Search Toolkit Book for CBlastQueryVector

#include <algo/blast/api/sseqloc.hpp>

Inheritance diagram for CBlastQueryVector:

Collaboration diagram for CBlastQueryVector:

Public Types
typedef CRef< CBlastSearchQuery >	value_type

typedef vector< value_type >::size_type	size_type
	size_type type definition More...

typedef vector< value_type >::const_iterator	const_iterator
	const_iterator type definition More...

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
void	AddQuery (CRef< CBlastSearchQuery > q)
	Add a query to the set. More...

bool	Empty () const
	Returns true if this query vector is empty. More...

size_type	Size () const
	Returns the number of queries found in this query vector. More...

CConstRef< objects::CSeq_loc >	GetQuerySeqLoc (size_type i) const
	Get the query Seq-loc for a query by index. More...

CRef< objects::CScope >	GetScope (size_type i) const
	Get the scope containing a query by index. More...

TMaskedQueryRegions	GetMaskedRegions (size_type i) const
	Get the masked regions for a query by number. More...

CRef< objects::CSeq_loc >	GetMasks (size_type i) const
	Convenience method to get a CSeq_loc representing the masking locations. More...

void	SetMaskedRegions (size_type i, TMaskedQueryRegions mqr)
	Assign a list of masked regions to one query. More...

void	AddMask (size_type i, CRef< CSeqLocInfo > sli)
	Add a masked region to the set for a query. More...

CRef< CBlastSearchQuery >	GetBlastSearchQuery (size_type i) const
	Get the CBlastSearchQuery object at index i. More...

CRef< CBlastSearchQuery >	operator[] (size_type i) const
	Get the CBlastSearchQuery object at index i. More...

size_type	size () const
	Identical to Size, provided to facilitate STL-style iteration. More...

const_iterator	begin () const
	Returns const_iterator to beginning of container, provided to facilitate STL-style iteration. More...

const_iterator	end () const
	Returns const_iterator to end of container, provided to facilitate STL-style iteration. More...

void	clear ()
	Clears the contents of this object. More...

void	push_back (const value_type &element)
	Add a value to the back of this container. 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 Attributes
vector< CRef< CBlastSearchQuery > >	m_Queries
	The set of queries used for a search. More...

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

Query Vector.

This class represents the data relevant to all queries in a blast search. The queries are represented as CBlastSearchQuery objects. Each contains a Seq-loc, scope, and a list of filtered regions.

Definition at line 276 of file sseqloc.hpp.

Member Typedef Documentation

◆ const_iterator

typedef vector<value_type>::const_iterator CBlastQueryVector::const_iterator

const_iterator type definition

Definition at line 285 of file sseqloc.hpp.

◆ size_type

typedef vector<value_type>::size_type CBlastQueryVector::size_type

size_type type definition

Definition at line 282 of file sseqloc.hpp.

◆ value_type

typedef CRef<CBlastSearchQuery> CBlastQueryVector::value_type

Definition at line 279 of file sseqloc.hpp.

Member Function Documentation

◆ AddMask()

void CBlastQueryVector::AddMask	(	size_type	i,
		CRef< CSeqLocInfo >	sli
	)

inline

Add a masked region to the set for a query.

Parameters

i	The index of the query.
sli	The masked region to add.

Definition at line 359 of file sseqloc.hpp.

References i, and m_Queries.

Referenced by CIgBlast::x_SetupDJSearch(), and CIgBlast::x_SetupNoOverlapDSearch().

◆ AddQuery()

void CBlastQueryVector::AddQuery ( CRef< CBlastSearchQuery > q )

inline

Add a query to the set.

The CBlastSearchQuery is added to the list of queries for this search.

Parameters

q	A query to add to the set.

Definition at line 293 of file sseqloc.hpp.

References m_Queries.

