NCBI C++ ToolKit
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CMergedPairwiseAln Class Reference

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+ Inheritance diagram for CMergedPairwiseAln:
+ Collaboration diagram for CMergedPairwiseAln:

Public Types

typedef CAnchoredAln::TPairwiseAlnVector TPairwiseAlnVector
- 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...

Public Member Functions

 CMergedPairwiseAln (const CAlnUserOptions::TMergeFlags &merge_flags)
void insert (const CRef< CPairwiseAln > &pairwise)
const TPairwiseAlnVectorGetPairwiseAlns () const
const CAlnUserOptions::TMergeFlagsGetMergedFlags () const
void SortInsertions (void)
- 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

void x_TruncateOverlaps (CRef< CPairwiseAln > &addition)
bool x_ValidNeighboursOnFirstDim (const CPairwiseAln::TAlnRng &left, const CPairwiseAln::TAlnRng &right)
bool x_ValidNeighboursOnSecondDim (const CPairwiseAln::TAlnRng &left, const CPairwiseAln::TAlnRng &right)
bool x_CanInsertRng (CPairwiseAln &a, const CPairwiseAln::TAlnRng &r)
void x_AddPairwise (const CPairwiseAln &addition)

Private Attributes

const CAlnUserOptions::TMergeFlags m_MergeFlags
TPairwiseAlnVector m_PairwiseAlns
size_t m_NumberOfDirectAlns

Additional Inherited Members

- 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 84 of file aln_builders.cpp.

Member Typedef Documentation

◆ TPairwiseAlnVector

Definition at line 87 of file aln_builders.cpp.

Constructor & Destructor Documentation

◆ CMergedPairwiseAln()

CMergedPairwiseAln::CMergedPairwiseAln ( const CAlnUserOptions::TMergeFlags merge_flags)

Definition at line 89 of file aln_builders.cpp.

Member Function Documentation

◆ GetMergedFlags()

const CAlnUserOptions::TMergeFlags& CMergedPairwiseAln::GetMergedFlags ( ) const

Definition at line 108 of file aln_builders.cpp.

References m_MergeFlags.

Referenced by operator<<().

◆ GetPairwiseAlns()

const TPairwiseAlnVector& CMergedPairwiseAln::GetPairwiseAlns ( void  ) const

Definition at line 104 of file aln_builders.cpp.

References m_PairwiseAlns.

Referenced by operator<<().

◆ insert()

void CMergedPairwiseAln::insert ( const CRef< CPairwiseAln > &  pairwise)

◆ SortInsertions()

void CMergedPairwiseAln::SortInsertions ( void  )

Definition at line 112 of file aln_builders.cpp.

References m_PairwiseAlns, and NON_CONST_ITERATE.

◆ x_AddPairwise()

void CMergedPairwiseAln::x_AddPairwise ( const CPairwiseAln addition)

◆ x_CanInsertRng()

bool CMergedPairwiseAln::x_CanInsertRng ( CPairwiseAln a,
const CPairwiseAln::TAlnRng r 

Definition at line 186 of file aln_builders.cpp.

References a, r(), x_ValidNeighboursOnFirstDim(), and x_ValidNeighboursOnSecondDim().

Referenced by x_AddPairwise().

◆ x_TruncateOverlaps()

void CMergedPairwiseAln::x_TruncateOverlaps ( CRef< CPairwiseAln > &  addition)

◆ x_ValidNeighboursOnFirstDim()

bool CMergedPairwiseAln::x_ValidNeighboursOnFirstDim ( const CPairwiseAln::TAlnRng left,
const CPairwiseAln::TAlnRng right 

◆ x_ValidNeighboursOnSecondDim()

bool CMergedPairwiseAln::x_ValidNeighboursOnSecondDim ( const CPairwiseAln::TAlnRng left,
const CPairwiseAln::TAlnRng right 

Member Data Documentation

◆ m_MergeFlags

const CAlnUserOptions::TMergeFlags CMergedPairwiseAln::m_MergeFlags

◆ m_NumberOfDirectAlns

size_t CMergedPairwiseAln::m_NumberOfDirectAlns

Definition at line 288 of file aln_builders.cpp.

Referenced by x_AddPairwise().

◆ m_PairwiseAlns

TPairwiseAlnVector CMergedPairwiseAln::m_PairwiseAlns

The documentation for this class was generated from the following file:
Modified on Fri Dec 01 04:44:42 2023 by rev. 669887