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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< Uint8TCounter
 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...
 
CObjectoperator= (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_MapperGetInstance (void)
 
static CConstRef< CSeq_idGetSeq_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_Treex_GetTree (CSeq_id::E_Choice type)
 
CSeq_id_Which_Treex_GetTree (const CSeq_id &id)
 
CSeq_id_Which_Treex_GetTree (const CSeq_id_Handle &idh)
 
 CSeq_id_Mapper (const CSeq_id_Mapper &)
 
CSeq_id_Mapperoperator= (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.


The documentation for this class was generated from the following files:
Modified on Mon May 20 05:00:03 2024 by modify_doxy.py rev. 669887