Search Toolkit Book for CAlignResultsSet

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

Inheritance diagram for CAlignResultsSet:

Collaboration diagram for CAlignResultsSet:

Public Types
typedef map< string, CRef< CQuerySet > >	TQueryToSubjectSet

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
	CAlignResultsSet ()

	CAlignResultsSet (bool AllowDupes)

	CAlignResultsSet (CRef< objects::CGC_Assembly > Gencoll, bool AllowDupes=false)

	CAlignResultsSet (const blast::CSearchResultSet &BlastResults)

TQueryToSubjectSet &	Get ()

const TQueryToSubjectSet &	Get () const

bool	QueryExists (const objects::CSeq_id &Id) const

CRef< CQuerySet >	GetQuerySet (const objects::CSeq_id &Id)

CConstRef< CQuerySet >	GetQuerySet (const objects::CSeq_id &Id) const

CRef< objects::CSeq_align_set >	ToSeqAlignSet () const

CRef< objects::CSeq_align_set >	ToBestSeqAlignSet () const

void	Insert (CRef< CQuerySet > QuerySet)

void	Insert (CRef< CAlignResultsSet > AlignSet)

void	Insert (const blast::CSearchResultSet &BlastResults)

void	Insert (CRef< objects::CSeq_align > Alignment)

void	Insert (const objects::CSeq_align_set &AlignSet)

size_t	size () const

bool	empty () const

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
void	DropQuery (const objects::CSeq_id &Id)

Private Attributes
bool	m_AllowDupes

TQueryToSubjectSet	m_QueryMap

CRef< objects::CGC_Assembly >	m_GenColl

Friends
class	CSplitSeqAlignMerger

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 121 of file result_set.hpp.

Member Typedef Documentation

◆ TQueryToSubjectSet

typedef map<string, CRef<CQuerySet> > CAlignResultsSet::TQueryToSubjectSet

Definition at line 124 of file result_set.hpp.

Constructor & Destructor Documentation

◆ CAlignResultsSet() [1/4]

CAlignResultsSet::CAlignResultsSet ( )

Definition at line 481 of file result_set.cpp.

◆ CAlignResultsSet() [2/4]

CAlignResultsSet::CAlignResultsSet ( bool AllowDupes )

Definition at line 486 of file result_set.cpp.

References m_AllowDupes.

◆ CAlignResultsSet() [3/4]

CAlignResultsSet::CAlignResultsSet	(	CRef< objects::CGC_Assembly >	Gencoll,
		bool	AllowDupes = `false`
	)

◆ CAlignResultsSet() [4/4]

CAlignResultsSet::CAlignResultsSet ( const blast::CSearchResultSet & BlastResults )

Definition at line 499 of file result_set.cpp.

References Insert().

Member Function Documentation

◆ DropQuery()

void CAlignResultsSet::DropQuery ( const objects::CSeq_id & Id )

private

Definition at line 645 of file result_set.cpp.

References CSeq_id::AsFastaString(), map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), and m_QueryMap.

◆ empty()

bool CAlignResultsSet::empty ( ) const

inline

Definition at line 152 of file result_set.hpp.

References map_checker< Container >::empty(), and m_QueryMap.

◆ Get() [1/2]

TQueryToSubjectSet& CAlignResultsSet::Get ( )

inline

Definition at line 132 of file result_set.hpp.

References m_QueryMap.

◆ Get() [2/2]

const TQueryToSubjectSet& CAlignResultsSet::Get ( ) const

inline

Definition at line 133 of file result_set.hpp.

References m_QueryMap.

◆ GetQuerySet() [1/2]

CRef<CQuerySet> CAlignResultsSet::GetQuerySet ( const objects::CSeq_id & Id )

Referenced by CSeqIdListSet::GetGiList(), and CSeqLocListSet::GetGiList().

◆ GetQuerySet() [2/2]

CConstRef<CQuerySet> CAlignResultsSet::GetQuerySet ( const objects::CSeq_id & Id ) const

◆ Insert() [1/5]

void CAlignResultsSet::Insert ( const blast::CSearchResultSet & BlastResults )

Definition at line 608 of file result_set.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), ITERATE, m_AllowDupes, m_GenColl, and m_QueryMap.

