Search Toolkit Book for CSourceFeatureItem

#include <objtools/format/items/feature_item.hpp>

Inheritance diagram for CSourceFeatureItem:

Collaboration diagram for CSourceFeatureItem:

Public Types
typedef CRange< TSeqPos >	TRange

Public Types inherited from IFlatItem
enum	EItem { eItem_None = 0 , eItem_StartSection , eItem_StartItem , eItem_HtmlAnchor , eItem_Head , eItem_Locus , eItem_Date , eItem_Defline , eItem_Accession , eItem_Version , eItem_Project , eItem_GenomeProject , eItem_DbSource , eItem_Keywords , eItem_Segment , eItem_Source , eItem_Reference , eItem_Cache , eItem_Comment , eItem_Primary , eItem_FeatHeader , eItem_SourceFeat , eItem_Feature , eItem_Gap , eItem_BaseCount , eItem_Origin , eItem_Sequence , eItem_Contig , eItem_Wgs , eItem_Tsa , eItem_Alignment , eItem_EndItem , eItem_EndSection , eItem_Slash }

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...

Public Member Functions
	CSourceFeatureItem (const CBioSource &src, TRange range, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree)

	CSourceFeatureItem (const CMappedFeat &feat, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree, const CSeq_loc *loc=nullptr)

void	SetObject (const CSerialObject &obj)

bool	WasDesc (void) const

const CBioSource &	GetSource (void) const

string	GetKey (void) const override

bool	IsFocus (void) const

bool	IsSynthetic (void) const

void	Subtract (const CSourceFeatureItem &other, CScope &scope)

void	SetLoc (const CSeq_loc &loc)

EItem	GetItemType () const override

Public Member Functions inherited from CFeatureItemBase
CConstRef< CFlatFeature >	Format (void) const

void	Format (IFormatter &formatter, IFlatTextOStream &text_os) const

bool	operator< (const CFeatureItemBase &f2) const

const CMappedFeat &	GetFeat (void) const

const CSeq_loc &	GetLoc (void) const

bool	IsSuppressAccession (void) const

Public Member Functions inherited from CFlatItem
bool	IsSetObject (void) const

const CSerialObject *	GetObject (void) const

CBioseqContext *	GetContext (void)

CBioseqContext *	GetContext (void) const

bool	Skip (void) const

bool	IsExternal (void) const

	~CFlatItem (void)

Public Member Functions inherited from IFlatItem
virtual	~IFlatItem (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

Private Types
typedef CQualContainer< ESourceQualifier >	TQuals

typedef TQuals::const_iterator	TQCI

typedef IFlatQVal::TFlags	TQualFlags

Private Member Functions
void	x_GatherInfo (CBioseqContext &ctx) override

void	x_AddQuals (CBioseqContext &ctx) override

void	x_AddQuals (const CBioSource &src, CBioseqContext &ctx) const

void	x_AddQuals (const COrg_ref &org, CBioseqContext &ctx) const

void	x_AddPcrPrimersQuals (const CBioSource &src, CBioseqContext &ctx) const

void	x_AddQual (ESourceQualifier slot, const IFlatQVal *value) const

void	x_FormatQuals (CFlatFeature &ff) const override

void	x_FormatGBNoteQuals (CFlatFeature &ff) const

void	x_FormatNoteQuals (CFlatFeature &ff) const

void	x_FormatQual (ESourceQualifier slot, const CTempString &name, CFlatFeature::TQuals &qvec, TQualFlags flags=0) const

void	x_FormatNoteQual (ESourceQualifier slot, const char *name, CFlatFeature::TQuals &qvec, TQualFlags flags=0) const

Private Attributes
bool	m_WasDesc

TQuals	m_Quals

bool	m_IsFocus

bool	m_IsSynthetic

CRef< feature::CFeatTree >	m_Feat_Tree

Additional Inherited Members
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 Member Functions inherited from CFeatureItemBase
	CFeatureItemBase (const CMappedFeat &feat, CBioseqContext &ctx, CRef< feature::CFeatTree > ftree, const CSeq_loc *loc=0, bool suppressAccession=false)

Protected Member Functions inherited from CFlatItem
	CFlatItem (CBioseqContext *ctx=0)

void	x_SetObject (const CSerialObject &obj)

void	x_SetContext (CBioseqContext &ctx)

void	x_SetSkip (void)

void	x_SetExternal (void)

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

Protected Attributes inherited from CFeatureItemBase
CMappedFeat	m_Feat

CRef< feature::CFeatTree >	m_Feat_Tree

CConstRef< CSeq_loc >	m_Loc

bool	m_SuppressAccession

Detailed Description

Definition at line 398 of file feature_item.hpp.

Member Typedef Documentation

◆ TQCI

typedef TQuals::const_iterator CSourceFeatureItem::TQCI

private

Definition at line 428 of file feature_item.hpp.

◆ TQualFlags

typedef IFlatQVal::TFlags CSourceFeatureItem::TQualFlags

private

Definition at line 429 of file feature_item.hpp.

◆ TQuals

typedef CQualContainer<ESourceQualifier> CSourceFeatureItem::TQuals

private

Definition at line 427 of file feature_item.hpp.

◆ TRange

typedef CRange<TSeqPos> CSourceFeatureItem::TRange

Definition at line 403 of file feature_item.hpp.

Constructor & Destructor Documentation

◆ CSourceFeatureItem() [1/2]

CSourceFeatureItem::CSourceFeatureItem	(	const CBioSource &	src,
		TRange	range,
		CBioseqContext &	ctx,
		CRef< feature::CFeatTree >	ftree
	)

◆ CSourceFeatureItem() [2/2]

CSourceFeatureItem::CSourceFeatureItem	(	const CMappedFeat &	feat,
		CBioseqContext &	ctx,
		CRef< feature::CFeatTree >	ftree,
		const CSeq_loc *	loc = `nullptr`
	)