Search Toolkit Book for CFlatFileConfig

#include <objtools/format/flat_file_config.hpp>

Collaboration diagram for CFlatFileConfig:

Classes
class	CGenbankBlockCallback

Public Types
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 }

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

Public Member Functions
	CFlatFileConfig (TFormat format=eFormat_GenBank, TMode mode=eMode_GBench, TStyle style=eStyle_Normal, TFlags flags=0, TView view=fViewNucleotides, TPolicy policy=ePolicy_Adaptive, TCustom custom=0)

	~CFlatFileConfig (void)

void	SetHTMLFormatter (CRef< IHTMLFormatter > html_fmt)

const IHTMLFormatter &	GetHTMLFormatter () const

const TFormat &	GetFormat (void) const

bool	IsFormatGenbank (void) const

bool	IsFormatEMBL (void) const

bool	IsFormatDDBJ (void) const

bool	IsFormatGBSeq (void) const

bool	IsFormatINSDSeq (void) const

bool	IsFormatFTable (void) const

bool	IsFormatAGP (void) const

bool	IsFormatLite (void) const

void	SetFormat (const TFormat &format)

void	SetFormatGenbank (void)

void	SetFormatEMBL (void)

void	SetFormatDDBJ (void)

void	SetFormatGBSeq (void)

void	SetFormatINSDSeq (void)

void	SetFormatFTable (void)

void	SetFormatAGP (void)

void	SetFormatLite (void)

const TMode &	GetMode (void) const

bool	IsModeRelease (void) const

bool	IsModeEntrez (void) const

bool	IsModeGBench (void) const

bool	IsModeDump (void) const

void	SetMode (const TMode &mode)

void	SetModeRelease (void)

void	SetModeEntrez (void)

void	SetModeGBench (void)

void	SetModeDump (void)

const TStyle &	GetStyle (void) const

bool	IsStyleNormal (void) const

bool	IsStyleSegment (void) const

bool	IsStyleMaster (void) const

bool	IsStyleContig (void) const

void	SetStyle (const TStyle &style)

void	SetStyleNormal (void)

void	SetStyleSegment (void)

void	SetStyleMaster (void)

void	SetStyleContig (void)

const TView &	GetView (void) const

bool	IsViewNuc (void) const

bool	IsViewProt (void) const

bool	IsViewAll (void) const

bool	IsViewFirst (void) const

void	SetView (const TView &view)

void	SetViewNuc (void)

void	SetViewProt (void)

void	SetViewAll (void)

void	SetViewFirst (bool enabled)

const TPolicy &	GetPolicy (void) const

bool	IsPolicyAdaptive (void) const

bool	IsPolicyInternal (void) const

bool	IsPolicyExternal (void) const

bool	IsPolicyExhaustive (void) const

bool	IsPolicyFtp (void) const

bool	IsPolicyWeb (void) const

bool	IsPolicyGenomes (void) const

void	SetPolicy (const TPolicy &Policy)

void	SetPolicyAdaptive (void)

void	SetPolicyInternal (void)

void	SetPolicyExternal (void)

void	SetPolicyExhaustive (void)

void	SetPolicyFtp (void)

void	SetPolicyWeb (void)

void	SetPolicyGenomes (void)

const TFlags &	GetFlags (void) const

bool	DoHTML (void) const

bool	HideImpFeatures (void) const

bool	HideSNPFeatures (void) const

bool	HideExonFeatures (void) const

bool	HideIntronFeatures (void) const

bool	HideMiscFeatures (void) const

bool	HideRemoteImpFeatures (void) const

bool	HideGeneRIFs (void) const

bool	OnlyGeneRIFs (void) const

bool	HideCDSProdFeatures (void) const

bool	HideCDDFeatures (void) const

bool	LatestGeneRIFs (void) const

bool	ShowContigFeatures (void) const

bool	ShowContigSources (void) const

bool	ShowContigAndSeq (void) const

bool	CopyGeneToCDNA (void) const

bool	ShowContigInMaster (void) const

bool	CopyCDSFromCDNA (void) const

bool	HideSourceFeatures (void) const

bool	AlwaysTranslateCDS (void) const

bool	OnlyNearFeatures (void) const

bool	FavorFarFeatures (void) const

bool	ShowFarTranslations (void) const

bool	TranslateIfNoProduct (void) const

bool	ShowTranscript (void) const

bool	ShowPeptides (void) const

bool	ShowFtableRefs (void) const

bool	OldFeaturesOrder (void) const

bool	HideGapFeatures (void) const

bool	NeverTranslateCDS (void) const

bool	ShowSeqSpans (void) const

bool	SuppressLocalId (void) const

bool	ValidateFeatures (void) const

bool	IgnorePatPubs (void) const

bool	DropShortAA (void) const

bool	AvoidLocusColl (void) const

bool	IupacaaOnly (void) const

bool	DropBadCitGens (void) const

bool	NoAffilOnUnpub (void) const

bool	DropIllegalQuals (void) const

bool	CheckQualSyntax (void) const

bool	NeedRequiredQuals (void) const

bool	NeedOrganismQual (void) const

bool	NeedAtLeastOneRef (void) const

bool	CitArtIsoJta (void) const

bool	DropBadDbxref (void) const

bool	UseEmblMolType (void) const

bool	HideBankItComment (void) const

bool	CheckCDSProductId (void) const

bool	FrequencyToNote (void) const

bool	SrcQualsToNote (void) const

bool	HideEmptySource (void) const

bool	GoQualsToNote (void) const

bool	SelenocysteineToNote (void) const

bool	ForGBRelease (void) const

bool	HideUnclassPartial (void) const

bool	CodonRecognizedToNote (void) const

bool	GoQualsEachMerge (void) const

bool	ShowOutOfBoundsFeats (void) const

bool	HideSpecificGeneMaps (void) const

void	SetFlags (const TFlags &flags)

CFlatFileConfig &	SetDoHTML (bool val=true)

CFlatFileConfig &	SetHideImpFeatures (bool val=true)

CFlatFileConfig &	SetHideSNPFeatures (bool val=true)

CFlatFileConfig &	SetHideExonFeatures (bool val=true)

CFlatFileConfig &	SetHideIntronFeatures (bool val=true)

CFlatFileConfig &	SetHideMiscFeatures (bool val=true)

CFlatFileConfig &	SetHideRemoteImpFeatures (bool val=true)

CFlatFileConfig &	SetHideGeneRIFs (bool val=true)

CFlatFileConfig &	SetOnlyGeneRIFs (bool val=true)

CFlatFileConfig &	SetHideCDSProdFeatures (bool val=true)

CFlatFileConfig &	SetHideCDDFeatures (bool val=true)

CFlatFileConfig &	SetLatestGeneRIFs (bool val=true)

CFlatFileConfig &	SetShowContigFeatures (bool val=true)

CFlatFileConfig &	SetShowContigSources (bool val=true)

CFlatFileConfig &	SetShowContigAndSeq (bool val=true)

CFlatFileConfig &	SetCopyGeneToCDNA (bool val=true)

CFlatFileConfig &	SetShowContigInMaster (bool val=true)

CFlatFileConfig &	SetCopyCDSFromCDNA (bool val=true)

CFlatFileConfig &	SetHideSourceFeatures (bool val=true)

CFlatFileConfig &	SetAlwaysTranslateCDS (bool val=true)

CFlatFileConfig &	SetOnlyNearFeatures (bool val=true)

CFlatFileConfig &	SetFavorFarFeatures (bool val=true)

CFlatFileConfig &	SetShowFarTranslations (bool val=true)

CFlatFileConfig &	SetTranslateIfNoProduct (bool val=true)

CFlatFileConfig &	SetShowTranscript (bool val=true)

CFlatFileConfig &	SetShowPeptides (bool val=true)

CFlatFileConfig &	SetShowFtableRefs (bool val=true)

CFlatFileConfig &	SetOldFeaturesOrder (bool val=true)

CFlatFileConfig &	SetHideGapFeatures (bool val=true)

CFlatFileConfig &	SetNeverTranslateCDS (bool val=true)

CFlatFileConfig &	SetShowSeqSpans (bool val=true)

const TCustom &	GetCustom (void) const

bool	HideProteinID (void) const

bool	HideGI (void) const

bool	LongLocusNames (void) const

bool	ExpandGaps (void) const

bool	ShowSNPFeatures (void) const

bool	ShowCDDFeatures (void) const

bool	ShowDebugTiming (void) const

bool	FasterReleaseSets (void) const

bool	DisableAnnotRefs (void) const

bool	UseSeqEntryIndexer (void) const

bool	UseAutoDef (void) const

bool	IgnoreExistingTitle (void) const

bool	GeneRNACDSFeatures (void) const

bool	ShowFtablePeptides (void) const

bool	DisableReferenceCache (void) const

bool	ShowDeflineModifiers (void) const

bool	DoNotUseAutoDef (void) const

bool	OldTpaDisplay (void) const

bool	DisableDefaultIndex (void) const

bool	GeoLocNameCountry (void) const

void	SetCustom (const TCustom &custom)

