Search Toolkit Book for CHitMatrixDataSource

#include <gui/widgets/hit_matrix/dense_ds.hpp>

Inheritance diagram for CHitMatrixDataSource:

Collaboration diagram for CHitMatrixDataSource:

Public Member Functions
	CHitMatrixDataSource ()
	CHitMatrixDataSource. More...

virtual	~CHitMatrixDataSource ()

IHitMatrixDataSource implementation
void	Init (objects::CScope &scope, TAlignVector &aligns)

virtual bool	CanCreateRowBased () const

virtual void	SetParams (const SParams &params, bool create_hits)

virtual void	GetParams (SParams &params) const

virtual bool	SelectIds (const IHitSeqId &q_id, const IHitSeqId &s_id)
	Creates Hits for all pairwise alignments between selected by Query and Subject IDs. More...

virtual bool	SelectDefaultIds ()
	selects default query and subject More...

virtual const TIdVector &	GetHitSeqIds ()
	returns list of all seq ids in the Data Source More...

virtual void	GetHitSeqIdsForParams (TIdVector &ids, const SParams &params) const
	returns a list of ids that Data Source will create if the given params are applied. More...

virtual void	GetAlignedIds (const IHitSeqId &id, TIdVector &aligned)

virtual void	GetAlignedIdsForParams (const IHitSeqId &id, const TIdVector &ids, TIdVector &aligned, const SParams &params)
	returns a list of ids that will be aligned with the specified id if the given params are applied. More...

virtual objects::CScope &	GetScope ()

virtual IHitSeqId &	GetQueryId () const

virtual IHitSeqId &	GetSubjectId () const

virtual objects::CBioseq_Handle	GetQueryHandle ()

virtual objects::CBioseq_Handle	GetSubjectHandle ()

virtual objects::CBioseq_Handle	GetBioseqHandle (const IHitSeqId &id)

virtual string	GetLabel (const IHitSeqId &id)

virtual void	GetScoreNames (vector< string > &names) const

TValueRange	GetScoreRange (const string &name) const

const THitAdapterCont &	GetHits () const

TSeqRange	GetQueryHitsRange ()

TSeqRange	GetSubjectHitsRange ()

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

Public Member Functions inherited from IHitMatrixDataSource
virtual	~IHitMatrixDataSource ()

Protected Types
typedef vector< CConstRef< objects::CSeq_id > >	TSeqIdRefVector

typedef objects::CSeq_align::TSegs::TStd	TStd

typedef vector< const CSeq_align * >	TAlnPtrVector

typedef CAlnSeqIdsExtract< CAlnSeqId >	TIdExtract

typedef CAlnIdMap< TAlnPtrVector, TIdExtract >	TAlnIdMap

typedef map< string, TValueRange >	TScoreMap

typedef CSeq_align::TDim	TDim

typedef const CSeq_id *	TSeqIdPtr

typedef vector< TSeqIdPtr >	TSeqIdVector

typedef CAlnStats< TAlnIdMap >	TAlnStats

typedef set< objects::CBioseq_Handle >	THIdToHandleMap

Protected Member Functions
void	x_TestAndSelectAligns (TAlignVector &aligns)

void	x_TestAndSelectAlign (const objects::CSeq_align &align)

bool	x_GoodSeg (const TStd &std_list)

TSeqRange	GetStdSegRange (const TStd &std_list, size_t row)

void	x_Clear ()

void	x_ClearHits ()

bool	x_CanCreateRowBased ()

void	x_UpdateScoreMap ()
	builds a map of all scores found in the alignments More...

void	x_GetSeqAlignIds (const objects::CSeq_align &align, TSeqIdRefVector &ids, bool unique) const

void	x_GetAlignedSeqIds (const CSeq_align &align, const IHitSeqId &id, TSeqIdRefVector &ids) const

void	x_CreateIds (TIdVector &seq_ids, const SParams &params) const

void	x_CreateHits (const objects::CSeq_align &align)

void	x_CreateHit (const objects::CSeq_align &align, size_t q_index, size_t s_index)

void	x_CreateHit_Denseg (const objects::CSeq_align &align, size_t q_index, size_t s_index)
	creates a single hit from 2 rows of a Seq-align More...

void	x_CreateHit_Std (const objects::CSeq_align &align, size_t q_index, size_t s_index)

void	x_CreateHits_Diagonal (const objects::CSeq_align &align, size_t q_index, size_t s_index)

void	x_CalculateHitsRange ()

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
TAlignVector	m_Aligns

CRef< objects::CScope >	m_Scope

unique_ptr< TAlnIdMap >	m_AlnIdMap

CRef< TAlnStats >	m_AlnStats

bool	m_CanCreateRowBased

SParams	m_Params

TIdVector	m_SeqIds

THIdToHandleMap	m_HIdToHandleMap
	list of Ids for all sequences More...

TScoreMap	m_ScoreMap

unique_ptr< IHitSeqId >	m_SubjectID

unique_ptr< IHitSeqId >	m_QueryID

objects::CBioseq_Handle	m_SubjectHandle

objects::CBioseq_Handle	m_QueryHandle

THitAdapterCont	m_Hits

TSeqRange	m_SubjectHitsRange

TSeqRange	m_QueryHitsRange

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...

Public Types inherited from IHitMatrixDataSource
typedef vector< CConstRef< objects::CSeq_align > >	TAlignVector

typedef vector< IHitSeqId * >	TIdVector

typedef vector< IHit * >	THitAdapterCont

typedef pair< double, double >	TValueRange

typedef IHit::TDirection	TDirection

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...

Detailed Description

CHitMatrixDataSource.

Definition at line 103 of file dense_ds.hpp.

Member Typedef Documentation

◆ TAlnIdMap

typedef CAlnIdMap<TAlnPtrVector, TIdExtract> CHitMatrixDataSource::TAlnIdMap

protected

Definition at line 158 of file dense_ds.hpp.

◆ TAlnPtrVector

typedef vector<const CSeq_align*> CHitMatrixDataSource::TAlnPtrVector

protected

Definition at line 156 of file dense_ds.hpp.

◆ TAlnStats

typedef CAlnStats<TAlnIdMap> CHitMatrixDataSource::TAlnStats

protected

Definition at line 198 of file dense_ds.hpp.

◆ TDim

typedef CSeq_align::TDim CHitMatrixDataSource::TDim

protected

Definition at line 195 of file dense_ds.hpp.

◆ THIdToHandleMap

typedef set<objects::CBioseq_Handle> CHitMatrixDataSource::THIdToHandleMap

protected

Definition at line 199 of file dense_ds.hpp.

◆ TIdExtract

typedef CAlnSeqIdsExtract<CAlnSeqId> CHitMatrixDataSource::TIdExtract

protected

Definition at line 157 of file dense_ds.hpp.

◆ TScoreMap

typedef map<string, TValueRange> CHitMatrixDataSource::TScoreMap

protected

Definition at line 194 of file dense_ds.hpp.

◆ TSeqIdPtr

typedef const CSeq_id* CHitMatrixDataSource::TSeqIdPtr

protected

Definition at line 196 of file dense_ds.hpp.

◆ TSeqIdRefVector

typedef vector<CConstRef<objects::CSeq_id> > CHitMatrixDataSource::TSeqIdRefVector

protected

Definition at line 153 of file dense_ds.hpp.

◆ TSeqIdVector

typedef vector<TSeqIdPtr> CHitMatrixDataSource::TSeqIdVector

protected

Definition at line 197 of file dense_ds.hpp.

◆ TStd

typedef objects::CSeq_align::TSegs::TStd CHitMatrixDataSource::TStd

protected

Definition at line 154 of file dense_ds.hpp.

Constructor & Destructor Documentation

◆ CHitMatrixDataSource()

CHitMatrixDataSource::CHitMatrixDataSource ( )

CHitMatrixDataSource.

Definition at line 115 of file dense_ds.cpp.

References CAlnUserOptions::eBothDirections, IHitMatrixDataSource::SParams::m_Direction, and m_Params.

◆ ~CHitMatrixDataSource()

CHitMatrixDataSource::~CHitMatrixDataSource ( )

virtual

Definition at line 121 of file dense_ds.cpp.

References x_Clear().

Member Function Documentation

◆ CanCreateRowBased()

bool CHitMatrixDataSource::CanCreateRowBased ( ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 343 of file dense_ds.cpp.

References m_CanCreateRowBased.

◆ GetAlignedIds()

void CHitMatrixDataSource::GetAlignedIds	(	const IHitSeqId &	id,
		TIdVector &	aligned
	)

virtual

Implements IHitMatrixDataSource.

