CSeq_id_Mapper Class Reference

Search Toolkit Book for CSeq_id_Mapper

#include <objects/seq/seq_id_mapper.hpp>

Inheritance diagram for CSeq_id_Mapper:

Collaboration diagram for CSeq_id_Mapper:

Public Types
enum	EDumpDetails { eCountTotalBytes , eDumpTotalBytes , eDumpStatistics , eDumpAllIds }
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
virtual	~CSeq_id_Mapper (void)
CSeq_id_Handle	GetGiHandle (TGi gi)
	Get seq-id handle. More...
CSeq_id_Handle	GetHandle (const CSeq_id &id, bool do_not_create=false)
bool	HaveMatchingHandles (const CSeq_id_Handle &id)
	Get the list of matching handles, do not create new handles. More...
void	GetMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set)
bool	HaveReverseMatch (const CSeq_id_Handle &id)
void	GetReverseMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set)
bool	HaveMatchingHandles (const CSeq_id_Handle &id, EAllowWeakMatch allow_weak_match)
void	GetMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set, EAllowWeakMatch allow_weak_match)
bool	HaveReverseMatch (const CSeq_id_Handle &id, EAllowWeakMatch allow_weak_match)
void	GetReverseMatchingHandles (const CSeq_id_Handle &id, TSeq_id_HandleSet &h_set, EAllowWeakMatch allow_weak_match)
void	GetMatchingHandlesStr (string sid, TSeq_id_HandleSet &h_set)
	Get the list of string-matching handles, do not create new handles. More...
size_t	Dump (CNcbiOstream &out, EDumpDetails details=eDumpTotalBytes) const
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

Static Public Member Functions
static CRef< CSeq_id_Mapper >	GetInstance (void)
static CConstRef< CSeq_id >	GetSeq_id (const CSeq_id_Handle &handle)
	Get seq-id for the given handle. 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)

Private Types
typedef vector< CRef< CSeq_id_Which_Tree > >	TTrees

Private Member Functions
	CSeq_id_Mapper (void)
bool	x_Match (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2)
bool	x_IsBetter (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2)
CSeq_id_Which_Tree &	x_GetTree (CSeq_id::E_Choice type)
CSeq_id_Which_Tree &	x_GetTree (const CSeq_id &id)
CSeq_id_Which_Tree &	x_GetTree (const CSeq_id_Handle &idh)
	CSeq_id_Mapper (const CSeq_id_Mapper &)
CSeq_id_Mapper &	operator= (const CSeq_id_Mapper &)

Private Attributes
TTrees	m_Trees
CMutex	m_IdMapMutex

Friends
class	CSeq_id_Handle
class	CSeq_id_Info

Additional Inherited Members
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 CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 72 of file seq_id_mapper.hpp.

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

• include/objects/seq/seq_id_mapper.hpp
• src/objects/seq/seq_id_mapper.cpp