CFlatFileConfig &	SetHideProteinID (bool val=true)

CFlatFileConfig &	SetHideGI (bool val=true)

CFlatFileConfig &	SetLongLocusNames (bool val=true)

CFlatFileConfig &	SetExpandGaps (bool val=true)

CFlatFileConfig &	SetShowSNPFeatures (bool val=true)

CFlatFileConfig &	SetShowCDDFeatures (bool val=true)

CFlatFileConfig &	SetShowDebugTiming (bool val=true)

CFlatFileConfig &	SetFasterReleaseSets (bool val=true)

CFlatFileConfig &	SetDisableAnnotRefs (bool val=true)

CFlatFileConfig &	SetUseSeqEntryIndexer (bool val=true)

CFlatFileConfig &	SetUseAutoDef (bool val=true)

CFlatFileConfig &	SetIgnoreExistingTitle (bool val=true)

CFlatFileConfig &	SetGeneRNACDSFeatures (bool val=true)

CFlatFileConfig &	SetShowFtablePeptides (bool val=true)

CFlatFileConfig &	SetDisableReferenceCache (bool val=true)

CFlatFileConfig &	SetShowDeflineModifiers (bool val=true)

CFlatFileConfig &	SetDoNotUseAutoDef (bool val=true)

CFlatFileConfig &	SetOldTpaDisplay (bool val=true)

CFlatFileConfig &	SetDisableDefaultIndex (bool val=true)

CFlatFileConfig &	SetGeoLocNameCountry (bool val=true)

void	SetRefSeqConventions (void)

void	SetSingleAccession (const string &accn)

const string &	GetSingleAccession (void) const

int	GetFeatDepth (void) const

void	SetFeatDepth (const int featDepth)

int	GetGapDepth (void) const

void	SetGapDepth (const int gapDepth)

void	SetGenbankBlocks (const TGenbankBlocks &genbank_blocks)

bool	IsShownGenbankBlock (FGenbankBlocks fTGenbankBlocksMask) const

void	ShowGenbankBlock (FGenbankBlocks fTGenbankBlocksMask)

void	SkipGenbankBlock (FGenbankBlocks fTGenbankBlocksMask)

CRef< CGenbankBlockCallback >	GetGenbankBlockCallback (void) const

void	SetGenbankBlockCallback (CGenbankBlockCallback *pGenbankBlockCallback)

const ICanceled *	GetCanceledCallback (void) const

void	SetCanceledCallback (ICanceled *pCallback)

bool	BasicCleanup (void) const

void	BasicCleanup (bool clean)

void	ThrowIfCanceled (void) const
	This throws a CFlatException if flatfile generation cancellation has been requested via ICanceled. More...

void	FromArguments (const CArgs &args)

Static Public Member Functions
static FGenbankBlocks	StringToGenbankBlock (const string &str)

static const vector< string > &	GetAllGenbankStrings (void)

static void	AddArgumentDescriptions (CArgDescriptions &args)

Static Public Attributes
static const size_t	SMARTFEATLIMIT = 1000000

Private Member Functions
void	x_ThrowHaltNow (void) const

Static Private Attributes
static const bool	sm_ModeFlags [4][32]

Detailed Description

Definition at line 116 of file flat_file_config.hpp.

Member Typedef Documentation

◆ TCustom

typedef unsigned int CFlatFileConfig::TCustom

Definition at line 276 of file flat_file_config.hpp.

◆ TFlags

typedef unsigned int CFlatFileConfig::TFlags

Definition at line 273 of file flat_file_config.hpp.

◆ TFormat

typedef EFormat CFlatFileConfig::TFormat

Definition at line 269 of file flat_file_config.hpp.

◆ TGenbankBlocks

typedef unsigned int CFlatFileConfig::TGenbankBlocks

Definition at line 275 of file flat_file_config.hpp.

◆ TMode

typedef EMode CFlatFileConfig::TMode

Definition at line 270 of file flat_file_config.hpp.

◆ TPolicy

typedef EPolicy CFlatFileConfig::TPolicy

Definition at line 272 of file flat_file_config.hpp.

◆ TStyle

typedef EStyle CFlatFileConfig::TStyle

Definition at line 271 of file flat_file_config.hpp.

◆ TView

typedef unsigned int CFlatFileConfig::TView

Definition at line 274 of file flat_file_config.hpp.

Member Enumeration Documentation

◆ ECustom

enum CFlatFileConfig::ECustom

Enumerator
fHideProteinID
fHideGI
fLongLocusNames
fExpandGaps
fShowSNPFeatures
fShowCDDFeatures
fShowDebugTiming
fFasterReleaseSets
fDisableAnnotRefs
fUseSeqEntryIndexer
fUseAutoDef
fIgnoreExistingTitle
fGeneRNACDSFeatures
fShowFtablePeptides
fDisableReferenceCache
fShowDeflineModifiers
fDoNotUseAutoDef
fOldTpaDisplay
fDisableDefaultIndex
fGeoLocNameCountry

Definition at line 186 of file flat_file_config.hpp.

◆ EFlags

enum CFlatFileConfig::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

enum CFlatFileConfig::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

enum CFlatFileConfig::EMode

Enumerator
eMode_Release
eMode_Entrez
eMode_GBench
eMode_Dump

Definition at line 134 of file flat_file_config.hpp.

◆ EPolicy

enum CFlatFileConfig::EPolicy

Enumerator
ePolicy_Adaptive
ePolicy_Internal
ePolicy_External
ePolicy_Exhaustive
ePolicy_Ftp
ePolicy_Web
ePolicy_Genomes

Definition at line 218 of file flat_file_config.hpp.

◆ EStyle

enum CFlatFileConfig::EStyle

Enumerator
eStyle_Normal
eStyle_Segment
eStyle_Master
eStyle_Contig

Definition at line 143 of file flat_file_config.hpp.

◆ EView

enum CFlatFileConfig::EView

Enumerator
fViewNucleotides
fViewProteins
fViewAll
fViewFirst

Definition at line 210 of file flat_file_config.hpp.

◆ FGenbankBlocks

enum CFlatFileConfig::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 230 of file flat_file_config.hpp.

Constructor & Destructor Documentation

◆ CFlatFileConfig()

CFlatFileConfig::CFlatFileConfig	(	TFormat	format = `eFormat_GenBank`,
		TMode	mode = `eMode_GBench`,
		TStyle	style = `eStyle_Normal`,
		TFlags	flags = `0`,
		TView	view = `fViewNucleotides`,
		TPolicy	policy = `ePolicy_Adaptive`,
		TCustom	custom = `0`
	)

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()

CFlatFileConfig::~CFlatFileConfig ( void )

Definition at line 338 of file flat_file_config.cpp.

Member Function Documentation

◆ AddArgumentDescriptions()

void CFlatFileConfig::AddArgumentDescriptions ( CArgDescriptions & args )

static

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

Definition at line 814 of file flat_file_config.hpp.

Referenced by CFeatureItem::x_AddQualTranslation(), CFeatureItem::x_GetAssociatedProtInfo(), and CFeatureItem::x_GetAssociatedProtInfoIdx().

◆ AvoidLocusColl()

bool CFlatFileConfig::AvoidLocusColl ( void ) const

Definition at line 389 of file flat_file_config.cpp.

◆ BasicCleanup() [1/2]

void CFlatFileConfig::BasicCleanup ( bool clean )

inline

Definition at line 725 of file flat_file_config.hpp.

References m_BasicCleanup.

◆ BasicCleanup() [2/2]

bool CFlatFileConfig::BasicCleanup ( void ) const

inline

Definition at line 723 of file flat_file_config.hpp.

References m_BasicCleanup.

Referenced by CFlatFileConfig(), CFlatFileGenerator::Generate(), and CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ CheckCDSProductId()

bool CFlatFileConfig::CheckCDSProductId ( void ) const

Definition at line 402 of file flat_file_config.cpp.

◆ CheckQualSyntax()

bool CFlatFileConfig::CheckQualSyntax ( void ) const

Definition at line 394 of file flat_file_config.cpp.

◆ CitArtIsoJta()

bool CFlatFileConfig::CitArtIsoJta ( void ) const

Definition at line 398 of file flat_file_config.cpp.

◆ CodonRecognizedToNote()

bool CFlatFileConfig::CodonRecognizedToNote ( void ) const

Definition at line 432 of file flat_file_config.cpp.

References false, m_Mode, m_RefSeqConventions, and sm_ModeFlags.

Referenced by CFeatureItem::x_FormatNoteQuals(), and CFeatureItem::x_FormatQuals().

◆ CopyCDSFromCDNA()

bool CFlatFileConfig::CopyCDSFromCDNA ( void ) const

inline

Definition at line 812 of file flat_file_config.hpp.

◆ CopyGeneToCDNA()

bool CFlatFileConfig::CopyGeneToCDNA ( void ) const

inline

Definition at line 810 of file flat_file_config.hpp.

Referenced by CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

◆ DisableAnnotRefs()

bool CFlatFileConfig::DisableAnnotRefs ( void ) const

inline

Definition at line 858 of file flat_file_config.hpp.

