Container mapping seq-aligns to vectors of participating seq-ids. More...

#include <objtools/alnmgr/aln_tests.hpp>

Inheritance diagram for CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >:

Collaboration diagram for CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >:

Public Types
typedef _TAlnVec	TAlnVec
	Container (vector) of seq-aligns. More...

typedef TAlnSeqIdExtract::TIdVec	TIdVec
	Container (vector) of seq-ids. More...

typedef TIdVec	value_type

typedef size_t	size_type

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
	CAlnIdMap (const TAlnSeqIdExtract &extract, size_t expected_number_of_alns=0)
	Constructor. More...

void	push_back (const CSeq_align &aln)
	Adding an alignment. More...

const TAlnVec &	GetAlnVec (void) const
	Accessing the vector of alignments. More...

const TIdVec &	operator[] (size_t aln_idx) const
	Accessing the seq-ids of a particular seq-align. More...

const TIdVec &	operator[] (const CSeq_align &aln) const
	Accessing the seq-ids of a particular seq-align. More...

size_type	size (void) const
	Size (number of alignments) More...

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 Types
typedef map< const CSeq_align *, size_t >	TAlnMap

typedef vector< TIdVec >	TAlnIdVec

Private Attributes
const TAlnSeqIdExtract &	m_Extract

TAlnMap	m_AlnMap

TAlnIdVec	m_AlnIdVec

TAlnVec	m_AlnVec

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

template<class _TAlnVec, class TAlnSeqIdExtract>
class CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >

Container mapping seq-aligns to vectors of participating seq-ids.

TAlnSeqIdExtract is a functor used to extract seq-ids from seq-aligns.

See also: CAlnSeqIdsExtract; TAlnIdMap; TScopeAlnIdMap

Definition at line 55 of file aln_tests.hpp.

Member Typedef Documentation

◆ size_type

template<class _TAlnVec , class TAlnSeqIdExtract >

typedef size_t CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::size_type

Definition at line 64 of file aln_tests.hpp.

◆ TAlnIdVec

template<class _TAlnVec , class TAlnSeqIdExtract >

typedef vector<TIdVec> CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::TAlnIdVec

private

Definition at line 153 of file aln_tests.hpp.

◆ TAlnMap

template<class _TAlnVec , class TAlnSeqIdExtract >

typedef map<const CSeq_align*, size_t> CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::TAlnMap

private

Definition at line 150 of file aln_tests.hpp.

◆ TAlnVec

template<class _TAlnVec , class TAlnSeqIdExtract >

typedef _TAlnVec CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::TAlnVec

Container (vector) of seq-aligns.

Definition at line 59 of file aln_tests.hpp.

◆ TIdVec

template<class _TAlnVec , class TAlnSeqIdExtract >

typedef TAlnSeqIdExtract::TIdVec CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::TIdVec

Container (vector) of seq-ids.

See also: TAlnSeqIdIRef

Definition at line 62 of file aln_tests.hpp.

◆ value_type

template<class _TAlnVec , class TAlnSeqIdExtract >

typedef TIdVec CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::value_type

Definition at line 63 of file aln_tests.hpp.

Constructor & Destructor Documentation

◆ CAlnIdMap()

template<class _TAlnVec , class TAlnSeqIdExtract >

CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::CAlnIdMap	(	const TAlnSeqIdExtract &	extract,
		size_t	expected_number_of_alns = `0`
	)

inline

Constructor.

Parameters

extract	Functor for extracting AlnSeqId from seq-aligns.
expected_number_of_alns	Hint for optimization - the expected number of alignments.

Definition at line 72 of file aln_tests.hpp.

References CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnIdVec, and CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnVec.

Member Function Documentation

◆ GetAlnVec()

template<class _TAlnVec , class TAlnSeqIdExtract >

const TAlnVec& CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::GetAlnVec ( void ) const

inline

Accessing the vector of alignments.

Definition at line 116 of file aln_tests.hpp.

References CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnVec.

