Search Toolkit Book for CBaseCountItem

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

Inheritance diagram for CBaseCountItem:

Collaboration diagram for CBaseCountItem:

Public Member Functions
	CBaseCountItem (CBioseqContext &ctx)

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

void	GetCounts (SIZE_TYPE &a, SIZE_TYPE &c, SIZE_TYPE &g, SIZE_TYPE &t, SIZE_TYPE &other) const

SIZE_TYPE	GetA (void) const

SIZE_TYPE	GetC (void) const

SIZE_TYPE	GetG (void) const

SIZE_TYPE	GetT (void) const

SIZE_TYPE	GetOther (void) const

EItem	GetItemType () const override

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 Member Functions
void	x_GatherInfo (CBioseqContext &ctx) override

Private Attributes
TSeqPos	m_A

TSeqPos	m_C

TSeqPos	m_G

TSeqPos	m_T

TSeqPos	m_Other

Additional Inherited Members
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...

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 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...

Detailed Description

Definition at line 56 of file basecount_item.hpp.

Constructor & Destructor Documentation

◆ CBaseCountItem()

CBaseCountItem::CBaseCountItem ( CBioseqContext & ctx )

Definition at line 48 of file basecount_item.cpp.

References ctx.

Member Function Documentation

◆ Format()

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

overridevirtual

Implements CFlatItem.

Definition at line 60 of file basecount_item.cpp.

References IFormatter::FormatBasecount().

◆ GetA()

SIZE_TYPE CBaseCountItem::GetA ( void ) const

inline

Definition at line 64 of file basecount_item.hpp.

References m_A.

Referenced by CGenbankFormatter::FormatBasecount().

◆ GetC()

SIZE_TYPE CBaseCountItem::GetC ( void ) const

inline

Definition at line 65 of file basecount_item.hpp.

References m_C.

Referenced by CGenbankFormatter::FormatBasecount().

◆ GetCounts()

void CBaseCountItem::GetCounts	(	SIZE_TYPE &	a,
		SIZE_TYPE &	c,
		SIZE_TYPE &	g,
		SIZE_TYPE &	t,
		SIZE_TYPE &	other
	)		const

inline

Definition at line 80 of file basecount_item.hpp.

References a, g(), m_A, m_C, m_G, m_Other, m_T, and t.

◆ GetG()

SIZE_TYPE CBaseCountItem::GetG ( void ) const

inline

Definition at line 66 of file basecount_item.hpp.

References m_G.

Referenced by CGenbankFormatter::FormatBasecount().

◆ GetItemType()

IFlatItem::EItem CBaseCountItem::GetItemType ( void ) const

overridevirtual

Implements IFlatItem.

Definition at line 55 of file basecount_item.cpp.

References IFlatItem::eItem_BaseCount.

◆ GetOther()

SIZE_TYPE CBaseCountItem::GetOther ( void ) const

inline

Definition at line 68 of file basecount_item.hpp.

References m_Other.

Referenced by CGenbankFormatter::FormatBasecount().

◆ GetT()

SIZE_TYPE CBaseCountItem::GetT ( void ) const

inline

Definition at line 67 of file basecount_item.hpp.

References m_T.

Referenced by CGenbankFormatter::FormatBasecount().

◆ x_GatherInfo()

void CBaseCountItem::x_GatherInfo ( CBioseqContext & ctx )

overrideprivatevirtual

Reimplemented from CFlatItem.

Definition at line 74 of file basecount_item.cpp.

References ctx, CSeqVectorTypes::eCaseConversion_lower, CBioseq_Handle::eCoding_Iupac, ITERATE_SIMPLE, kMax_UChar, m_A, m_C, m_G, m_Other, m_T, min(), CSeqVector::size(), and CFlatItem::x_SetSkip().

Member Data Documentation

◆ m_A

TSeqPos CBaseCountItem::m_A

mutableprivate

Definition at line 75 of file basecount_item.hpp.

Referenced by GetA(), GetCounts(), and x_GatherInfo().

◆ m_C

TSeqPos CBaseCountItem::m_C

private

Definition at line 75 of file basecount_item.hpp.

Referenced by GetC(), GetCounts(), and x_GatherInfo().

◆ m_G

TSeqPos CBaseCountItem::m_G

private

Definition at line 75 of file basecount_item.hpp.

Referenced by GetCounts(), GetG(), and x_GatherInfo().

◆ m_Other

TSeqPos CBaseCountItem::m_Other

private

Definition at line 75 of file basecount_item.hpp.

Referenced by GetCounts(), GetOther(), and x_GatherInfo().

◆ m_T

TSeqPos CBaseCountItem::m_T

private

Definition at line 75 of file basecount_item.hpp.

Referenced by GetCounts(), GetT(), and x_GatherInfo().

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

include/objtools/format/items/basecount_item.hpp
src/objtools/format/basecount_item.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBaseCountItem()

Member Function Documentation

◆ Format()

◆ GetA()

◆ GetC()

◆ GetCounts()

◆ GetG()

◆ GetItemType()

◆ GetOther()

◆ GetT()

◆ x_GatherInfo()

Member Data Documentation

◆ m_A

◆ m_C

◆ m_G

◆ m_Other

◆ m_T