Referenced by CFlatGatherer::x_GatherReferences().

◆ DisableDefaultIndex()

bool CFlatFileConfig::DisableDefaultIndex ( void ) const

inline

Definition at line 868 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate().

◆ DisableReferenceCache()

bool CFlatFileConfig::DisableReferenceCache ( void ) const

inline

Definition at line 864 of file flat_file_config.hpp.

Referenced by CFlatGatherer::x_DoMultipleSections(), and CFlatGatherer::x_GatherBioseq().

◆ DoHTML()

bool CFlatFileConfig::DoHTML ( void ) const

inline

Definition at line 795 of file flat_file_config.hpp.

◆ DoNotUseAutoDef()

bool CFlatFileConfig::DoNotUseAutoDef ( void ) const

inline

Definition at line 866 of file flat_file_config.hpp.

◆ DropBadCitGens()

bool CFlatFileConfig::DropBadCitGens ( void ) const

Definition at line 391 of file flat_file_config.cpp.

Referenced by s_FormatCitGen().

◆ DropBadDbxref()

bool CFlatFileConfig::DropBadDbxref ( void ) const

Definition at line 399 of file flat_file_config.cpp.

◆ DropIllegalQuals()

bool CFlatFileConfig::DropIllegalQuals ( void ) const

Definition at line 393 of file flat_file_config.cpp.

Referenced by CFeatureItem::x_AddQualProtEcNumber(), and CFeatureItem::x_AddQualsRna().

◆ DropShortAA()

bool CFlatFileConfig::DropShortAA ( void ) const

Definition at line 388 of file flat_file_config.cpp.

◆ ExpandGaps()

bool CFlatFileConfig::ExpandGaps ( void ) const

inline

Definition at line 853 of file flat_file_config.hpp.

Referenced by CGenbankFormatter::FormatSequence().

◆ FasterReleaseSets()

bool CFlatFileConfig::FasterReleaseSets ( void ) const

inline

Definition at line 857 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate().

◆ FavorFarFeatures()

bool CFlatFileConfig::FavorFarFeatures ( void ) const

inline

Definition at line 816 of file flat_file_config.hpp.

◆ ForGBRelease()

bool CFlatFileConfig::ForGBRelease ( void ) const

Definition at line 408 of file flat_file_config.cpp.

Referenced by CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

◆ FrequencyToNote()

bool CFlatFileConfig::FrequencyToNote ( void ) const

Definition at line 403 of file flat_file_config.cpp.

◆ FromArguments()

void CFlatFileConfig::FromArguments ( const CArgs & args )

Definition at line 1056 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

Definition at line 862 of file flat_file_config.hpp.

Referenced by s_SkipFeature().

◆ GeoLocNameCountry()

bool CFlatFileConfig::GeoLocNameCountry ( void ) const

inline

Definition at line 869 of file flat_file_config.hpp.

◆ GetAllGenbankStrings()

const vector< string > & CFlatFileConfig::GetAllGenbankStrings ( void )

static

Definition at line 479 of file flat_file_config.cpp.

References set< Key, Compare >::begin(), copy(), set< Key, Compare >::end(), set< Key, Compare >::insert(), and ITERATE.

Referenced by AddArgumentDescriptions().

◆ GetCanceledCallback()

const ICanceled* CFlatFileConfig::GetCanceledCallback ( void ) const

inline

Definition at line 714 of file flat_file_config.hpp.

References m_pCanceledCallback.

Referenced by CFlatFileGenerator::Generate().

◆ GetCustom()

const TCustom& CFlatFileConfig::GetCustom ( void ) const

inline

Definition at line 618 of file flat_file_config.hpp.

References m_Custom.

◆ GetFeatDepth()

int CFlatFileConfig::GetFeatDepth ( void ) const

inline

Definition at line 670 of file flat_file_config.hpp.

References m_FeatDepth.

Referenced by CFlatFileGenerator::Generate().

◆ GetFlags()

const TFlags& CFlatFileConfig::GetFlags ( void ) const

inline

Definition at line 518 of file flat_file_config.hpp.

References m_Flags.

◆ GetFormat()

const TFormat& CFlatFileConfig::GetFormat ( void ) const

inline

Definition at line 417 of file flat_file_config.hpp.

References m_Format.

Referenced by CFlatFileGenerator::Generate(), CFlatFileGenerator::GetSeqFeatText(), and s_FormatPatent().

◆ GetGapDepth()

int CFlatFileConfig::GetGapDepth ( void ) const

inline

Definition at line 673 of file flat_file_config.hpp.

References m_GapDepth.

Referenced by CFlatFileGenerator::Generate().

◆ GetGenbankBlockCallback()

CRef<CGenbankBlockCallback> CFlatFileConfig::GetGenbankBlockCallback ( void ) const

inline

Definition at line 708 of file flat_file_config.hpp.

References m_GenbankBlockCallback.

Referenced by CGenbankGatherer::x_DoSingleSection().

◆ GetHTMLFormatter()

const IHTMLFormatter& CFlatFileConfig::GetHTMLFormatter ( ) const

inline

Definition at line 410 of file flat_file_config.hpp.

References m_html_formatter.

Referenced by CGenbankFormatter::FormatSequence(), s_GetLinkFeatureKey(), CDBSourceItem::x_FormatDBSourceID(), and CGenbankFormatter::x_FormatOrganismLine().

◆ GetMode()

const TMode& CFlatFileConfig::GetMode ( void ) const

inline

Definition at line 440 of file flat_file_config.hpp.

References m_Mode.

Referenced by s_FormatPatent().

◆ GetPolicy()

const TPolicy& CFlatFileConfig::GetPolicy ( void ) const

inline

Definition at line 498 of file flat_file_config.hpp.

References m_Policy.

◆ GetSingleAccession()

const string& CFlatFileConfig::GetSingleAccession ( void ) const

inline

Definition at line 668 of file flat_file_config.hpp.

References m_SingleAccession.

Referenced by CFlatFileGenerator::Generate().

◆ GetStyle()

const TStyle& CFlatFileConfig::GetStyle ( void ) const

inline

Definition at line 454 of file flat_file_config.hpp.

References m_Style.

◆ GetView()

const TView& CFlatFileConfig::GetView ( void ) const

inline

Definition at line 468 of file flat_file_config.hpp.

References m_View.

◆ GoQualsEachMerge()

bool CFlatFileConfig::GoQualsEachMerge ( void ) const

Definition at line 411 of file flat_file_config.cpp.

Referenced by CFeatureItem::x_FormatQuals().

◆ GoQualsToNote()

bool CFlatFileConfig::GoQualsToNote ( void ) const

Definition at line 422 of file flat_file_config.cpp.

References false, m_Mode, m_RefSeqConventions, and sm_ModeFlags.

Referenced by CFeatureItem::x_FormatQuals().

◆ HideBankItComment()

bool CFlatFileConfig::HideBankItComment ( void ) const

Definition at line 401 of file flat_file_config.cpp.

◆ HideCDDFeatures()

bool CFlatFileConfig::HideCDDFeatures ( void ) const

inline

Definition at line 805 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate(), s_SetSelection(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ HideCDSProdFeatures()

bool CFlatFileConfig::HideCDSProdFeatures ( void ) const

inline

Definition at line 804 of file flat_file_config.hpp.

Referenced by CFlatGatherer::x_GetFeatsOnCdsProduct(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ HideEmptySource()

bool CFlatFileConfig::HideEmptySource ( void ) const

Definition at line 405 of file flat_file_config.cpp.

Referenced by CFlatGatherer::x_GatherSourceFeatures().

◆ HideExonFeatures()

bool CFlatFileConfig::HideExonFeatures ( void ) const

inline

Definition at line 798 of file flat_file_config.hpp.

Referenced by s_SetSelection(), and s_SkipFeature().

◆ HideGapFeatures()

bool CFlatFileConfig::HideGapFeatures ( void ) const

inline

Definition at line 823 of file flat_file_config.hpp.

Referenced by s_SetSelection().

◆ HideGeneRIFs()

bool CFlatFileConfig::HideGeneRIFs ( void ) const

inline

Definition at line 802 of file flat_file_config.hpp.

Referenced by s_FilterPubdesc().

◆ HideGI()

bool CFlatFileConfig::HideGI ( void ) const

inline

Definition at line 851 of file flat_file_config.hpp.

Referenced by CGenbankFormatter::FormatVersion(), CFeatureItem::x_AddProductIdQuals(), and CFeatureItem::x_AddQualProteinId().

◆ HideImpFeatures()

bool CFlatFileConfig::HideImpFeatures ( void ) const

inline

Definition at line 796 of file flat_file_config.hpp.

Referenced by s_SetSelection(), and s_SkipFeature().

◆ HideIntronFeatures()

bool CFlatFileConfig::HideIntronFeatures ( void ) const

inline

Definition at line 799 of file flat_file_config.hpp.

Referenced by s_SetSelection(), and s_SkipFeature().

