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CAlnMap::CAlnChunk Class Reference

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#include <objtools/alnmgr/alnmap.hpp>

+ Inheritance diagram for CAlnMap::CAlnChunk:
+ Collaboration diagram for CAlnMap::CAlnChunk:

Public Member Functions

TSegTypeFlags GetType (void) const
 
CAlnChunkSetType (TSegTypeFlags type_flags)
 
const TSignedRangeGetRange (void) const
 
const TSignedRangeGetAlnRange (void) const
 
bool IsGap (void) 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

 CAlnChunk (void)
 
TSignedRangeSetRange (void)
 
TSignedRangeSetAlnRange (void)
 

Private Attributes

TSegTypeFlags m_TypeFlags
 
TSignedRange m_SeqRange
 
TSignedRange m_AlnRange
 

Friends

CConstRef< CAlnChunkCAlnChunkVec::operator[] (TNumchunk i) const
 

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 293 of file alnmap.hpp.

Constructor & Destructor Documentation

◆ CAlnChunk()

CAlnMap::CAlnChunk::CAlnChunk ( void  )
inlineprivate

Definition at line 310 of file alnmap.hpp.

Member Function Documentation

◆ GetAlnRange()

const TSignedRange& CAlnMap::CAlnChunk::GetAlnRange ( void  ) const
inline

Definition at line 302 of file alnmap.hpp.

References m_AlnRange.

◆ GetRange()

const TSignedRange& CAlnMap::CAlnChunk::GetRange ( void  ) const
inline

Definition at line 300 of file alnmap.hpp.

References m_SeqRange.

◆ GetType()

TSegTypeFlags CAlnMap::CAlnChunk::GetType ( void  ) const
inline

Definition at line 296 of file alnmap.hpp.

References m_TypeFlags.

◆ IsGap()

bool CAlnMap::CAlnChunk::IsGap ( void  ) const
inline

Definition at line 304 of file alnmap.hpp.

References CRange_Base::GetFrom(), and m_SeqRange.

◆ SetAlnRange()

TSignedRange& CAlnMap::CAlnChunk::SetAlnRange ( void  )
inlineprivate

Definition at line 312 of file alnmap.hpp.

References m_AlnRange.

◆ SetRange()

TSignedRange& CAlnMap::CAlnChunk::SetRange ( void  )
inlineprivate

Definition at line 311 of file alnmap.hpp.

References m_SeqRange.

◆ SetType()

CAlnChunk& CAlnMap::CAlnChunk::SetType ( TSegTypeFlags  type_flags)
inline

Definition at line 297 of file alnmap.hpp.

References m_TypeFlags.

Friends And Related Function Documentation

◆ CAlnChunkVec::operator[]

CConstRef<CAlnChunk> CAlnChunkVec::operator[] ( TNumchunk  i) const
friend

Member Data Documentation

◆ m_AlnRange

TSignedRange CAlnMap::CAlnChunk::m_AlnRange
private

Definition at line 316 of file alnmap.hpp.

Referenced by GetAlnRange(), and SetAlnRange().

◆ m_SeqRange

TSignedRange CAlnMap::CAlnChunk::m_SeqRange
private

Definition at line 315 of file alnmap.hpp.

Referenced by GetRange(), IsGap(), and SetRange().

◆ m_TypeFlags

TSegTypeFlags CAlnMap::CAlnChunk::m_TypeFlags
private

Definition at line 314 of file alnmap.hpp.

Referenced by GetType(), and SetType().


The documentation for this class was generated from the following file:
Modified on Mon Jul 15 05:36:22 2024 by modify_doxy.py rev. 669887