Definition at line 571 of file dense_ds.cpp.

References GetAlignedIdsForParams(), m_Params, and m_SeqIds.

◆ GetAlignedIdsForParams()

void CHitMatrixDataSource::GetAlignedIdsForParams	(	const IHitSeqId &	id,
		const TIdVector &	ids,
		TIdVector &	aligned,
		const SParams &	params
	)

virtual

returns a list of ids that will be aligned with the specified id if the given params are applied.

Implements IHitMatrixDataSource.

Definition at line 578 of file dense_ds.cpp.

References _ASSERT, find_id(), GetSeqId(), IAlnSeqId::GetSeqId(), ITERATE, m_AlnStats, and IHitMatrixDataSource::SParams::m_RowBased.

Referenced by GetAlignedIds().

◆ GetBioseqHandle()

CBioseq_Handle CHitMatrixDataSource::GetBioseqHandle ( const IHitSeqId & id )

virtual

Implements IHitMatrixDataSource.

Definition at line 880 of file dense_ds.cpp.

References _ASSERT, and m_Scope.

◆ GetHits()

const CHitMatrixDataSource::THitAdapterCont & CHitMatrixDataSource::GetHits ( ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 906 of file dense_ds.cpp.

References m_Hits.

◆ GetHitSeqIds()

const CHitMatrixDataSource::TIdVector & CHitMatrixDataSource::GetHitSeqIds ( )

virtual

returns list of all seq ids in the Data Source

Implements IHitMatrixDataSource.

Definition at line 549 of file dense_ds.cpp.

References m_SeqIds.

◆ GetHitSeqIdsForParams()

void CHitMatrixDataSource::GetHitSeqIdsForParams	(	TIdVector &	ids,
		const SParams &	params
	)		const

virtual

returns a list of ids that Data Source will create if the given params are applied.

The caller is responsible for deleting ids.

Implements IHitMatrixDataSource.

Definition at line 555 of file dense_ds.cpp.

References i, m_Params, m_SeqIds, and x_CreateIds().

◆ GetLabel()

string CHitMatrixDataSource::GetLabel ( const IHitSeqId & id )

virtual

Implements IHitMatrixDataSource.

Definition at line 892 of file dense_ds.cpp.

References _ASSERT, CLabel::eDefault, CLabel::GetLabel(), CRef< C, Locker >::GetPointer(), CHitSeqRowId::GetRow(), GetSeqId(), NStr::IntToString(), and m_Scope.

◆ GetParams()

void CHitMatrixDataSource::GetParams ( SParams & params ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 349 of file dense_ds.cpp.

References m_Params.

◆ GetQueryHandle()

CBioseq_Handle CHitMatrixDataSource::GetQueryHandle ( )

virtual

Implements IHitMatrixDataSource.

Definition at line 868 of file dense_ds.cpp.

References m_QueryHandle.

◆ GetQueryHitsRange()

TSeqRange CHitMatrixDataSource::GetQueryHitsRange ( )

virtual

Implements IHitMatrixDataSource.

Definition at line 929 of file dense_ds.cpp.

References m_QueryHitsRange.

◆ GetQueryId()

IHitSeqId & CHitMatrixDataSource::GetQueryId ( void ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 856 of file dense_ds.cpp.

References m_QueryID.

◆ GetScope()

CScope & CHitMatrixDataSource::GetScope ( void )

virtual

Implements IHitMatrixDataSource.

Definition at line 850 of file dense_ds.cpp.

References CRef< C, Locker >::GetObject(), and m_Scope.

◆ GetScoreNames()

void CHitMatrixDataSource::GetScoreNames ( vector< string > & names ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 912 of file dense_ds.cpp.

References ITERATE, m_ScoreMap, and names.

◆ GetScoreRange()

CHitMatrixDataSource::TValueRange CHitMatrixDataSource::GetScoreRange ( const string & name ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 921 of file dense_ds.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), and m_ScoreMap.

◆ GetStdSegRange()

TSeqRange CHitMatrixDataSource::GetStdSegRange	(	const TStd &	std_list,
		size_t	row
	)

protected

Definition at line 769 of file dense_ds.cpp.

References COpenRange< TSeqPos >::GetEmpty(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), ITERATE, r(), compile_time_bits::range(), and row.