◆ HideMiscFeatures()

bool CFlatFileConfig::HideMiscFeatures ( void ) const

inline

Definition at line 800 of file flat_file_config.hpp.

Referenced by s_SetSelection(), and s_SkipFeature().

◆ HideProteinID()

bool CFlatFileConfig::HideProteinID ( void ) const

inline

Definition at line 850 of file flat_file_config.hpp.

Referenced by CFeatureItem::x_AddFTableCdregionQuals(), CFeatureItem::x_AddFTableQuals(), and CFeatureItem::x_AddFTableRnaQuals().

◆ HideRemoteImpFeatures()

bool CFlatFileConfig::HideRemoteImpFeatures ( void ) const

inline

Definition at line 801 of file flat_file_config.hpp.

Referenced by s_SetSelection(), and s_SkipFeature().

◆ HideSNPFeatures()

bool CFlatFileConfig::HideSNPFeatures ( void ) const

inline

Definition at line 797 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate(), and s_SetSelection().

◆ HideSourceFeatures()

bool CFlatFileConfig::HideSourceFeatures ( void ) const

inline

Definition at line 813 of file flat_file_config.hpp.

Referenced by CEmblGatherer::x_DoSingleSection(), and CGenbankGatherer::x_DoSingleSection().

◆ HideSpecificGeneMaps()

bool CFlatFileConfig::HideSpecificGeneMaps ( void ) const

Definition at line 413 of file flat_file_config.cpp.

◆ HideUnclassPartial()

bool CFlatFileConfig::HideUnclassPartial ( void ) const

Definition at line 409 of file flat_file_config.cpp.

◆ IgnoreExistingTitle()

bool CFlatFileConfig::IgnoreExistingTitle ( void ) const

inline

Definition at line 861 of file flat_file_config.hpp.

◆ IgnorePatPubs()

bool CFlatFileConfig::IgnorePatPubs ( void ) const

Definition at line 387 of file flat_file_config.cpp.

◆ IsFormatAGP()

bool CFlatFileConfig::IsFormatAGP ( void ) const

inline

Definition at line 424 of file flat_file_config.hpp.

References eFormat_AGP, and m_Format.

◆ IsFormatDDBJ()

bool CFlatFileConfig::IsFormatDDBJ ( void ) const

inline

Definition at line 420 of file flat_file_config.hpp.

References eFormat_DDBJ, and m_Format.

Referenced by s_SkipFeature().

◆ IsFormatEMBL()

bool CFlatFileConfig::IsFormatEMBL ( void ) const

inline

Definition at line 419 of file flat_file_config.hpp.

References eFormat_EMBL, and m_Format.

Referenced by s_FormatCitGen(), s_FormatJournal(), and CFlatItemFormatter::x_FormatRefJournal().

◆ IsFormatFTable()

bool CFlatFileConfig::IsFormatFTable ( void ) const

inline

Definition at line 423 of file flat_file_config.hpp.

References eFormat_FTable, and m_Format.

Referenced by CFlatGatherer::x_CollectBioSources(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), CFeatureItem::x_FormatQuals(), and CFlatGatherer::x_GatherBioseq().

◆ IsFormatGBSeq()

bool CFlatFileConfig::IsFormatGBSeq ( void ) const

inline

Definition at line 421 of file flat_file_config.hpp.

References eFormat_GBSeq, and m_Format.

Referenced by s_FormatJournal(), and CFeatureItem::x_AddQualsRna().

◆ IsFormatGenbank()

bool CFlatFileConfig::IsFormatGenbank ( void ) const

inline

Definition at line 418 of file flat_file_config.hpp.

References eFormat_GenBank, and m_Format.

Referenced by s_FormatCitGen(), s_FormatJournal(), and CFlatItemFormatter::x_FormatRefJournal().

◆ IsFormatINSDSeq()

bool CFlatFileConfig::IsFormatINSDSeq ( void ) const

inline

Definition at line 422 of file flat_file_config.hpp.

References eFormat_INSDSeq, and m_Format.

Referenced by s_FormatJournal(), and CFeatureItem::x_AddQualsRna().

◆ IsFormatLite()

bool CFlatFileConfig::IsFormatLite ( void ) const

inline

Definition at line 425 of file flat_file_config.hpp.

References eFormat_Lite, and m_Format.

Referenced by CGenbankGatherer::x_DoSingleSection().

◆ IsModeDump()

bool CFlatFileConfig::IsModeDump ( void ) const

inline

Definition at line 444 of file flat_file_config.hpp.

References eMode_Dump, and m_Mode.

Referenced by s_ShowBaseCount(), CFeatureItem::x_AddQualCdsProduct(), CFeatureItem::x_AddQualsRna(), CFlatGatherer::x_CollectBioSources(), CFlatGatherer::x_CollectBioSourcesOnBioseq(), CEmblGatherer::x_DoSingleSection(), CFlatGatherer::x_GatherSourceFeatures(), and CFlatGatherer::x_RefSeqComments().

◆ IsModeEntrez()

bool CFlatFileConfig::IsModeEntrez ( void ) const

inline

Definition at line 442 of file flat_file_config.hpp.

References eMode_Entrez, and m_Mode.

Referenced by CFlatItemFormatter::End(), CGenbankFormatter::EndSection(), CGenbankFormatter::FormatSequence(), CFlatItemFormatter::Start(), and CGenbankGatherer::x_DoSingleSection().

◆ IsModeGBench()

bool CFlatFileConfig::IsModeGBench ( void ) const

inline

Definition at line 443 of file flat_file_config.hpp.

References eMode_GBench, and m_Mode.

Referenced by s_ShowBaseCount(), CFeatureItem::x_AddQualsRna(), and CEmblGatherer::x_DoSingleSection().

◆ IsModeRelease()

bool CFlatFileConfig::IsModeRelease ( void ) const

inline

Definition at line 441 of file flat_file_config.hpp.

References eMode_Release, and m_Mode.

Referenced by CFlatGatherer::x_GatherBioseq().

◆ IsPolicyAdaptive()

bool CFlatFileConfig::IsPolicyAdaptive ( void ) const

inline

Definition at line 499 of file flat_file_config.hpp.

References ePolicy_Adaptive, and m_Policy.

◆ IsPolicyExhaustive()

bool CFlatFileConfig::IsPolicyExhaustive ( void ) const

inline

Definition at line 502 of file flat_file_config.hpp.

References ePolicy_Exhaustive, and m_Policy.

Referenced by CFlatFileGenerator::Generate().

◆ IsPolicyExternal()

bool CFlatFileConfig::IsPolicyExternal ( void ) const

inline

Definition at line 501 of file flat_file_config.hpp.

References ePolicy_External, and m_Policy.

Referenced by CFlatFileGenerator::Generate().

◆ IsPolicyFtp()

bool CFlatFileConfig::IsPolicyFtp ( void ) const

inline

Definition at line 503 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 505 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

Definition at line 500 of file flat_file_config.hpp.

References ePolicy_Internal, and m_Policy.

Referenced by CFlatFileGenerator::Generate(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ IsPolicyWeb()

bool CFlatFileConfig::IsPolicyWeb ( void ) const

inline

Definition at line 504 of file flat_file_config.hpp.

References ePolicy_Web, and m_Policy.

Referenced by CFlatFileGenerator::Generate().

◆ IsShownGenbankBlock()

bool CFlatFileConfig::IsShownGenbankBlock ( FGenbankBlocks fTGenbankBlocksMask ) const

inline

Definition at line 683 of file flat_file_config.hpp.

References m_fGenbankBlocks.

Referenced by CFlatGatherer::x_GatherSourceOrganism().

◆ IsStyleContig()

bool CFlatFileConfig::IsStyleContig ( void ) const

inline

Definition at line 458 of file flat_file_config.hpp.

References eStyle_Contig, and m_Style.

Referenced by CBioseqContext::DoContigStyle(), and CFlatGatherer::x_GatherBioseq().

◆ IsStyleMaster()

bool CFlatFileConfig::IsStyleMaster ( void ) const

inline

Definition at line 457 of file flat_file_config.hpp.

References eStyle_Master, and m_Style.

◆ IsStyleNormal()

bool CFlatFileConfig::IsStyleNormal ( void ) const

inline

Definition at line 455 of file flat_file_config.hpp.

References eStyle_Normal, and m_Style.

Referenced by CBioseqContext::DoContigStyle(), CFlatFileGenerator::Generate(), and CFlatGatherer::x_GatherBioseq().

◆ IsStyleSegment()

bool CFlatFileConfig::IsStyleSegment ( void ) const

inline

Definition at line 456 of file flat_file_config.hpp.

References eStyle_Segment, and m_Style.

Referenced by CFlatGatherer::x_GatherBioseq().

◆ IsViewAll()

bool CFlatFileConfig::IsViewAll ( void ) const

inline

Definition at line 471 of file flat_file_config.hpp.

References IsViewNuc(), and IsViewProt().

Referenced by CFlatFileGenerator::Generate(), and CGather_Iter::x_AddSeqEntryToStack().