◆ operator[]() [1/2]

template<class _TAlnVec , class TAlnSeqIdExtract >

const TIdVec& CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::operator[] ( const CSeq_align & aln ) const

inline

Accessing the seq-ids of a particular seq-align.

Definition at line 129 of file aln_tests.hpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnIdVec, CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnMap, and NCBI_THROW.

◆ operator[]() [2/2]

template<class _TAlnVec , class TAlnSeqIdExtract >

const TIdVec& CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::operator[] ( size_t aln_idx ) const

inline

Accessing the seq-ids of a particular seq-align.

Definition at line 122 of file aln_tests.hpp.

References _ASSERT, and CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnIdVec.

◆ push_back()

template<class _TAlnVec , class TAlnSeqIdExtract >

void CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back ( const CSeq_align & aln )

inline

Adding an alignment.

NB #1: An exception might be thrown here if the alignment's seq-ids are inconsistent. NB #2: Only seq-ids are validated in release mode. The alignment is assumed to be otherwise valid. For efficiency (to avoid multiple validation), it is up to the user to assure the validity of the alignments.

Definition at line 87 of file aln_tests.hpp.

References _ASSERT, ctll::empty(), map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), map_checker< Container >::insert(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnIdVec, CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnMap, CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnVec, CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_Extract, NCBI_EXCEPTION_THROW, NCBI_THROW, and CSeq_align::Validate().

Referenced by BuildAlignDataSource(), CAlnSpanVertModel::CAlnSpanVertModel(), ConvertSeq_align(), CAlignCleanup::CreatePairwiseFromMultiple(), CAlnBuildApp::Run(), CAlnTestApp::Run(), CAlignCleanup::x_Cleanup_AnchoredAln(), CMergeAlignmentsJob::x_CreateProjectItems(), CTreeBuilderJob::x_CreateProjectItems(), CAlnMultiDSBuilder::x_PreCreateSparseDataSource(), and CValidError_align::x_ValidateAlignPercentIdentity().

◆ size()

template<class _TAlnVec , class TAlnSeqIdExtract >

size_type CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::size ( void ) const

inline

Size (number of alignments)

Definition at line 142 of file aln_tests.hpp.

References CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnIdVec.

Referenced by CAlnTestApp::Run().

Member Data Documentation

◆ m_AlnIdVec

template<class _TAlnVec , class TAlnSeqIdExtract >

TAlnIdVec CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnIdVec

private

Definition at line 154 of file aln_tests.hpp.

Referenced by CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::CAlnIdMap(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::operator[](), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back(), and CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::size().

◆ m_AlnMap

template<class _TAlnVec , class TAlnSeqIdExtract >

TAlnMap CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnMap

private

Definition at line 151 of file aln_tests.hpp.

Referenced by CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::operator[](), and CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back().

◆ m_AlnVec

template<class _TAlnVec , class TAlnSeqIdExtract >

TAlnVec CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_AlnVec

private

Definition at line 156 of file aln_tests.hpp.

Referenced by CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::CAlnIdMap(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::GetAlnVec(), and CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back().

◆ m_Extract

template<class _TAlnVec , class TAlnSeqIdExtract >

const TAlnSeqIdExtract& CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::m_Extract

private

Definition at line 148 of file aln_tests.hpp.

Referenced by CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back().

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

include/objtools/alnmgr/aln_tests.hpp

Public Types

Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

template<class _TAlnVec, class TAlnSeqIdExtract> class CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >

Member Typedef Documentation

◆ size_type

◆ TAlnIdVec

◆ TAlnMap

◆ TAlnVec

◆ TIdVec

◆ value_type

Constructor & Destructor Documentation

◆ CAlnIdMap()

Member Function Documentation

◆ GetAlnVec()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ push_back()

◆ size()

Member Data Documentation

◆ m_AlnIdVec

◆ m_AlnMap

◆ m_AlnVec

◆ m_Extract

template<class _TAlnVec, class TAlnSeqIdExtract>
class CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >