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NCBI C++ ToolKit: CBaseCountItem Class Reference
Search Toolkit Book for CBaseCountItem
#include <objtools/format/items/basecount_item.hpp>
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 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) virtual ~IFlatItem (void) 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...
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 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
} 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 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 void EnableDebugDump (bool on) 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...
CFlatItem (CBioseqContext *ctx=0) void x_SetObject (const CSerialObject &obj) void x_SetContext (CBioseqContext &ctx) void x_SetSkip (void) void x_SetExternal (void) virtual void DeleteThis (void) Virtual method "deleting" this object. More...
Definition at line 56 of file basecount_item.hpp.
◆ CBaseCountItem() ◆ Format() ◆ GetA() SIZE_TYPE CBaseCountItem::GetA ( void ) const inline ◆ GetC() SIZE_TYPE CBaseCountItem::GetC ( void ) const inline ◆ GetCounts() ◆ GetG() SIZE_TYPE CBaseCountItem::GetG ( void ) const inline ◆ GetItemType() ◆ GetOther() SIZE_TYPE CBaseCountItem::GetOther ( void ) const inline ◆ GetT() SIZE_TYPE CBaseCountItem::GetT ( void ) const inline ◆ x_GatherInfo()
Reimplemented from CFlatItem.
Definition at line 74 of file basecount_item.cpp.
References count, 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().
◆ m_A ◆ m_C ◆ m_G ◆ m_Other ◆ m_T
The documentation for this class was generated from the following files:
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