◆ IsViewFirst()

bool CFlatFileConfig::IsViewFirst ( void ) const

inline

Definition at line 472 of file flat_file_config.hpp.

References fViewFirst, and m_View.

Referenced by CGather_Iter::x_AddSeqEntryToStack().

◆ IsViewNuc()

bool CFlatFileConfig::IsViewNuc ( void ) const

inline

Definition at line 469 of file flat_file_config.hpp.

References fViewNucleotides, and m_View.

Referenced by CFlatFileGenerator::Generate(), IsViewAll(), and CGather_Iter::x_AddSeqEntryToStack().

◆ IsViewProt()

bool CFlatFileConfig::IsViewProt ( void ) const

inline

Definition at line 470 of file flat_file_config.hpp.

References fViewProteins, and m_View.

Referenced by CFlatFileGenerator::Generate(), IsViewAll(), and CGather_Iter::x_AddSeqEntryToStack().

◆ IupacaaOnly()

bool CFlatFileConfig::IupacaaOnly ( void ) const

Definition at line 390 of file flat_file_config.cpp.

Referenced by CFeatureItem::x_AddQualsRna().

◆ LatestGeneRIFs()

bool CFlatFileConfig::LatestGeneRIFs ( void ) const

inline

Definition at line 806 of file flat_file_config.hpp.

Referenced by s_FilterPubdesc().

◆ LongLocusNames()

bool CFlatFileConfig::LongLocusNames ( void ) const

inline

Definition at line 852 of file flat_file_config.hpp.

Referenced by CGenbankFormatter::FormatLocus().

◆ NeedAtLeastOneRef()

bool CFlatFileConfig::NeedAtLeastOneRef ( void ) const

Definition at line 397 of file flat_file_config.cpp.

◆ NeedOrganismQual()

bool CFlatFileConfig::NeedOrganismQual ( void ) const

Definition at line 396 of file flat_file_config.cpp.

◆ NeedRequiredQuals()

bool CFlatFileConfig::NeedRequiredQuals ( void ) const

Definition at line 395 of file flat_file_config.cpp.

Referenced by s_SkipFeature().

◆ NeverTranslateCDS()

bool CFlatFileConfig::NeverTranslateCDS ( void ) const

inline

Definition at line 824 of file flat_file_config.hpp.

Referenced by CFeatureItem::x_AddQualTranslation().

◆ NoAffilOnUnpub()

bool CFlatFileConfig::NoAffilOnUnpub ( void ) const

Definition at line 392 of file flat_file_config.cpp.

Referenced by s_FormatCitGen().

◆ OldFeaturesOrder()

bool CFlatFileConfig::OldFeaturesOrder ( void ) const

inline

Definition at line 822 of file flat_file_config.hpp.

◆ OldTpaDisplay()

bool CFlatFileConfig::OldTpaDisplay ( void ) const

inline

Definition at line 867 of file flat_file_config.hpp.

◆ OnlyGeneRIFs()

bool CFlatFileConfig::OnlyGeneRIFs ( void ) const

inline

Definition at line 803 of file flat_file_config.hpp.

Referenced by s_FilterPubdesc().

◆ OnlyNearFeatures()

bool CFlatFileConfig::OnlyNearFeatures ( void ) const

inline

Definition at line 815 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate().

◆ SelenocysteineToNote()

bool CFlatFileConfig::SelenocysteineToNote ( void ) const

Definition at line 427 of file flat_file_config.cpp.

References false, m_Mode, m_RefSeqConventions, and sm_ModeFlags.

◆ SetAlwaysTranslateCDS()

CFlatFileConfig & CFlatFileConfig::SetAlwaysTranslateCDS ( bool val = true )

inline

Definition at line 814 of file flat_file_config.hpp.

◆ SetCanceledCallback()

void CFlatFileConfig::SetCanceledCallback ( ICanceled * pCallback )

inline

Definition at line 717 of file flat_file_config.hpp.

References m_pCanceledCallback.

Referenced by CFlatFileConfig(), and CFlatFileExportJob::Run().

◆ SetCopyCDSFromCDNA()

CFlatFileConfig & CFlatFileConfig::SetCopyCDSFromCDNA ( bool val = true )

inline

Definition at line 812 of file flat_file_config.hpp.

◆ SetCopyGeneToCDNA()

CFlatFileConfig & CFlatFileConfig::SetCopyGeneToCDNA ( bool val = true )

inline

Definition at line 810 of file flat_file_config.hpp.

◆ SetCustom()

void CFlatFileConfig::SetCustom ( const TCustom & custom )

inline

Definition at line 641 of file flat_file_config.hpp.

References m_Custom.

Referenced by FromArguments().

◆ SetDisableAnnotRefs()

CFlatFileConfig & CFlatFileConfig::SetDisableAnnotRefs ( bool val = true )

inline

Definition at line 858 of file flat_file_config.hpp.

◆ SetDisableDefaultIndex()

CFlatFileConfig & CFlatFileConfig::SetDisableDefaultIndex ( bool val = true )

inline

Definition at line 868 of file flat_file_config.hpp.

◆ SetDisableReferenceCache()

CFlatFileConfig & CFlatFileConfig::SetDisableReferenceCache ( bool val = true )

inline

Definition at line 864 of file flat_file_config.hpp.

◆ SetDoHTML()

CFlatFileConfig & CFlatFileConfig::SetDoHTML ( bool val = true )

inline

Definition at line 795 of file flat_file_config.hpp.

◆ SetDoNotUseAutoDef()

CFlatFileConfig & CFlatFileConfig::SetDoNotUseAutoDef ( bool val = true )

inline

Definition at line 866 of file flat_file_config.hpp.

◆ SetExpandGaps()

CFlatFileConfig & CFlatFileConfig::SetExpandGaps ( bool val = true )

inline

Definition at line 853 of file flat_file_config.hpp.

◆ SetFasterReleaseSets()

CFlatFileConfig & CFlatFileConfig::SetFasterReleaseSets ( bool val = true )

inline

Definition at line 857 of file flat_file_config.hpp.

◆ SetFavorFarFeatures()

CFlatFileConfig & CFlatFileConfig::SetFavorFarFeatures ( bool val = true )

inline

Definition at line 816 of file flat_file_config.hpp.

◆ SetFeatDepth()

void CFlatFileConfig::SetFeatDepth ( const int featDepth )

inline

Definition at line 671 of file flat_file_config.hpp.

References m_FeatDepth.

Referenced by FromArguments().

◆ SetFlags()

void CFlatFileConfig::SetFlags ( const TFlags & flags )

inline

Definition at line 583 of file flat_file_config.hpp.

References flags, and m_Flags.

Referenced by FromArguments().

◆ SetFormat()

void CFlatFileConfig::SetFormat ( const TFormat & format )

inline

Definition at line 428 of file flat_file_config.hpp.

References format, and m_Format.

Referenced by FromArguments().

◆ SetFormatAGP()

void CFlatFileConfig::SetFormatAGP ( void )

inline

Definition at line 435 of file flat_file_config.hpp.

References eFormat_AGP, and m_Format.

◆ SetFormatDDBJ()

void CFlatFileConfig::SetFormatDDBJ ( void )

inline

Definition at line 431 of file flat_file_config.hpp.

References eFormat_DDBJ, and m_Format.

◆ SetFormatEMBL()

void CFlatFileConfig::SetFormatEMBL ( void )

inline

Definition at line 430 of file flat_file_config.hpp.

References eFormat_EMBL, and m_Format.

◆ SetFormatFTable()

void CFlatFileConfig::SetFormatFTable ( void )

inline

Definition at line 434 of file flat_file_config.hpp.

References eFormat_FTable, and m_Format.

Referenced by C5ColExportJob::Run(), and s_Create5ColFeatTable().

◆ SetFormatGBSeq()

void CFlatFileConfig::SetFormatGBSeq ( void )

inline

Definition at line 432 of file flat_file_config.hpp.

References eFormat_GBSeq, and m_Format.

◆ SetFormatGenbank()

void CFlatFileConfig::SetFormatGenbank ( void )

inline

Definition at line 429 of file flat_file_config.hpp.

References eFormat_GenBank, and m_Format.

Referenced by CEditingActionFlatFile::Find(), CFlatFileField::GetVal(), and CId1FetchApp::LookUpGI().

◆ SetFormatINSDSeq()

void CFlatFileConfig::SetFormatINSDSeq ( void )

inline

Definition at line 433 of file flat_file_config.hpp.

References eFormat_INSDSeq, and m_Format.

◆ SetFormatLite()

void CFlatFileConfig::SetFormatLite ( void )

inline

Definition at line 436 of file flat_file_config.hpp.

References eFormat_Lite, and m_Format.

◆ SetGapDepth()

void CFlatFileConfig::SetGapDepth ( const int gapDepth )

inline

Definition at line 674 of file flat_file_config.hpp.

References m_GapDepth.

Referenced by FromArguments().

◆ SetGenbankBlockCallback()

void CFlatFileConfig::SetGenbankBlockCallback ( CGenbankBlockCallback * pGenbankBlockCallback )

inline

Definition at line 710 of file flat_file_config.hpp.

