Search Toolkit Book for CSplitSeqLocListSet

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

Inheritance diagram for CSplitSeqLocListSet:

Collaboration diagram for CSplitSeqLocListSet:

Public Member Functions
	CSplitSeqLocListSet (CUnorderedSplitter *Splitter)

void	AddSeqLoc (CRef< objects::CSeq_loc > Loc)

void	SetSeqMasker (CSeqMasker *SeqMasker)

bool	Empty ()

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...

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

Protected Attributes
list< CRef< objects::CSeq_loc > >	m_OrigSeqLocList

CSeqIdListSet	m_SeqIdListSet

CUnorderedSplitter *	m_Splitter

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< Uint8 >	TCounter
	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 157 of file unordered_spliter.hpp.

Constructor & Destructor Documentation

◆ CSplitSeqLocListSet()

CSplitSeqLocListSet::CSplitSeqLocListSet ( CUnorderedSplitter * Splitter )

Definition at line 762 of file unordered_spliter.cpp.

Member Function Documentation

◆ AddSeqLoc()

void CSplitSeqLocListSet::AddSeqLoc ( CRef< objects::CSeq_loc > Loc )

Definition at line 769 of file unordered_spliter.cpp.

References Loc, m_OrigSeqLocList, m_SeqIdListSet, m_Splitter, CSeqIdListSet::SetIdList(), and CUnorderedSplitter::SplitLoc().

◆ CreateLocalDbAdapter()

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

virtual

Implements ISequenceSet.

Definition at line 812 of file unordered_spliter.cpp.

References CSeqIdListSet::CreateLocalDbAdapter(), m_OrigSeqLocList, m_SeqIdListSet, and NCBI_THROW.

◆ CreateQueryFactory() [1/2]

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

virtual

Implements ISequenceSet.

◆ CreateQueryFactory() [2/2]

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

virtual

Implements ISequenceSet.

◆ Empty()

bool CSplitSeqLocListSet::Empty ( )

inline

Definition at line 165 of file unordered_spliter.hpp.

References m_SeqIdListSet, and CSeqIdListSet::SetIdList().

◆ SetSeqMasker()

void CSplitSeqLocListSet::SetSeqMasker ( CSeqMasker * SeqMasker )

Definition at line 776 of file unordered_spliter.cpp.

References m_SeqIdListSet, and CSeqIdListSet::SetSeqMasker().

Member Data Documentation

◆ m_OrigSeqLocList

list<CRef<objects::CSeq_loc> > CSplitSeqLocListSet::m_OrigSeqLocList

protected

Definition at line 178 of file unordered_spliter.hpp.

Referenced by AddSeqLoc(), and CreateLocalDbAdapter().

◆ m_SeqIdListSet

CSeqIdListSet CSplitSeqLocListSet::m_SeqIdListSet

protected

Definition at line 179 of file unordered_spliter.hpp.

Referenced by AddSeqLoc(), CreateLocalDbAdapter(), Empty(), and SetSeqMasker().

◆ m_Splitter

CUnorderedSplitter* CSplitSeqLocListSet::m_Splitter

protected

Definition at line 180 of file unordered_spliter.hpp.

Referenced by AddSeqLoc().

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

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

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSplitSeqLocListSet()

Member Function Documentation

◆ AddSeqLoc()

◆ CreateLocalDbAdapter()

◆ CreateQueryFactory() [1/2]

◆ CreateQueryFactory() [2/2]

◆ Empty()

◆ SetSeqMasker()

Member Data Documentation

◆ m_OrigSeqLocList

◆ m_SeqIdListSet

◆ m_Splitter