◆ GetSubjectHandle()

CBioseq_Handle CHitMatrixDataSource::GetSubjectHandle ( )

virtual

Implements IHitMatrixDataSource.

Definition at line 874 of file dense_ds.cpp.

References m_SubjectHandle.

◆ GetSubjectHitsRange()

TSeqRange CHitMatrixDataSource::GetSubjectHitsRange ( )

virtual

Implements IHitMatrixDataSource.

Definition at line 935 of file dense_ds.cpp.

References m_SubjectHitsRange.

◆ GetSubjectId()

IHitSeqId & CHitMatrixDataSource::GetSubjectId ( ) const

virtual

Implements IHitMatrixDataSource.

Definition at line 862 of file dense_ds.cpp.

References m_SubjectID.

◆ Init()

void CHitMatrixDataSource::Init	(	objects::CScope &	scope,
		TAlignVector &	aligns
	)

virtual

Implements IHitMatrixDataSource.

Definition at line 180 of file dense_ds.cpp.

References m_CanCreateRowBased, m_Params, IHitMatrixDataSource::SParams::m_RowBased, m_Scope, m_SeqIds, CRef< C, Locker >::Reset(), x_CanCreateRowBased(), x_Clear(), x_CreateIds(), x_TestAndSelectAligns(), and x_UpdateScoreMap().

◆ SelectDefaultIds()

bool CHitMatrixDataSource::SelectDefaultIds ( )

virtual

selects default query and subject

Implements IHitMatrixDataSource.

Definition at line 635 of file dense_ds.cpp.

References m_SeqIds, and SelectIds().

◆ SelectIds()

bool CHitMatrixDataSource::SelectIds	(	const IHitSeqId &	q_id,
		const IHitSeqId &	s_id
	)

virtual

Creates Hits for all pairwise alignments between selected by Query and Subject IDs.

Implements IHitMatrixDataSource.

Definition at line 646 of file dense_ds.cpp.

References IHitSeqId::Clone(), find_id(), ITERATE, m_Aligns, m_QueryHandle, m_QueryID, m_Scope, m_SeqIds, m_SubjectHandle, m_SubjectID, x_CalculateHitsRange(), x_ClearHits(), and x_CreateHits().

Referenced by SelectDefaultIds(), and SetParams().

◆ SetParams()

void CHitMatrixDataSource::SetParams	(	const SParams &	params,
		bool	create_hits
	)

virtual

Implements IHitMatrixDataSource.

Definition at line 308 of file dense_ds.cpp.

References _ASSERT, m_CanCreateRowBased, IHitMatrixDataSource::SParams::m_Direction, m_Params, m_QueryID, IHitMatrixDataSource::SParams::m_RowBased, m_SeqIds, m_SubjectID, SelectIds(), x_ClearHits(), and x_CreateIds().

◆ x_CalculateHitsRange()

void CHitMatrixDataSource::x_CalculateHitsRange ( )

protected

Definition at line 820 of file dense_ds.cpp.

References COpenRange< Position >::Empty(), IHit::GetElem(), IHit::GetElemsCount(), IHitElement::GetQueryLength(), IHitElement::GetQueryStart(), IHitElement::GetSubjectLength(), IHitElement::GetSubjectStart(), i, m_Hits, m_QueryHitsRange, m_SubjectHitsRange, and COpenRange< Position >::Set().

Referenced by SelectIds().

◆ x_CanCreateRowBased()

bool CHitMatrixDataSource::x_CanCreateRowBased ( )

protected

Definition at line 290 of file dense_ds.cpp.

References i, m_AlnIdMap, and NULL.

Referenced by Init().

◆ x_Clear()

void CHitMatrixDataSource::x_Clear ( void )

protected

Definition at line 146 of file dense_ds.cpp.

References map_checker< Container >::clear(), set< Key, Compare >::clear(), ITERATE, m_Aligns, m_AlnIdMap, m_AlnStats, m_CanCreateRowBased, m_HIdToHandleMap, m_Scope, m_ScoreMap, m_SeqIds, CRef< C, Locker >::Reset(), and x_ClearHits().

Referenced by Init(), and ~CHitMatrixDataSource().

◆ x_ClearHits()

void CHitMatrixDataSource::x_ClearHits ( )

protected

Definition at line 127 of file dense_ds.cpp.