References m_GenbankBlockCallback.

Referenced by CFlatFileConfig(), and CSUCDataGenerator::GetSUCResults().

◆ SetGenbankBlocks()

void CFlatFileConfig::SetGenbankBlocks ( const TGenbankBlocks & genbank_blocks )

inline

Definition at line 677 of file flat_file_config.hpp.

References m_fGenbankBlocks.

Referenced by CFlatFileConfig(), and CSUCDataGenerator::GetSUCResults().

◆ SetGeneRNACDSFeatures()

CFlatFileConfig & CFlatFileConfig::SetGeneRNACDSFeatures ( bool val = true )

inline

Definition at line 862 of file flat_file_config.hpp.

◆ SetGeoLocNameCountry()

CFlatFileConfig & CFlatFileConfig::SetGeoLocNameCountry ( bool val = true )

inline

Definition at line 869 of file flat_file_config.hpp.

◆ SetHideCDDFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideCDDFeatures ( bool val = true )

inline

Definition at line 805 of file flat_file_config.hpp.

◆ SetHideCDSProdFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideCDSProdFeatures ( bool val = true )

inline

Definition at line 804 of file flat_file_config.hpp.

◆ SetHideExonFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideExonFeatures ( bool val = true )

inline

Definition at line 798 of file flat_file_config.hpp.

◆ SetHideGapFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideGapFeatures ( bool val = true )

inline

Definition at line 823 of file flat_file_config.hpp.

◆ SetHideGeneRIFs()

CFlatFileConfig & CFlatFileConfig::SetHideGeneRIFs ( bool val = true )

inline

Definition at line 802 of file flat_file_config.hpp.

◆ SetHideGI()

CFlatFileConfig & CFlatFileConfig::SetHideGI ( bool val = true )

inline

Definition at line 851 of file flat_file_config.hpp.

◆ SetHideImpFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideImpFeatures ( bool val = true )

inline

Definition at line 796 of file flat_file_config.hpp.

◆ SetHideIntronFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideIntronFeatures ( bool val = true )

inline

Definition at line 799 of file flat_file_config.hpp.

◆ SetHideMiscFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideMiscFeatures ( bool val = true )

inline

Definition at line 800 of file flat_file_config.hpp.

◆ SetHideProteinID()

CFlatFileConfig & CFlatFileConfig::SetHideProteinID ( bool val = true )

inline

Definition at line 850 of file flat_file_config.hpp.

Referenced by s_Create5ColFeatTable().

◆ SetHideRemoteImpFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideRemoteImpFeatures ( bool val = true )

inline

Definition at line 801 of file flat_file_config.hpp.

◆ SetHideSNPFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideSNPFeatures ( bool val = true )

inline

Definition at line 797 of file flat_file_config.hpp.

Referenced by CId1FetchApp::LookUpGI(), and CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ SetHideSourceFeatures()

CFlatFileConfig & CFlatFileConfig::SetHideSourceFeatures ( bool val = true )

inline

Definition at line 813 of file flat_file_config.hpp.

Referenced by s_Create5ColFeatTable().

◆ SetHTMLFormatter()

void CFlatFileConfig::SetHTMLFormatter ( CRef< IHTMLFormatter > html_fmt )

inline

Definition at line 406 of file flat_file_config.hpp.

References m_html_formatter.

Referenced by CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ SetIgnoreExistingTitle()

CFlatFileConfig & CFlatFileConfig::SetIgnoreExistingTitle ( bool val = true )

inline

Definition at line 861 of file flat_file_config.hpp.

◆ SetLatestGeneRIFs()

CFlatFileConfig & CFlatFileConfig::SetLatestGeneRIFs ( bool val = true )

inline

Definition at line 806 of file flat_file_config.hpp.

◆ SetLongLocusNames()

CFlatFileConfig & CFlatFileConfig::SetLongLocusNames ( bool val = true )

inline

Definition at line 852 of file flat_file_config.hpp.

◆ SetMode()

void CFlatFileConfig::SetMode ( const TMode & mode )

inline

Definition at line 446 of file flat_file_config.hpp.

References m_Mode.

Referenced by FromArguments(), CId1FetchApp::LookUpGI(), and CFlatFileExportJob::Run().

◆ SetModeDump()

void CFlatFileConfig::SetModeDump ( void )

inline

Definition at line 450 of file flat_file_config.hpp.

References eMode_Dump, and m_Mode.

◆ SetModeEntrez()

void CFlatFileConfig::SetModeEntrez ( void )

inline

Definition at line 448 of file flat_file_config.hpp.

References eMode_Entrez, and m_Mode.

◆ SetModeGBench()

void CFlatFileConfig::SetModeGBench ( void )

inline

Definition at line 449 of file flat_file_config.hpp.

References eMode_GBench, and m_Mode.

Referenced by CEditingActionFlatFile::Find(), and CFlatFileField::GetVal().

◆ SetModeRelease()

void CFlatFileConfig::SetModeRelease ( void )

inline

Definition at line 447 of file flat_file_config.hpp.

References eMode_Release, and m_Mode.

◆ SetNeverTranslateCDS()

CFlatFileConfig & CFlatFileConfig::SetNeverTranslateCDS ( bool val = true )

inline

Definition at line 824 of file flat_file_config.hpp.

Referenced by CConvertCdsWithGapsToMiscFeat::GetCommand(), and s_Render_SeqFeat().

◆ SetOldFeaturesOrder()

CFlatFileConfig & CFlatFileConfig::SetOldFeaturesOrder ( bool val = true )

inline

Definition at line 822 of file flat_file_config.hpp.

◆ SetOldTpaDisplay()

CFlatFileConfig & CFlatFileConfig::SetOldTpaDisplay ( bool val = true )

inline

Definition at line 867 of file flat_file_config.hpp.

◆ SetOnlyGeneRIFs()

CFlatFileConfig & CFlatFileConfig::SetOnlyGeneRIFs ( bool val = true )

inline

Definition at line 803 of file flat_file_config.hpp.

◆ SetOnlyNearFeatures()

CFlatFileConfig & CFlatFileConfig::SetOnlyNearFeatures ( bool val = true )

inline

Definition at line 815 of file flat_file_config.hpp.

◆ SetPolicy()

void CFlatFileConfig::SetPolicy ( const TPolicy & Policy )

inline

Definition at line 507 of file flat_file_config.hpp.

References m_Policy.

Referenced by FromArguments().

◆ SetPolicyAdaptive()

void CFlatFileConfig::SetPolicyAdaptive ( void )

inline

Definition at line 508 of file flat_file_config.hpp.

References ePolicy_Adaptive, and m_Policy.

◆ SetPolicyExhaustive()

void CFlatFileConfig::SetPolicyExhaustive ( void )

inline

Definition at line 511 of file flat_file_config.hpp.

References ePolicy_Exhaustive, and m_Policy.

◆ SetPolicyExternal()

void CFlatFileConfig::SetPolicyExternal ( void )

inline

Definition at line 510 of file flat_file_config.hpp.

References ePolicy_External, and m_Policy.

◆ SetPolicyFtp()

void CFlatFileConfig::SetPolicyFtp ( void )

inline

Definition at line 512 of file flat_file_config.hpp.

References ePolicy_Ftp, and m_Policy.

◆ SetPolicyGenomes()

void CFlatFileConfig::SetPolicyGenomes ( void )

inline

Definition at line 514 of file flat_file_config.hpp.

References ePolicy_Genomes, and m_Policy.

◆ SetPolicyInternal()

void CFlatFileConfig::SetPolicyInternal ( void )

inline

Definition at line 509 of file flat_file_config.hpp.

References ePolicy_Internal, and m_Policy.

◆ SetPolicyWeb()

void CFlatFileConfig::SetPolicyWeb ( void )

inline

Definition at line 513 of file flat_file_config.hpp.

References ePolicy_Web, and m_Policy.

◆ SetRefSeqConventions()

void CFlatFileConfig::SetRefSeqConventions ( void )

inline

Definition at line 880 of file flat_file_config.hpp.

References m_RefSeqConventions.

Referenced by CBioseqContext::x_Init().

◆ SetShowCDDFeatures()

CFlatFileConfig & CFlatFileConfig::SetShowCDDFeatures ( bool val = true )

inline

Definition at line 855 of file flat_file_config.hpp.

◆ SetShowContigAndSeq()

CFlatFileConfig & CFlatFileConfig::SetShowContigAndSeq ( bool val = true )

inline

Definition at line 809 of file flat_file_config.hpp.

◆ SetShowContigFeatures()

CFlatFileConfig & CFlatFileConfig::SetShowContigFeatures ( bool val = true )

inline

Definition at line 807 of file flat_file_config.hpp.

Referenced by CSUCDataGenerator::GetSUCResults(), CId1FetchApp::LookUpGI(), C5ColExportJob::Run(), CFlatFileExportJob::Run(), and s_Create5ColFeatTable().

