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CAlnMap::CAlnChunkVec Class Reference

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#include <objtools/alnmgr/alnmap.hpp>

+ Inheritance diagram for CAlnMap::CAlnChunkVec:
+ Collaboration diagram for CAlnMap::CAlnChunkVec:

Public Member Functions

 CAlnChunkVec (const CAlnMap &aln_map, TNumrow row)
 
CConstRef< CAlnChunkoperator[] (TNumchunk i) const
 
TNumchunk size (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

 CAlnChunkVec (void)
 

Private Attributes

const CAlnMapm_AlnMap
 
TNumrow m_Row
 
vector< TNumsegm_StartSegs
 
vector< TNumsegm_StopSegs
 
TSeqPos m_LeftDelta
 
TSeqPos m_RightDelta
 

Friends

CRef< CAlnChunkVecCAlnMap::GetAlnChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags) const
 
CRef< CAlnChunkVecCAlnMap::GetSeqChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags) const
 
void CAlnMap::x_GetChunks (CAlnChunkVec *vec, TNumrow row, TNumseg left_seg, TNumseg right_seg, TGetChunkFlags flags) 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 247 of file alnmap.hpp.

Constructor & Destructor Documentation

◆ CAlnChunkVec() [1/2]

CAlnMap::CAlnChunkVec::CAlnChunkVec ( const CAlnMap aln_map,
TNumrow  row 
)
inline

Definition at line 250 of file alnmap.hpp.

◆ CAlnChunkVec() [2/2]

CAlnMap::CAlnChunkVec::CAlnChunkVec ( void  )
private

Member Function Documentation

◆ operator[]()

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

◆ size()

TNumchunk CAlnMap::CAlnChunkVec::size ( void  ) const
inline

Definition at line 258 of file alnmap.hpp.

References m_StartSegs.

Referenced by operator[]().

Friends And Related Function Documentation

◆ CAlnMap::GetAlnChunks

CRef<CAlnChunkVec> CAlnMap::GetAlnChunks ( TNumrow  row,
const TSignedRange range,
TGetChunkFlags  flags 
) const
friend

◆ CAlnMap::GetSeqChunks

CRef<CAlnChunkVec> CAlnMap::GetSeqChunks ( TNumrow  row,
const TSignedRange range,
TGetChunkFlags  flags 
) const
friend

◆ CAlnMap::x_GetChunks

void CAlnMap::x_GetChunks ( CAlnChunkVec vec,
TNumrow  row,
TNumseg  left_seg,
TNumseg  right_seg,
TGetChunkFlags  flags 
) const
friend

Member Data Documentation

◆ m_AlnMap

const CAlnMap& CAlnMap::CAlnChunkVec::m_AlnMap
private

Definition at line 285 of file alnmap.hpp.

Referenced by operator[]().

◆ m_LeftDelta

TSeqPos CAlnMap::CAlnChunkVec::m_LeftDelta
private

Definition at line 289 of file alnmap.hpp.

Referenced by operator[](), and CAlnMap::x_GetChunks().

◆ m_RightDelta

TSeqPos CAlnMap::CAlnChunkVec::m_RightDelta
private

Definition at line 290 of file alnmap.hpp.

Referenced by operator[](), and CAlnMap::x_GetChunks().

◆ m_Row

TNumrow CAlnMap::CAlnChunkVec::m_Row
private

Definition at line 286 of file alnmap.hpp.

Referenced by operator[]().

◆ m_StartSegs

vector<TNumseg> CAlnMap::CAlnChunkVec::m_StartSegs
private

Definition at line 287 of file alnmap.hpp.

Referenced by operator[](), size(), and CAlnMap::x_GetChunks().

◆ m_StopSegs

vector<TNumseg> CAlnMap::CAlnChunkVec::m_StopSegs
private

Definition at line 288 of file alnmap.hpp.

Referenced by operator[](), and CAlnMap::x_GetChunks().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:03:20 2024 by modify_doxy.py rev. 669887