Referenced by CdBlaster::blast(), Blast_FindRepeatFilterLoc(), BOOST_AUTO_TEST_CASE(), CSimpleB2SWrapper::DoBlast2Seqs(), CBlastInput::GetAllSeqs(), CBlastInput::GetNextSeqBatch(), CdBlaster::psiBlast(), s_GetBlastQueryVector(), CQueryDataTestFixture::s_ObjMgr_QueryFactory_LocalDataFromBlastQueryVector(), CBlastFormatterApp::x_ExtractQueries(), and CBlastFormatterVdbApp::x_ExtractQueries().

◆ begin()

const_iterator CBlastQueryVector::begin ( ) const

inline

Returns const_iterator to beginning of container, provided to facilitate STL-style iteration.

Definition at line 386 of file sseqloc.hpp.

References m_Queries.

◆ clear()

void CBlastQueryVector::clear ( )

inline

Clears the contents of this object.

Definition at line 393 of file sseqloc.hpp.

References m_Queries.

◆ Empty()

bool CBlastQueryVector::Empty ( ) const

inline

Returns true if this query vector is empty.

Definition at line 299 of file sseqloc.hpp.

References m_Queries.

Referenced by CheckForEmptySequences(), and CObjMgr_QueryFactory::CObjMgr_QueryFactory().

◆ end()

const_iterator CBlastQueryVector::end ( ) const

inline

Returns const_iterator to end of container, provided to facilitate STL-style iteration.

Definition at line 390 of file sseqloc.hpp.

References m_Queries.

◆ GetBlastSearchQuery()

CRef<CBlastSearchQuery> CBlastQueryVector::GetBlastSearchQuery ( size_type i ) const

inline

Get the CBlastSearchQuery object at index i.

Parameters

i	The index of a query.

Definition at line 367 of file sseqloc.hpp.

References _ASSERT, i, and m_Queries.

Referenced by Blast_FindWindowMaskerLoc(), CBlastQuerySourceOM::GetGeneticCodeId(), operator[](), s_AddSeqDataToPssm(), s_AddSeqTitleToPssm(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CIgBlast::x_ConvertResultType(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), and CIgBlast::x_SetupNoOverlapDSearch().

◆ GetMaskedRegions()

TMaskedQueryRegions CBlastQueryVector::GetMaskedRegions ( size_type i ) const

inline

Get the masked regions for a query by number.

Parameters

i	The index of a query.

Returns: The masked (filtered) regions of that query.

Definition at line 331 of file sseqloc.hpp.

References _ASSERT, i, and m_Queries.

Referenced by BOOST_AUTO_TEST_CASE(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CBlastQuerySourceOM::GetMask(), CBlastQuerySourceOM::GetMaskedRegions(), GetMasks(), and CObjMgr_QueryFactory::GetTSeqLocVector().

◆ GetMasks()

CRef<objects::CSeq_loc> CBlastQueryVector::GetMasks ( size_type i ) const

inline

Convenience method to get a CSeq_loc representing the masking locations.

Parameters

i	The index of a query.

Returns: The masked (filtered) regions of that query.

Exceptions

CBlastException in case of errors in conversion

Definition at line 341 of file sseqloc.hpp.

References GetMaskedRegions(), i, and MaskedQueryRegionsToPackedSeqLoc().

Referenced by Blast_FindDustFilterLoc(), and BOOST_AUTO_TEST_CASE().

◆ GetQuerySeqLoc()

CConstRef<objects::CSeq_loc> CBlastQueryVector::GetQuerySeqLoc ( size_type i ) const

inline

Get the query Seq-loc for a query by index.

Parameters

i	The index of a query.

Returns: The Seq-loc representing the query.

Definition at line 313 of file sseqloc.hpp.

References _ASSERT, i, and m_Queries.

Referenced by Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), CBlastQuerySourceOM::GetBlastSequence(), CBlastQuerySourceOM::GetLength(), CBlastQuerySourceOM::GetSeqId(), CBlastQuerySourceOM::GetSeqLoc(), CBlastQuerySourceOM::GetStrand(), CObjMgr_QueryFactory::GetTSeqLocVector(), operator<<(), CVecScreenApp::Run(), s_QueryVectorToBioseqSet(), s_QueryVectorToTSeqLocs(), and CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk().