◆ SetShowContigInMaster()

CFlatFileConfig & CFlatFileConfig::SetShowContigInMaster ( bool val = true )

inline

Definition at line 811 of file flat_file_config.hpp.

◆ SetShowContigSources()

CFlatFileConfig & CFlatFileConfig::SetShowContigSources ( bool val = true )

inline

Definition at line 808 of file flat_file_config.hpp.

Referenced by CSUCDataGenerator::GetSUCResults(), CId1FetchApp::LookUpGI(), C5ColExportJob::Run(), CFlatFileExportJob::Run(), and s_Create5ColFeatTable().

◆ SetShowDebugTiming()

CFlatFileConfig & CFlatFileConfig::SetShowDebugTiming ( bool val = true )

inline

Definition at line 856 of file flat_file_config.hpp.

◆ SetShowDeflineModifiers()

CFlatFileConfig & CFlatFileConfig::SetShowDeflineModifiers ( bool val = true )

inline

Definition at line 865 of file flat_file_config.hpp.

◆ SetShowFarTranslations()

CFlatFileConfig & CFlatFileConfig::SetShowFarTranslations ( bool val = true )

inline

Definition at line 817 of file flat_file_config.hpp.

◆ SetShowFtablePeptides()

CFlatFileConfig & CFlatFileConfig::SetShowFtablePeptides ( bool val = true )

inline

Definition at line 863 of file flat_file_config.hpp.

Referenced by s_Create5ColFeatTable().

◆ SetShowFtableRefs()

CFlatFileConfig & CFlatFileConfig::SetShowFtableRefs ( bool val = true )

inline

Definition at line 821 of file flat_file_config.hpp.

◆ SetShowPeptides()

CFlatFileConfig & CFlatFileConfig::SetShowPeptides ( bool val = true )

inline

Definition at line 820 of file flat_file_config.hpp.

Referenced by s_Create5ColFeatTable().

◆ SetShowSeqSpans()

CFlatFileConfig & CFlatFileConfig::SetShowSeqSpans ( bool val = true )

inline

Definition at line 825 of file flat_file_config.hpp.

◆ SetShowSNPFeatures()

CFlatFileConfig & CFlatFileConfig::SetShowSNPFeatures ( bool val = true )

inline

Definition at line 854 of file flat_file_config.hpp.

◆ SetShowTranscript()

CFlatFileConfig & CFlatFileConfig::SetShowTranscript ( bool val = true )

inline

Definition at line 819 of file flat_file_config.hpp.

◆ SetSingleAccession()

void CFlatFileConfig::SetSingleAccession ( const string & accn )

inline

Definition at line 667 of file flat_file_config.hpp.

References m_SingleAccession.

Referenced by FromArguments().

◆ SetStyle()

void CFlatFileConfig::SetStyle ( const TStyle & style )

inline

Definition at line 460 of file flat_file_config.hpp.

References m_Style.

Referenced by FromArguments().

◆ SetStyleContig()

void CFlatFileConfig::SetStyleContig ( void )

inline

Definition at line 464 of file flat_file_config.hpp.

References eStyle_Contig, and m_Style.

◆ SetStyleMaster()

void CFlatFileConfig::SetStyleMaster ( void )

inline

Definition at line 463 of file flat_file_config.hpp.

References eStyle_Master, and m_Style.

Referenced by CFlatFileGenerator::Generate().

◆ SetStyleNormal()

void CFlatFileConfig::SetStyleNormal ( void )

inline

Definition at line 461 of file flat_file_config.hpp.

References eStyle_Normal, and m_Style.

Referenced by CEditingActionFlatFile::Find(), and CFlatFileField::GetVal().

◆ SetStyleSegment()

void CFlatFileConfig::SetStyleSegment ( void )

inline

Definition at line 462 of file flat_file_config.hpp.

References eStyle_Segment, and m_Style.

◆ SetTranslateIfNoProduct()

CFlatFileConfig & CFlatFileConfig::SetTranslateIfNoProduct ( bool val = true )

inline

Definition at line 818 of file flat_file_config.hpp.

◆ SetUseAutoDef()

CFlatFileConfig & CFlatFileConfig::SetUseAutoDef ( bool val = true )

inline

Definition at line 860 of file flat_file_config.hpp.

◆ SetUseSeqEntryIndexer()

CFlatFileConfig & CFlatFileConfig::SetUseSeqEntryIndexer ( bool val = true )

inline

Definition at line 859 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate().

◆ SetView()

void CFlatFileConfig::SetView ( const TView & view )

inline

Definition at line 474 of file flat_file_config.hpp.

References m_View.

Referenced by FromArguments().

◆ SetViewAll()

void CFlatFileConfig::SetViewAll ( void )

inline

Definition at line 483 of file flat_file_config.hpp.

References fViewAll, and m_View.

Referenced by s_Create5ColFeatTable(), and CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ SetViewFirst()

void CFlatFileConfig::SetViewFirst ( bool enabled )

inline

Definition at line 487 of file flat_file_config.hpp.

References fViewFirst, and m_View.

◆ SetViewNuc()

void CFlatFileConfig::SetViewNuc ( void )

inline

Definition at line 475 of file flat_file_config.hpp.

References fViewAll, fViewNucleotides, and m_View.

Referenced by s_Create5ColFeatTable(), and CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ SetViewProt()

void CFlatFileConfig::SetViewProt ( void )

inline

Definition at line 479 of file flat_file_config.hpp.

References fViewAll, fViewProteins, and m_View.

Referenced by CId1FetchApp::LookUpGI(), and CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ ShowCDDFeatures()

bool CFlatFileConfig::ShowCDDFeatures ( void ) const

inline

Definition at line 855 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate(), and CFlatGatherer::x_GetFeatsOnCdsProductIdx().

◆ ShowContigAndSeq()

bool CFlatFileConfig::ShowContigAndSeq ( void ) const

inline

Definition at line 809 of file flat_file_config.hpp.

Referenced by CGenbankGatherer::x_DoSingleSection(), and CGenbankFormatter::x_LocusHtmlPrefix().

◆ ShowContigFeatures()

bool CFlatFileConfig::ShowContigFeatures ( void ) const

inline

Definition at line 807 of file flat_file_config.hpp.

Referenced by s_SetSelection(), and CGenbankGatherer::x_DoSingleSection().

◆ ShowContigInMaster()

bool CFlatFileConfig::ShowContigInMaster ( void ) const

inline

Definition at line 811 of file flat_file_config.hpp.

◆ ShowContigSources()

bool CFlatFileConfig::ShowContigSources ( void ) const

inline

Definition at line 808 of file flat_file_config.hpp.

Referenced by CFlatGatherer::x_CollectBioSourcesOnBioseq().

◆ ShowDebugTiming()

bool CFlatFileConfig::ShowDebugTiming ( void ) const

inline

Definition at line 856 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate().

◆ ShowDeflineModifiers()

bool CFlatFileConfig::ShowDeflineModifiers ( void ) const

inline

Definition at line 865 of file flat_file_config.hpp.

◆ ShowFarTranslations()

bool CFlatFileConfig::ShowFarTranslations ( void ) const

inline

Definition at line 817 of file flat_file_config.hpp.

Referenced by CFeatureItem::x_GetAssociatedProtInfo(), and CFeatureItem::x_GetAssociatedProtInfoIdx().

◆ ShowFtablePeptides()

bool CFlatFileConfig::ShowFtablePeptides ( void ) const

inline

Definition at line 863 of file flat_file_config.hpp.

Referenced by CFlatGatherer::x_GatherBioseq().

◆ ShowFtableRefs()

bool CFlatFileConfig::ShowFtableRefs ( void ) const

inline

Definition at line 821 of file flat_file_config.hpp.

◆ ShowGenbankBlock()

void CFlatFileConfig::ShowGenbankBlock ( FGenbankBlocks fTGenbankBlocksMask )

inline

Definition at line 689 of file flat_file_config.hpp.

References m_fGenbankBlocks.

◆ ShowOutOfBoundsFeats()

bool CFlatFileConfig::ShowOutOfBoundsFeats ( void ) const

Definition at line 412 of file flat_file_config.cpp.

◆ ShowPeptides()

bool CFlatFileConfig::ShowPeptides ( void ) const

inline

Definition at line 820 of file flat_file_config.hpp.

◆ ShowSeqSpans()

bool CFlatFileConfig::ShowSeqSpans ( void ) const

inline

Definition at line 825 of file flat_file_config.hpp.

Referenced by s_FormatRegularSequencePiece().

◆ ShowSNPFeatures()

bool CFlatFileConfig::ShowSNPFeatures ( void ) const

inline

Definition at line 854 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate(), and CAsn2FlatApp::x_CreateFlatFileGenerator().

◆ ShowTranscript()

bool CFlatFileConfig::ShowTranscript ( void ) const

inline

Definition at line 819 of file flat_file_config.hpp.

Referenced by CFeatureItem::x_AddQualsRna().

◆ SkipGenbankBlock()

void CFlatFileConfig::SkipGenbankBlock ( FGenbankBlocks fTGenbankBlocksMask )

inline

Definition at line 696 of file flat_file_config.hpp.