References COpenRange< TSeqPos >::GetEmpty(), ITERATE, m_Hits, m_QueryHandle, m_QueryHitsRange, m_QueryID, m_SubjectHandle, m_SubjectHitsRange, and m_SubjectID.

Referenced by SelectIds(), SetParams(), and x_Clear().

◆ x_CreateHit()

void CHitMatrixDataSource::x_CreateHit	(	const objects::CSeq_align &	align,
		size_t	q_index,
		size_t	s_index
	)

protected

Definition at line 727 of file dense_ds.cpp.

References CSeq_align_Base::GetSegs(), Info(), CSeq_align_Base::IsSetSegs(), LOG_POST, CSeq_align_Base::C_Segs::Which(), x_CreateHit_Std(), and x_CreateHits_Diagonal().

Referenced by x_CreateHits().

◆ x_CreateHit_Denseg()

void CHitMatrixDataSource::x_CreateHit_Denseg	(	const objects::CSeq_align &	align,
		size_t	q_index,
		size_t	s_index
	)

protected

creates a single hit from 2 rows of a Seq-align

Definition at line 755 of file dense_ds.cpp.

References _ASSERT, CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CDenseSegHit::HasAlignment(), CSeq_align_Base::C_Segs::IsDenseg(), IHitMatrixDataSource::SParams::m_Direction, m_Hits, and m_Params.

◆ x_CreateHit_Std()

void CHitMatrixDataSource::x_CreateHit_Std	(	const objects::CSeq_align &	align,
		size_t	q_index,
		size_t	s_index
	)

protected

Definition at line 787 of file dense_ds.cpp.

References _ASSERT, CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetStd(), CStdSegHit::HasAlignment(), CSeq_align_Base::C_Segs::IsStd(), IHitMatrixDataSource::SParams::m_Direction, m_Hits, and m_Params.

Referenced by x_CreateHit().

◆ x_CreateHits()

void CHitMatrixDataSource::x_CreateHits ( const objects::CSeq_align & align )

protected

Definition at line 678 of file dense_ds.cpp.

References _ASSERT, CHitSeqRowId::GetRow(), i, CSeq_align_Base::IsSetSegs(), m_Params, m_QueryID, IHitMatrixDataSource::SParams::m_RowBased, m_SubjectID, x_CreateHit(), and x_GetSeqAlignIds().

Referenced by SelectIds().

◆ x_CreateHits_Diagonal()

void CHitMatrixDataSource::x_CreateHits_Diagonal	(	const objects::CSeq_align &	align,
		size_t	q_index,
		size_t	s_index
	)

protected

Definition at line 803 of file dense_ds.cpp.

References ConvertSeqAlignToPairwiseAln(), IHitMatrixDataSource::SParams::m_Direction, m_Hits, and m_Params.

Referenced by x_CreateHit().

◆ x_CreateIds()

void CHitMatrixDataSource::x_CreateIds	(	TIdVector &	seq_ids,
		const SParams &	params
	)		const

protected

Definition at line 503 of file dense_ds.cpp.

References CScope::GetBioseqHandle(), CRef< C, Locker >::GetObject(), i, set< Key, Compare >::insert(), ITERATE, m_Aligns, m_HIdToHandleMap, IHitMatrixDataSource::SParams::m_RowBased, m_Scope, m_SeqIds, row, and x_GetSeqAlignIds().

Referenced by GetHitSeqIdsForParams(), Init(), and SetParams().

◆ x_GetAlignedSeqIds()

void CHitMatrixDataSource::x_GetAlignedSeqIds	(	const CSeq_align &	align,
		const IHitSeqId &	id,
		TSeqIdRefVector &	ids
	)		const

protected

Definition at line 423 of file dense_ds.cpp.

References _ASSERT, CSeq_align_Base::CanGetSegs(), CSeq_align_Base::GetSegs(), IAlnSeqId::GetSeqId(), ITERATE, and CSeq_align_Base::C_Segs::Which().

◆ x_GetSeqAlignIds()

void CHitMatrixDataSource::x_GetSeqAlignIds	(	const objects::CSeq_align &	align,
		TSeqIdRefVector &	ids,
		bool	unique
	)		const

protected

Definition at line 468 of file dense_ds.cpp.

References _ASSERT, CSeq_align_Base::CanGetSegs(), CSeq_align_Base::GetSegs(), IAlnSeqId::GetSeqId(), ITERATE, and CSeq_align_Base::C_Segs::Which().

