToNote(), GetMode(), GoQualsToNote(), IsModeDump(), IsModeEntrez(), IsModeGBench(), IsModeRelease(), SelenocysteineToNote(), SetMode(), SetModeDump(), SetModeEntrez(), SetModeGBench(), SetModeRelease(), and SrcQualsToNote().

◆ m_pCanceledCallback ◆ m_Policy

Definition at line 758 of file flat_file_config.hpp.

Referenced by GetPolicy(), IsPolicyAdaptive(), IsPolicyExhaustive(), IsPolicyExternal(), IsPolicyFtp(), IsPolicyGenomes(), IsPolicyInternal(), IsPolicyWeb(), SetPolicy(), SetPolicyAdaptive(), SetPolicyExhaustive(), SetPolicyExternal(), SetPolicyFtp(), SetPolicyGenomes(), SetPolicyInternal(), and SetPolicyWeb().

◆ m_RefSeqConventions bool CFlatFileConfig::m_RefSeqConventions private ◆ m_SingleAccession string CFlatFileConfig::m_SingleAccession private ◆ m_Style TStyle CFlatFileConfig::m_Style private

Definition at line 755 of file flat_file_config.hpp.

Referenced by CFlatFileConfig(), GetStyle(), IsStyleContig(), IsStyleMaster(), IsStyleNormal(), IsStyleSegment(), SetStyle(), SetStyleContig(), SetStyleMaster(), SetStyleNormal(), and SetStyleSegment().

◆ m_View TView CFlatFileConfig::m_View private ◆ sm_ModeFlags ◆ SMARTFEATLIMIT const size_t CFlatFileConfig::SMARTFEATLIMIT = 1000000 static

The documentation for this class was generated from the following files:

include/objtools/format/flat_file_config.hpp
src/objtools/format/flat_file_config.cpp

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