#include <objtools/format/embl_gather.hpp>

Inheritance diagram for CEmblGatherer:

Collaboration diagram for CEmblGatherer:

Public Member Functions
	CEmblGatherer (void)

virtual void	x_DoSingleSection (CBioseqContext &ctx) const

Public Member Functions inherited from CFlatGatherer
virtual void	Gather (CFlatFileContext &ctx, CFlatItemOStream &os, bool doNuc=true, bool doProt=true) const

virtual void	Gather (CFlatFileContext &ctx, CFlatItemOStream &os, const CSeq_entry_Handle &entry, CBioseq_Handle bsh, bool useSeqEntryIndexing, bool doNuc=true, bool doProt=true, bool fasterSets=false) const

virtual void	SetCanceledCallback (const ICanceled *pCanceledCallback)

virtual	~CFlatGatherer (void)

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CFlatGatherer
static CFlatGatherer *	New (CFlatFileConfig::TFormat format)

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Types inherited from CFlatGatherer
enum	EGenomeAnnotComment { eGenomeAnnotComment_No = 0 , eGenomeAnnotComment_Yes }

typedef CRange< TSeqPos >	TRange

typedef CBioseqContext::TReferences	TReferences

typedef CRef< CSourceFeatureItem >	TSFItem

typedef deque< TSFItem >	TSourceFeatSet

typedef vector< CRef< CCommentItem > >	TCommentVec

Protected Member Functions inherited from CFlatGatherer
	CFlatGatherer ()

CFlatItemOStream &	ItemOS (void) const

CBioseqContext &	Context (void) const

const CFlatFileConfig &	Config (void) const

vector< string > &	RefCache (void) const

virtual void	x_GatherSeqEntry (CFlatFileContext &ctx, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >(), bool doNuc=true, bool doProt=true) const

virtual void	x_GatherSeqEntry (CFlatFileContext &ctx, const CSeq_entry_Handle &entry, CBioseq_Handle bsh, bool useSeqEntryIndexing, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >(), bool doNuc=true, bool doProt=true) const

virtual void	x_GatherBioseq (const CBioseq_Handle &prev_seq, const CBioseq_Handle &this_seq, const CBioseq_Handle &next_seq, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >()) const

virtual void	x_DoMultipleSections (const CBioseq_Handle &seq) const

virtual CFeatureItem *	x_NewFeatureItem (const CMappedFeat &feat, CBioseqContext &ctx, const CSeq_loc *loc, CRef< feature::CFeatTree > ftree, CFeatureItem::EMapped mapped=CFeatureItem::eMapped_not_mapped, bool suppressAccession=false, CConstRef< CFeatureItem > parentFeatureItem=CConstRef< CFeatureItem >()) const

void	x_GatherSourceOrganism (void) const

void	x_GatherReferences (void) const

void	x_GatherReferences (const CSeq_loc &loc, TReferences &refs) const

void	x_GatherReferencesIdx (const CSeq_loc &loc, TReferences &refs) const

void	x_GatherCDSReferences (TReferences &refs) const

void	x_GatherFeatures (void) const

void	x_GatherFeaturesIdx (void) const

void	x_GetFeatsOnCdsProduct (const CSeq_feat &feat, CBioseqContext &ctx, CRef< CSeq_loc_Mapper > slice_mapper, CConstRef< CFeatureItem > cdsFeatureItem=CConstRef< CFeatureItem >()) const

void	x_GetFeatsOnCdsProductIdx (const CSeq_feat &feat, CBioseqContext &ctx, CRef< CSeq_loc_Mapper > slice_mapper, CConstRef< CFeatureItem > cdsFeatureItem=CConstRef< CFeatureItem >()) const

void	x_CopyCDSFromCDNA (const CSeq_feat &feat, CBioseqContext &ctx) const

bool	x_SkipFeature (const CSeq_feat &feat, const CBioseqContext &ctx) const

virtual void	x_GatherFeaturesOnLocation (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void	x_GatherFeaturesOnWholeLocationIdx (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void	x_GatherFeaturesOnWholeLocation (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void	x_GatherFeaturesOnRangeIdx (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void	x_GatherFeaturesOnRange (const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void	x_GatherSourceFeatures (void) const

void	x_CollectBioSources (TSourceFeatSet &srcs) const

void	x_CollectBioSourcesOnBioseq (const CBioseq_Handle &bh, const TRange &range, CBioseqContext &ctx, TSourceFeatSet &srcs) const