◆ GetScope()

CRef<objects::CScope> CBlastQueryVector::GetScope ( size_type i ) const

inline

Get the scope containing a query by index.

Parameters

i	The index of a query.

Returns: The CScope containing the query.

Definition at line 322 of file sseqloc.hpp.

References _ASSERT, i, and m_Queries.

Referenced by Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), Blast_FindWindowMaskerLoc(), CObjMgr_QueryFactory::ExtractScopes(), CBlastQuerySourceOM::GetBlastSequence(), CBlastQuerySourceOM::GetLength(), CBlastQuerySourceOM::GetSeqId(), CBlastQuerySourceOM::GetStrand(), CBlastQuerySourceOM::GetTitle(), CObjMgr_QueryFactory::GetTSeqLocVector(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CVecScreenApp::Run(), and s_QueryVectorToBioseqSet().

◆ operator[]()

CRef<CBlastSearchQuery> CBlastQueryVector::operator[] ( size_type i ) const

inline

Get the CBlastSearchQuery object at index i.

Parameters

i	The index of a query.

Definition at line 376 of file sseqloc.hpp.

References GetBlastSearchQuery(), and i.

◆ push_back()

void CBlastQueryVector::push_back ( const value_type & element )

inline

Add a value to the back of this container.

Parameters

element element to add [in]

Definition at line 397 of file sseqloc.hpp.

References m_Queries.

Referenced by BOOST_AUTO_TEST_CASE(), and s_CloneBlastQueryVector().

◆ SetMaskedRegions()

void CBlastQueryVector::SetMaskedRegions	(	size_type	i,
		TMaskedQueryRegions	mqr
	)

inline

Assign a list of masked regions to one query.

Parameters

i	The index of the query.
mqr	The masked regions for this query.

Definition at line 350 of file sseqloc.hpp.

References _ASSERT, i, and m_Queries.

Referenced by Blast_FindDustFilterLoc(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), and CIgBlast::x_SetupNoOverlapDSearch().

◆ Size()

size_type CBlastQueryVector::Size ( ) const

inline

Returns the number of queries found in this query vector.

Definition at line 305 of file sseqloc.hpp.

References m_Queries.

Referenced by CdBlaster::blast(), Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), Blast_FindWindowMaskerLoc(), CObjMgr_QueryFactory::ExtractScopes(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CBlastInput::GetNextSeqBatch(), CObjMgr_QueryFactory::GetTSeqLocVector(), operator<<(), CVecScreenApp::Run(), s_QueryVectorToBioseqSet(), s_QueryVectorToTSeqLocs(), size(), CBlastQuerySourceOM::Size(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CIgBlast::x_ConvertResultType(), and CSplitQueryTestFixture::x_ValidateQuerySeqLocsPerChunk().

◆ size()

size_type CBlastQueryVector::size ( ) const

inline

Identical to Size, provided to facilitate STL-style iteration.

Definition at line 382 of file sseqloc.hpp.

References Size().

Referenced by CSequenceInputStats::AddQueryBatch(), CBlastFormatterApp::x_ExtractQueries(), and CBlastFormatterVdbApp::x_ExtractQueries().

Member Data Documentation

◆ m_Queries

vector< CRef<CBlastSearchQuery> > CBlastQueryVector::m_Queries

private

The set of queries used for a search.

Definition at line 401 of file sseqloc.hpp.

Referenced by AddMask(), AddQuery(), begin(), clear(), Empty(), end(), GetBlastSearchQuery(), GetMaskedRegions(), GetQuerySeqLoc(), GetScope(), push_back(), SetMaskedRegions(), and Size().

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

include/algo/blast/api/sseqloc.hpp

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ size_type

◆ value_type

Member Function Documentation

◆ AddMask()

◆ AddQuery()

◆ begin()

◆ clear()

◆ Empty()

◆ end()

◆ GetBlastSearchQuery()

◆ GetMaskedRegions()

◆ GetMasks()

◆ GetQuerySeqLoc()

◆ GetScope()

◆ operator[]()

◆ push_back()

◆ SetMaskedRegions()

◆ Size()

◆ size()

Member Data Documentation

◆ m_Queries