NCBI C++ ToolKit
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Search Toolkit Book for CSeqIdListSet
#include <algo/align/ngalign/sequence_set.hpp>
Public Member Functions | |
CSeqIdListSet () | |
list< CRef< objects::CSeq_id > > & | SetIdList () |
void | SetSeqMasker (CSeqMasker *SeqMasker) |
void | GetGiList (vector< TGi > &GiList, objects::CScope &Scope, const CAlignResultsSet &Alignments, int Threshold) |
CRef< blast::IQueryFactory > | CreateQueryFactory (objects::CScope &Scope, const blast::CBlastOptionsHandle &BlastOpts) |
CRef< blast::IQueryFactory > | CreateQueryFactory (objects::CScope &Scope, const blast::CBlastOptionsHandle &BlastOpts, const CAlignResultsSet &Alignments, int Threshold) |
CRef< blast::CLocalDbAdapter > | CreateLocalDbAdapter (objects::CScope &Scope, const blast::CBlastOptionsHandle &BlastOpts) |
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 |
Protected Attributes | |
list< CRef< objects::CSeq_id > > | m_SeqIdList |
CSeqMasker * | m_SeqMasker |
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< Uint8 > | TCounter |
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... | |
Definition at line 111 of file sequence_set.hpp.
CSeqIdListSet::CSeqIdListSet | ( | ) |
Definition at line 148 of file sequence_set.cpp.
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virtual |
Implements ISequenceSet.
Definition at line 462 of file sequence_set.cpp.
References CreateQueryFactory(), m_SeqIdList, NCBI_THROW, and CRef< C, Locker >::Reset().
Referenced by CSplitSeqIdListSet::CreateLocalDbAdapter(), and CSplitSeqLocListSet::CreateLocalDbAdapter().
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Implements ISequenceSet.
Referenced by CreateLocalDbAdapter().
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virtual |
Implements ISequenceSet.
void CSeqIdListSet::GetGiList | ( | vector< TGi > & | GiList, |
objects::CScope & | Scope, | ||
const CAlignResultsSet & | Alignments, | ||
int | Threshold | ||
) |
Definition at line 166 of file sequence_set.cpp.
References GetGiForId(), CAlignResultsSet::GetQuerySet(), INVALID_GI, ITERATE, m_SeqIdList, CAlignResultsSet::QueryExists(), and ZERO_GI.
Referenced by CBlastAligner::GenerateAlignments().
Definition at line 154 of file sequence_set.cpp.
References m_SeqIdList.
Referenced by CSplitSeqIdListSet::AddSeqId(), CSplitSeqLocListSet::AddSeqLoc(), CSplitSeqIdListSet::Empty(), and CSplitSeqLocListSet::Empty().
void CSeqIdListSet::SetSeqMasker | ( | CSeqMasker * | SeqMasker | ) |
Definition at line 160 of file sequence_set.cpp.
References m_SeqMasker.
Referenced by CSplitSeqIdListSet::SetSeqMasker(), and CSplitSeqLocListSet::SetSeqMasker().
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protected |
Definition at line 131 of file sequence_set.hpp.
Referenced by CreateLocalDbAdapter(), GetGiList(), and SetIdList().
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protected |
Definition at line 132 of file sequence_set.hpp.
Referenced by SetSeqMasker().