void	x_CollectSourceDescriptors (const CBioseq_Handle &bh, CBioseqContext &ctx, TSourceFeatSet &srcs) const

void	x_CollectSourceFeatures (const CBioseq_Handle &bh, const TRange &range, CBioseqContext &ctx, TSourceFeatSet &srcs) const

void	x_MergeEqualBioSources (TSourceFeatSet &srcs) const

bool	x_BiosourcesEqualForMergingPurposes (const CSourceFeatureItem &src1, const CSourceFeatureItem &src2) const

void	x_SubtractFromFocus (TSourceFeatSet &srcs) const

void	x_GatherAlignments (void) const

void	x_GatherComments (void) const

void	x_AddComment (CCommentItem *comment) const

void	x_AddGSDBComment (const CDbtag &dbtag, CBioseqContext &ctx) const

void	x_RemoveDupComments (void) const

void	x_RemoveExcessNewlines (void) const

void	x_FlushComments (void) const

void	x_UnverifiedComment (CBioseqContext &ctx) const

void	x_UnreviewedComment (CBioseqContext &ctx) const

void	x_AuthorizedAccessComment (CBioseqContext &ctx) const

void	x_MapComment (CBioseqContext &ctx) const

void	x_BasemodComment (CBioseqContext &ctx) const

void	x_IdComments (CBioseqContext &ctx, EGenomeAnnotComment eGenomeAnnotComment) const

void	x_RefSeqComments (CBioseqContext &ctx, EGenomeAnnotComment eGenomeAnnotComment) const

void	x_HistoryComments (CBioseqContext &ctx) const

void	x_RefSeqGenomeComments (CBioseqContext &ctx) const

void	x_WGSComment (CBioseqContext &ctx) const

void	x_TSAComment (CBioseqContext &ctx) const

void	x_TLSComment (CBioseqContext &ctx) const

void	x_GBBSourceComment (CBioseqContext &ctx) const

void	x_BarcodeComment (CBioseqContext &ctx) const

void	x_DescComments (CBioseqContext &ctx) const

void	x_MaplocComments (CBioseqContext &ctx) const

void	x_RegionComments (CBioseqContext &ctx) const

void	x_HTGSComments (CBioseqContext &ctx) const

void	x_AnnotComments (CBioseqContext &ctx) const

CConstRef< CUser_object >	x_PrepareAnnotDescStrucComment (CBioseqContext &ctx) const

CConstRef< CUser_object >	x_GetAnnotDescStrucCommentFromBioseqHandle (CBioseq_Handle bsh) const

void	x_FeatComments (CBioseqContext &ctx) const

void	x_NameComments (CBioseqContext &ctx) const

void	x_StructuredComments (CBioseqContext &ctx) const

void	x_UnorderedComments (CBioseqContext &ctx) const

void	x_GatherSequence (void) const

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Static Protected Member Functions inherited from CFlatGatherer
static void	x_GiveOneResidueIntervalsBogusFuzz (CSeq_loc &loc)

static void	x_RemoveBogusFuzzFromIntervals (CSeq_loc &loc)

Protected Attributes inherited from CFlatGatherer
CRef< CFlatItemOStream >	m_ItemOS

CRef< CFlatFileContext >	m_Context

CRef< CBioseqContext >	m_Current

TCommentVec	m_Comments

vector< string >	m_RefCache

CConstRef< CUser_object >	m_FirstGenAnnotSCAD

const ICanceled *	m_pCanceledCallback

CRef< feature::CFeatTree >	m_Feat_Tree

CSeq_entry_Handle	m_TopSEH

Detailed Description

Definition at line 45 of file embl_gather.hpp.

Constructor & Destructor Documentation

◆ CEmblGatherer()

CEmblGatherer::CEmblGatherer ( void )

Definition at line 61 of file embl_gather.cpp.

Member Function Documentation

◆ x_DoSingleSection()

void CEmblGatherer::x_DoSingleSection ( CBioseqContext & ctx ) const

virtual

Implements CFlatGatherer.

Definition at line 66 of file embl_gather.cpp.

References ctx, CFlatFileConfig::HideSourceFeatures(), CFlatFileConfig::IsModeDump(), CFlatFileConfig::IsModeGBench(), CFlatGatherer::ItemOS(), CConstRef< C, Locker >::Reset(), CFlatGatherer::x_GatherComments(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherReferences(), CFlatGatherer::x_GatherSequence(), and CFlatGatherer::x_GatherSourceFeatures().

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CEmblGatherer()

Member Function Documentation

◆ x_DoSingleSection()