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

Inheritance diagram for CMergeAligner:

Collaboration diagram for CMergeAligner:

Public Types
enum	EMode { eAlignCleanup , eTreeAlignMerger , eDefault = eAlignCleanup }

typedef EMode	TMode

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...

Public Member Functions
	CMergeAligner (int Threshold, TMode mode=eAlignCleanup)

string	GetName () const

TAlignResultsRef	GenerateAlignments (objects::CScope &Scope, ISequenceSet QuerySet, ISequenceSet SubjectSet, TAlignResultsRef AccumResults)

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

Private Member Functions
CRef< objects::CSeq_align_set >	x_MergeAlignments (CQuerySet &QueryAligns, objects::CScope &Scope)

CRef< objects::CSeq_align_set >	x_MergeSeqAlignSet (objects::CSeq_align_set &InAligns, objects::CScope &Scope)

void	x_SortAlignSet (objects::CSeq_align_set &AlignSet, int CompartFlags=0)

Private Attributes
int	m_Threshold

TMode	m_Mode

CTreeAlignMerger	m_TreeAlignMerger

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 66 of file merge_aligner.hpp.

Member Typedef Documentation

◆ TMode

typedef EMode CMergeAligner::TMode

Definition at line 78 of file merge_aligner.hpp.

Member Enumeration Documentation

◆ EMode

enum CMergeAligner::EMode

Enumerator
eAlignCleanup	Use the older (CAlignCleanup) merge algorithm.
eTreeAlignMerger	Use the new (CTreeAlignMerger) merge algorithm.
eDefault

Definition at line 69 of file merge_aligner.hpp.

Constructor & Destructor Documentation

◆ CMergeAligner()

CMergeAligner::CMergeAligner	(	int	Threshold,
		TMode	mode = `eAlignCleanup`
	)

inline

Definition at line 80 of file merge_aligner.hpp.

Member Function Documentation

◆ GenerateAlignments()

TAlignResultsRef CMergeAligner::GenerateAlignments	(	objects::CScope &	Scope,
		ISequenceSet *	QuerySet,
		ISequenceSet *	SubjectSet,
		TAlignResultsRef	AccumResults
	)

virtual

Implements IAlignmentFactory.

Definition at line 64 of file merge_aligner.cpp.

References _TRACE, ERR_POST, CSeq_align_set_Base::Get(), Info(), and NON_CONST_ITERATE.

◆ GetName()

string CMergeAligner::GetName ( ) const

inlinevirtual

Implements IAlignmentFactory.

Definition at line 85 of file merge_aligner.hpp.

Referenced by x_MergeSeqAlignSet().

◆ x_MergeAlignments()

CRef< CSeq_align_set > CMergeAligner::x_MergeAlignments	(	CQuerySet &	QueryAligns,
		objects::CScope &	Scope
	)

private

Definition at line 96 of file merge_aligner.cpp.

References eNa_strand_minus, eNa_strand_plus, fCompart_AllowIntersections, fCompart_SortByScore, FindCompartments(), CQuerySet::Get(), CSeq_align_set_Base::Get(), i, CRef< C, Locker >::IsNull(), ITERATE, NON_CONST_ITERATE, out(), CSeq_align_set_Base::Set(), x_MergeSeqAlignSet(), and x_SortAlignSet().

◆ x_MergeSeqAlignSet()

CRef< objects::CSeq_align_set > CMergeAligner::x_MergeSeqAlignSet	(	objects::CSeq_align_set &	InAligns,
		objects::CScope &	Scope
	)

private

◆ x_SortAlignSet()

void CMergeAligner::x_SortAlignSet	(	objects::CSeq_align_set &	AlignSet,
		int	CompartFlags = `0`
	)

private

Definition at line 243 of file merge_aligner.cpp.

References copy(), fCompart_SortByScore, s_SortByAlignedLength(), s_SortByScore(), CSeq_align_set_Base::Set(), and ct::sort().

Referenced by x_MergeAlignments().

Member Data Documentation

◆ m_Mode

TMode CMergeAligner::m_Mode

private

Definition at line 103 of file merge_aligner.hpp.

Referenced by x_MergeSeqAlignSet().

◆ m_Threshold

int CMergeAligner::m_Threshold

private

Definition at line 102 of file merge_aligner.hpp.

◆ m_TreeAlignMerger

CTreeAlignMerger CMergeAligner::m_TreeAlignMerger

private

Definition at line 104 of file merge_aligner.hpp.

Referenced by x_MergeSeqAlignSet().

The documentation for this class was generated from the following files:

include/algo/align/ngalign/merge_aligner.hpp
src/algo/align/ngalign/merge_aligner.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TMode

Member Enumeration Documentation

◆ EMode

Constructor & Destructor Documentation

◆ CMergeAligner()

Member Function Documentation

◆ GenerateAlignments()

◆ GetName()

◆ x_MergeAlignments()

◆ x_MergeSeqAlignSet()

◆ x_SortAlignSet()

Member Data Documentation

◆ m_Mode

◆ m_Threshold

◆ m_TreeAlignMerger