NCBI C++ ToolKit
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Search Toolkit Book for CSeq_id_Giim_Tree
#include "seq_id_tree.hpp"
(Private to src/objects/seq
.)
Public Member Functions | |
CSeq_id_Giim_Tree (CSeq_id_Mapper *mapper) | |
~CSeq_id_Giim_Tree (void) | |
virtual bool | Empty (void) const |
virtual CSeq_id_Handle | FindInfo (const CSeq_id &id) const |
virtual CSeq_id_Handle | FindOrCreate (const CSeq_id &id) |
virtual void | FindMatchStr (const string &sid, TSeq_id_MatchList &id_list) const |
virtual size_t | Dump (CNcbiOstream &out, CSeq_id::E_Choice type, int details) const |
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CSeq_id_Which_Tree (CSeq_id_Mapper *mapper) | |
virtual | ~CSeq_id_Which_Tree (void) |
virtual CSeq_id_Handle | GetGiHandle (TGi gi) |
virtual void | DropInfo (const CSeq_id_Info *info) |
virtual bool | HaveMatch (const CSeq_id_Handle &id) const |
virtual void | FindMatch (const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) const |
virtual bool | Match (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const |
virtual bool | IsBetterVersion (const CSeq_id_Handle &h1, const CSeq_id_Handle &h2) const |
virtual bool | HaveReverseMatch (const CSeq_id_Handle &id) const |
virtual void | FindReverseMatch (const CSeq_id_Handle &id, TSeq_id_MatchList &id_list) |
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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 vector< CSeq_id_Info * > | TGiimList |
typedef map< TPacked, TGiimList > | TIdMap |
Private Member Functions | |
virtual void | x_Unindex (const CSeq_id_Info *info) |
CSeq_id_Info * | x_FindInfo (const CGiimport_id &gid) const |
Private Attributes | |
TIdMap | m_IdMap |
Additional Inherited Members | |
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typedef set< CSeq_id_Handle > | TSeq_id_MatchList |
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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 void | Initialize (CSeq_id_Mapper *mapper, vector< CRef< CSeq_id_Which_Tree > > &v) |
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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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typedef CSeq_id_Info::TPacked | TPacked |
typedef CFastMutex | TTreeLock |
typedef TTreeLock::TReadLockGuard | TReadLockGuard |
typedef TTreeLock::TWriteLockGuard | TWriteLockGuard |
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CSeq_id_Info * | CreateInfo (CSeq_id::E_Choice type) |
CSeq_id_Info * | CreateInfo (const CSeq_id &id) |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
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static const CSeq_id_Info * | GetInfo (const CSeq_id_Handle &id) |
static const CSeq_id * | GetSeqId (const CSeq_id_Info *info) |
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TTreeLock | m_TreeLock |
CSeq_id_Mapper * | m_Mapper |
Definition at line 938 of file seq_id_tree.hpp.
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private |
Definition at line 961 of file seq_id_tree.hpp.
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private |
Definition at line 962 of file seq_id_tree.hpp.
CSeq_id_Giim_Tree::CSeq_id_Giim_Tree | ( | CSeq_id_Mapper * | mapper | ) |
Definition at line 2874 of file seq_id_tree.cpp.
CSeq_id_Giim_Tree::~CSeq_id_Giim_Tree | ( | void | ) |
Definition at line 2880 of file seq_id_tree.cpp.
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Implements CSeq_id_Which_Tree.
Definition at line 2972 of file seq_id_tree.cpp.
References count, CSeq_id_Mapper::eDumpAllIds, CSeq_id_Mapper::eDumpStatistics, int, ITERATE, kMallocOverhead, m_IdMap, out(), CSeq_id_Base::SelectionName(), and sx_StringMemory().
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Implements CSeq_id_Which_Tree.
Definition at line 2885 of file seq_id_tree.cpp.
References map_checker< Container >::empty(), and m_IdMap.
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Implements CSeq_id_Which_Tree.
Definition at line 2909 of file seq_id_tree.cpp.
References _ASSERT, CSeq_id_Which_Tree::m_TreeLock, and x_FindInfo().
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Implements CSeq_id_Which_Tree.
Definition at line 2952 of file seq_id_tree.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), set< Key, Compare >::insert(), ITERATE, m_IdMap, CSeq_id_Which_Tree::m_TreeLock, and rapidjson::value.
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Implements CSeq_id_Which_Tree.
Definition at line 2918 of file seq_id_tree.cpp.
References _ASSERT, CSeq_id_Which_Tree::CreateInfo(), CGiimport_id_Base::GetId(), info, m_IdMap, CSeq_id_Which_Tree::m_TreeLock, and x_FindInfo().
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private |
Definition at line 2891 of file seq_id_tree.cpp.
References map_checker< Container >::end(), CSerialObject::Equals(), map_checker< Container >::find(), CGiimport_id_Base::GetId(), ITERATE, and m_IdMap.
Referenced by FindInfo(), and FindOrCreate().
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privatevirtual |
Implements CSeq_id_Which_Tree.
Definition at line 2932 of file seq_id_tree.cpp.
References _ASSERT, map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CGiimport_id_Base::GetId(), info, CSeq_id_Base::IsGiim(), m_IdMap, and NON_CONST_ITERATE.
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private |
Definition at line 964 of file seq_id_tree.hpp.
Referenced by Dump(), Empty(), FindMatchStr(), FindOrCreate(), x_FindInfo(), and x_Unindex().