References m_fGenbankBlocks.

Referenced by CEditingActionFlatFile::Find(), and CFlatFileField::GetVal().

◆ SrcQualsToNote()

bool CFlatFileConfig::SrcQualsToNote ( void ) const

Definition at line 417 of file flat_file_config.cpp.

References false, m_Mode, m_RefSeqConventions, and sm_ModeFlags.

◆ StringToGenbankBlock()

CFlatFileConfig::FGenbankBlocks CFlatFileConfig::StringToGenbankBlock ( const string & str )

static

Definition at line 468 of file flat_file_config.cpp.

References str().

◆ SuppressLocalId()

bool CFlatFileConfig::SuppressLocalId ( void ) const

Definition at line 385 of file flat_file_config.cpp.

Referenced by CGather_Iter::x_IsBioseqHandleOkay().

◆ ThrowIfCanceled()

void CFlatFileConfig::ThrowIfCanceled ( void ) const

inline

This throws a CFlatException if flatfile generation cancellation has been requested via ICanceled.

Definition at line 729 of file flat_file_config.hpp.

References ICanceled::IsCanceled(), m_pCanceledCallback, and x_ThrowHaltNow().

Referenced by CBioseqContext::ThrowIfCanceled().

◆ TranslateIfNoProduct()

bool CFlatFileConfig::TranslateIfNoProduct ( void ) const

inline

Definition at line 818 of file flat_file_config.hpp.

Referenced by CFeatureItem::x_AddQualTranslation().

◆ UseAutoDef()

bool CFlatFileConfig::UseAutoDef ( void ) const

inline

Definition at line 860 of file flat_file_config.hpp.

◆ UseEmblMolType()

bool CFlatFileConfig::UseEmblMolType ( void ) const

Definition at line 400 of file flat_file_config.cpp.

◆ UseSeqEntryIndexer()

bool CFlatFileConfig::UseSeqEntryIndexer ( void ) const

inline

Definition at line 859 of file flat_file_config.hpp.

Referenced by CFlatFileGenerator::Generate(), CFlatGatherer::x_GatherFeatures(), and CFlatGatherer::x_GatherFeaturesIdx().

◆ ValidateFeatures()

bool CFlatFileConfig::ValidateFeatures ( void ) const

Definition at line 386 of file flat_file_config.cpp.

Referenced by s_SkipFeature().

◆ x_ThrowHaltNow()

void CFlatFileConfig::x_ThrowHaltNow ( void ) const

private

Definition at line 500 of file flat_file_config.cpp.

References NCBI_THROW.

Referenced by ThrowIfCanceled().

Member Data Documentation

◆ m_BasicCleanup

bool CFlatFileConfig::m_BasicCleanup

private

Definition at line 760 of file flat_file_config.hpp.

Referenced by BasicCleanup(), and FromArguments().

◆ m_Custom

TCustom CFlatFileConfig::m_Custom

private

Definition at line 761 of file flat_file_config.hpp.

Referenced by GetCustom(), and SetCustom().

◆ m_FeatDepth

int CFlatFileConfig::m_FeatDepth

private

Definition at line 762 of file flat_file_config.hpp.

Referenced by CFlatFileConfig(), GetFeatDepth(), and SetFeatDepth().

◆ m_fGenbankBlocks

TGenbankBlocks CFlatFileConfig::m_fGenbankBlocks

private

Definition at line 757 of file flat_file_config.hpp.

Referenced by FromArguments(), IsShownGenbankBlock(), SetGenbankBlocks(), ShowGenbankBlock(), and SkipGenbankBlock().

◆ m_Flags

TFlags CFlatFileConfig::m_Flags

private

Definition at line 753 of file flat_file_config.hpp.

Referenced by GetFlags(), and SetFlags().

◆ m_Format

TFormat CFlatFileConfig::m_Format

private

Definition at line 750 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

Definition at line 763 of file flat_file_config.hpp.

Referenced by CFlatFileConfig(), GetGapDepth(), and SetGapDepth().

◆ m_GenbankBlockCallback

CRef<CGenbankBlockCallback> CFlatFileConfig::m_GenbankBlockCallback

private

Definition at line 758 of file flat_file_config.hpp.

Referenced by GetGenbankBlockCallback(), and SetGenbankBlockCallback().

◆ m_html_formatter

CRef<IHTMLFormatter> CFlatFileConfig::m_html_formatter

private

Definition at line 765 of file flat_file_config.hpp.

Referenced by CFlatFileConfig(), GetHTMLFormatter(), and SetHTMLFormatter().

◆ m_Mode

TMode CFlatFileConfig::m_Mode

private

Definition at line 751 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

const ICanceled* CFlatFileConfig::m_pCanceledCallback

private

Definition at line 759 of file flat_file_config.hpp.

Referenced by GetCanceledCallback(), SetCanceledCallback(), and ThrowIfCanceled().

◆ m_Policy

TPolicy CFlatFileConfig::m_Policy

private

Definition at line 755 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

Definition at line 756 of file flat_file_config.hpp.

Referenced by CFlatFileConfig(), CodonRecognizedToNote(), GoQualsToNote(), SelenocysteineToNote(), SetRefSeqConventions(), and SrcQualsToNote().

◆ m_SingleAccession

string CFlatFileConfig::m_SingleAccession

private

Definition at line 764 of file flat_file_config.hpp.

Referenced by GetSingleAccession(), and SetSingleAccession().

◆ m_Style

TStyle CFlatFileConfig::m_Style

private

Definition at line 752 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

Definition at line 754 of file flat_file_config.hpp.

Referenced by GetView(), IsViewFirst(), IsViewNuc(), IsViewProt(), SetView(), SetViewAll(), SetViewFirst(), SetViewNuc(), and SetViewProt().

◆ sm_ModeFlags

const bool CFlatFileConfig::sm_ModeFlags

staticprivate

Definition at line 745 of file flat_file_config.hpp.

Referenced by CodonRecognizedToNote(), GoQualsToNote(), SelenocysteineToNote(), and SrcQualsToNote().

◆ SMARTFEATLIMIT

const size_t CFlatFileConfig::SMARTFEATLIMIT = 1000000

static

Definition at line 741 of file flat_file_config.hpp.

Referenced by CGenbankGatherer::x_DoSingleSection().

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

Private Attributes
TFormat	m_Format

TMode	m_Mode

TStyle	m_Style

TFlags	m_Flags

TView	m_View

TPolicy	m_Policy

bool	m_RefSeqConventions

TGenbankBlocks	m_fGenbankBlocks

CRef< CGenbankBlockCallback >	m_GenbankBlockCallback

const ICanceled *	m_pCanceledCallback

bool	m_BasicCleanup

TCustom	m_Custom

int	m_FeatDepth

int	m_GapDepth

string	m_SingleAccession

CRef< IHTMLFormatter >	m_html_formatter

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ TCustom

◆ TFlags

◆ TFormat

◆ TGenbankBlocks

◆ TMode

◆ TPolicy

◆ TStyle

◆ TView

Member Enumeration Documentation

◆ ECustom

◆ EFlags

◆ EFormat

◆ EMode

◆ EPolicy

◆ EStyle

◆ EView

◆ FGenbankBlocks

Constructor & Destructor Documentation

◆ CFlatFileConfig()

◆ ~CFlatFileConfig()

Member Function Documentation

◆ AddArgumentDescriptions()

◆ AlwaysTranslateCDS()

◆ AvoidLocusColl()

◆ BasicCleanup() [1/2]

◆ BasicCleanup() [2/2]

◆ CheckCDSProductId()

◆ CheckQualSyntax()

◆ CitArtIsoJta()

◆ CodonRecognizedToNote()

◆ CopyCDSFromCDNA()

◆ CopyGeneToCDNA()

◆ DisableAnnotRefs()

◆ DisableDefaultIndex()

◆ DisableReferenceCache()

◆ DoHTML()

◆ DoNotUseAutoDef()

◆ DropBadCitGens()

◆ DropBadDbxref()

◆ DropIllegalQuals()

◆ DropShortAA()

◆ ExpandGaps()

◆ FasterReleaseSets()

◆ FavorFarFeatures()

◆ ForGBRelease()

◆ FrequencyToNote()

◆ FromArguments()

◆ GeneRNACDSFeatures()

◆ GeoLocNameCountry()

◆ GetAllGenbankStrings()

◆ GetCanceledCallback()

◆ GetCustom()

◆ GetFeatDepth()

◆ GetFlags()

◆ GetFormat()

◆ GetGapDepth()

◆ GetGenbankBlockCallback()

◆ GetHTMLFormatter()

◆ GetMode()

◆ GetPolicy()

◆ GetSingleAccession()

◆ GetStyle()

◆ GetView()

◆ GoQualsEachMerge()

◆ GoQualsToNote()

◆ HideBankItComment()

◆ HideCDDFeatures()

◆ HideCDSProdFeatures()

◆ HideEmptySource()

◆ HideExonFeatures()