◆ Insert() [2/5]

void CAlignResultsSet::Insert ( const objects::CSeq_align_set & AlignSet )

◆ Insert() [3/5]

void CAlignResultsSet::Insert ( CRef< CAlignResultsSet > AlignSet )

Definition at line 600 of file result_set.cpp.

References Insert(), and ITERATE.

◆ Insert() [4/5]

void CAlignResultsSet::Insert ( CRef< CQuerySet > QuerySet )

Definition at line 579 of file result_set.cpp.

References CSeq_align_set_Base::CanGet(), map_checker< Container >::end(), map_checker< Container >::find(), CSeq_align_set_Base::Get(), CQuerySet::GetQueryId(), m_AllowDupes, m_GenColl, m_QueryMap, and CQuerySet::ToSeqAlignSet().

Referenced by CAlignResultsSet(), and Insert().

◆ Insert() [5/5]

void CAlignResultsSet::Insert ( CRef< objects::CSeq_align > Alignment )

◆ QueryExists()

bool CAlignResultsSet::QueryExists ( const objects::CSeq_id & Id ) const

Definition at line 506 of file result_set.cpp.

References CSeq_id::AsFastaString(), map_checker< Container >::end(), map_checker< Container >::find(), and m_QueryMap.

Referenced by CSeqIdListSet::GetGiList(), and CSeqLocListSet::GetGiList().

◆ size()

size_t CAlignResultsSet::size ( ) const

inline

Definition at line 151 of file result_set.hpp.

References m_QueryMap, and map_checker< Container >::size().

◆ ToBestSeqAlignSet()

CRef< CSeq_align_set > CAlignResultsSet::ToBestSeqAlignSet ( ) const

Definition at line 560 of file result_set.cpp.

References CSeq_align_set_Base::Get(), CRef< C, Locker >::IsNull(), ITERATE, m_QueryMap, and Out().

◆ ToSeqAlignSet()

CRef< CSeq_align_set > CAlignResultsSet::ToSeqAlignSet ( ) const

Definition at line 543 of file result_set.cpp.

References ITERATE, m_QueryMap, and Out().

Friends And Related Function Documentation

◆ CSplitSeqAlignMerger

friend class CSplitSeqAlignMerger

friend

Definition at line 164 of file result_set.hpp.

Member Data Documentation

◆ m_AllowDupes

bool CAlignResultsSet::m_AllowDupes

private

Definition at line 156 of file result_set.hpp.

Referenced by CAlignResultsSet(), and Insert().

◆ m_GenColl

CRef<objects::CGC_Assembly> CAlignResultsSet::m_GenColl

private

Definition at line 160 of file result_set.hpp.

Referenced by Insert().

◆ m_QueryMap

TQueryToSubjectSet CAlignResultsSet::m_QueryMap

private

Definition at line 158 of file result_set.hpp.

Referenced by DropQuery(), empty(), Get(), Insert(), QueryExists(), size(), ToBestSeqAlignSet(), and ToSeqAlignSet().

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TQueryToSubjectSet

Constructor & Destructor Documentation

◆ CAlignResultsSet() [1/4]

◆ CAlignResultsSet() [2/4]

◆ CAlignResultsSet() [3/4]

◆ CAlignResultsSet() [4/4]

Member Function Documentation

◆ DropQuery()

◆ empty()

◆ Get() [1/2]

◆ Get() [2/2]

◆ GetQuerySet() [1/2]

◆ GetQuerySet() [2/2]

◆ Insert() [1/5]

◆ Insert() [2/5]

◆ Insert() [3/5]

◆ Insert() [4/5]

◆ Insert() [5/5]

◆ QueryExists()

◆ size()

◆ ToBestSeqAlignSet()

◆ ToSeqAlignSet()

Friends And Related Function Documentation

◆ CSplitSeqAlignMerger

Member Data Documentation

◆ m_AllowDupes

◆ m_GenColl

◆ m_QueryMap