NCBI C++ ToolKit
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CIdResolver Class Reference

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#include <objtools/import/id_resolver.hpp>

+ Inheritance diagram for CIdResolver:
+ Collaboration diagram for CIdResolver:

Public Member Functions

 CIdResolver ()
 
virtual ~CIdResolver ()
 
virtual CRef< CSeq_idoperator() (const string &) const
 
 CIdResolver (CScope &scope)
 
CSeq_id_Handle GetAccessionVersion (const string &identifier) 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
 

Private Member Functions

bool x_TryProcessLRG (const string &identifier, CSeq_id_Handle &idh) const
 
bool x_TryProcessGenomicLRG (const string &identifier, CSeq_id_Handle &idh) const
 
bool x_LooksLikeLRG (const string &identifier) const
 
bool x_LooksLikeCCDS (const string &identifier) const
 

Private Attributes

CScopem_Scope
 
unique_ptr< CRegexpm_LRGregex
 
unique_ptr< CRegexpm_CCDSregex
 
unique_ptr< CEntrez2Clientm_E2Client
 

Additional Inherited Members

- 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...
 
- 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 CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 43 of file id_resolver.hpp.

Constructor & Destructor Documentation

◆ CIdResolver() [1/2]

CIdResolver::CIdResolver ( )

Definition at line 43 of file id_resolver.cpp.

◆ ~CIdResolver()

CIdResolver::~CIdResolver ( )
virtual

Definition at line 49 of file id_resolver.cpp.

◆ CIdResolver() [2/2]

CIdResolver::CIdResolver ( CScope scope)

Definition at line 11 of file id_resolver.cpp.

Member Function Documentation

◆ GetAccessionVersion()

CSeq_id_Handle CIdResolver::GetAccessionVersion ( const string identifier) const

◆ operator()()

CRef< CSeq_id > CIdResolver::operator() ( const string rawId) const
virtual

Reimplemented in CIdResolverPrefix, and CIdResolverCanonical.

Definition at line 56 of file id_resolver.cpp.

◆ x_LooksLikeCCDS()

bool CIdResolver::x_LooksLikeCCDS ( const string identifier) const
private

Definition at line 201 of file id_resolver.cpp.

References m_CCDSregex.

◆ x_LooksLikeLRG()

bool CIdResolver::x_LooksLikeLRG ( const string identifier) const
private

Definition at line 195 of file id_resolver.cpp.

References m_LRGregex.

Referenced by x_TryProcessGenomicLRG().

◆ x_TryProcessGenomicLRG()

bool CIdResolver::x_TryProcessGenomicLRG ( const string identifier,
CSeq_id_Handle idh 
) const
private

◆ x_TryProcessLRG()

bool CIdResolver::x_TryProcessLRG ( const string identifier,
CSeq_id_Handle idh 
) const
private

Member Data Documentation

◆ m_CCDSregex

unique_ptr<CRegexp> CIdResolver::m_CCDSregex
private

Definition at line 26 of file id_resolver.hpp.

Referenced by x_LooksLikeCCDS().

◆ m_E2Client

unique_ptr<CEntrez2Client> CIdResolver::m_E2Client
private

Definition at line 27 of file id_resolver.hpp.

◆ m_LRGregex

unique_ptr<CRegexp> CIdResolver::m_LRGregex
private

Definition at line 25 of file id_resolver.hpp.

Referenced by x_LooksLikeLRG(), and x_TryProcessLRG().

◆ m_Scope

CScope& CIdResolver::m_Scope
private

Definition at line 24 of file id_resolver.hpp.

Referenced by GetAccessionVersion(), x_TryProcessGenomicLRG(), and x_TryProcessLRG().


The documentation for this class was generated from the following files:
Modified on Mon Jun 17 05:04:44 2024 by modify_doxy.py rev. 669887