NCBI C++ ToolKit
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CSeqIdListSet Class Reference

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#include <algo/align/ngalign/sequence_set.hpp>

+ Inheritance diagram for CSeqIdListSet:
+ Collaboration diagram for CSeqIdListSet:

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...
 
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
 

Protected Attributes

list< CRef< objects::CSeq_id > > m_SeqIdList
 
CSeqMaskerm_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< 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 111 of file sequence_set.hpp.

Constructor & Destructor Documentation

◆ CSeqIdListSet()

CSeqIdListSet::CSeqIdListSet ( )

Definition at line 148 of file sequence_set.cpp.

Member Function Documentation

◆ CreateLocalDbAdapter()

CRef< CLocalDbAdapter > CSeqIdListSet::CreateLocalDbAdapter ( objects::CScope &  Scope,
const blast::CBlastOptionsHandle &  BlastOpts 
)
virtual

◆ CreateQueryFactory() [1/2]

CRef<blast::IQueryFactory> CSeqIdListSet::CreateQueryFactory ( objects::CScope &  Scope,
const blast::CBlastOptionsHandle &  BlastOpts 
)
virtual

Implements ISequenceSet.

Referenced by CreateLocalDbAdapter().

◆ CreateQueryFactory() [2/2]

CRef<blast::IQueryFactory> CSeqIdListSet::CreateQueryFactory ( objects::CScope &  Scope,
const blast::CBlastOptionsHandle &  BlastOpts,
const CAlignResultsSet Alignments,
int  Threshold 
)
virtual

Implements ISequenceSet.

◆ GetGiList()

void CSeqIdListSet::GetGiList ( vector< TGi > &  GiList,
objects::CScope &  Scope,
const CAlignResultsSet Alignments,
int  Threshold 
)

◆ SetIdList()

list< CRef< CSeq_id > > & CSeqIdListSet::SetIdList ( )

◆ SetSeqMasker()

void CSeqIdListSet::SetSeqMasker ( CSeqMasker SeqMasker)

Definition at line 160 of file sequence_set.cpp.

References m_SeqMasker.

Referenced by CSplitSeqIdListSet::SetSeqMasker(), and CSplitSeqLocListSet::SetSeqMasker().

Member Data Documentation

◆ m_SeqIdList

list<CRef<objects::CSeq_id> > CSeqIdListSet::m_SeqIdList
protected

Definition at line 131 of file sequence_set.hpp.

Referenced by CreateLocalDbAdapter(), GetGiList(), and SetIdList().

◆ m_SeqMasker

CSeqMasker* CSeqIdListSet::m_SeqMasker
protected

Definition at line 132 of file sequence_set.hpp.

Referenced by SetSeqMasker().


The documentation for this class was generated from the following files:
Modified on Fri Mar 01 10:06:19 2024 by modify_doxy.py rev. 669887