NCBI C++ ToolKit
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Search Toolkit Book for CTestMapperSeqInfo
Public Member Functions | |
CTestMapperSeqInfo (void) | |
virtual TSeqType | GetSequenceType (const CSeq_id_Handle &idh) |
Get information about sequence type (nuc or prot). More... | |
virtual TSeqPos | GetSequenceLength (const CSeq_id_Handle &idh) |
Get sequence length or kInvalidSeqPos. More... | |
virtual void | CollectSynonyms (const CSeq_id_Handle &id, TSynonyms &synonyms) |
Collect all synonyms for the id including the id itself. More... | |
void | AddSeq (TGi gi, TSeqType seqtype, TSeqPos len) |
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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... | |
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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 Types | |
typedef map< TGi, TSeqType > | TTypeMap |
typedef map< TGi, TSeqPos > | TLenMap |
Private Attributes | |
TTypeMap | m_Types |
TLenMap | m_Lengths |
Additional Inherited Members | |
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typedef CSeq_loc_Mapper_Base::ESeqType | TSeqType |
typedef CSeq_loc_Mapper_Base::TSynonyms | TSynonyms |
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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... | |
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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... | |
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static void | EnableDebugDump (bool on) |
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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... | |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Definition at line 788 of file mapper_unit_test.cpp.
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private |
Definition at line 820 of file mapper_unit_test.cpp.
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private |
Definition at line 819 of file mapper_unit_test.cpp.
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inline |
Definition at line 791 of file mapper_unit_test.cpp.
Definition at line 812 of file mapper_unit_test.cpp.
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inlinevirtual |
Collect all synonyms for the id including the id itself.
Any derived class must add at least the original id to the collection.
Implements IMapper_Sequence_Info.
Definition at line 806 of file mapper_unit_test.cpp.
References set< Key, Compare >::insert().
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inlinevirtual |
Get sequence length or kInvalidSeqPos.
Implements IMapper_Sequence_Info.
Definition at line 799 of file mapper_unit_test.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::IsGi(), kInvalidSeqPos, and m_Lengths.
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inlinevirtual |
Get information about sequence type (nuc or prot).
Implements IMapper_Sequence_Info.
Definition at line 792 of file mapper_unit_test.cpp.
References map_checker< Container >::end(), CSeq_loc_Mapper_Base::eSeq_unknown, map_checker< Container >::find(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::IsGi(), and m_Types.
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private |
Definition at line 823 of file mapper_unit_test.cpp.
Referenced by AddSeq(), and GetSequenceLength().
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private |
Definition at line 822 of file mapper_unit_test.cpp.
Referenced by AddSeq(), and GetSequenceType().