Referenced by x_CreateHits(), and x_CreateIds().

◆ x_GoodSeg()

bool CHitMatrixDataSource::x_GoodSeg ( const TStd & std_list )

protected

Definition at line 270 of file dense_ds.cpp.

References eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, CStd_seg_Base::GetLoc(), CSeq_loc::GetStrand(), Info(), ITERATE, and LOG_POST.

Referenced by x_TestAndSelectAlign().

◆ x_TestAndSelectAlign()

void CHitMatrixDataSource::x_TestAndSelectAlign ( const objects::CSeq_align & align )

protected

Definition at line 215 of file dense_ds.cpp.

References ERR_POST, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, m_Aligns, m_AlnIdMap, CSeq_align_Base::C_Segs::Which(), and x_GoodSeg().

Referenced by x_TestAndSelectAligns().

◆ x_TestAndSelectAligns()

void CHitMatrixDataSource::x_TestAndSelectAligns ( TAlignVector & aligns )

protected

Definition at line 256 of file dense_ds.cpp.

References ITERATE, m_AlnIdMap, m_AlnStats, and x_TestAndSelectAlign().

Referenced by Init().

◆ x_UpdateScoreMap()

void CHitMatrixDataSource::x_UpdateScoreMap ( )

protected

builds a map of all scores found in the alignments

Definition at line 356 of file dense_ds.cpp.

References _ASSERT, CScore_Base::CanGetId(), CSeq_align_Base::CanGetSegs(), CScore_Base::C_Value::e_Int, CScore_Base::C_Value::e_Real, map_checker< Container >::end(), map_checker< Container >::find(), CScore_Base::GetId(), CSeq_align_Base::GetScore(), CScore_Base::GetValue(), i, ITERATE, m_Aligns, m_ScoreMap, max(), min(), compile_time_bits::range(), val, and rapidjson::value.

Referenced by Init().

Member Data Documentation

◆ m_Aligns

TAlignVector CHitMatrixDataSource::m_Aligns

protected

Definition at line 201 of file dense_ds.hpp.

Referenced by SelectIds(), x_Clear(), x_CreateIds(), x_TestAndSelectAlign(), and x_UpdateScoreMap().

◆ m_AlnIdMap

unique_ptr<TAlnIdMap> CHitMatrixDataSource::m_AlnIdMap

protected

Definition at line 204 of file dense_ds.hpp.

Referenced by x_CanCreateRowBased(), x_Clear(), x_TestAndSelectAlign(), and x_TestAndSelectAligns().

◆ m_AlnStats

CRef<TAlnStats> CHitMatrixDataSource::m_AlnStats

protected

Definition at line 205 of file dense_ds.hpp.

Referenced by GetAlignedIdsForParams(), x_Clear(), and x_TestAndSelectAligns().

◆ m_CanCreateRowBased

bool CHitMatrixDataSource::m_CanCreateRowBased

protected

Definition at line 208 of file dense_ds.hpp.

Referenced by CanCreateRowBased(), Init(), SetParams(), and x_Clear().

◆ m_HIdToHandleMap

THIdToHandleMap CHitMatrixDataSource::m_HIdToHandleMap

mutableprotected

list of Ids for all sequences

Definition at line 212 of file dense_ds.hpp.

Referenced by x_Clear(), and x_CreateIds().

◆ m_Hits

THitAdapterCont CHitMatrixDataSource::m_Hits

protected

Definition at line 221 of file dense_ds.hpp.

Referenced by GetHits(), x_CalculateHitsRange(), x_ClearHits(), x_CreateHit_Denseg(), x_CreateHit_Std(), and x_CreateHits_Diagonal().

◆ m_Params

SParams CHitMatrixDataSource::m_Params

protected

Definition at line 209 of file dense_ds.hpp.

Referenced by CHitMatrixDataSource(), GetAlignedIds(), GetHitSeqIdsForParams(), GetParams(), Init(), SetParams(), x_CreateHit_Denseg(), x_CreateHit_Std(), x_CreateHits(), and x_CreateHits_Diagonal().

◆ m_QueryHandle

objects::CBioseq_Handle CHitMatrixDataSource::m_QueryHandle

protected

Definition at line 219 of file dense_ds.hpp.

Referenced by GetQueryHandle(), SelectIds(), and x_ClearHits().

◆ m_QueryHitsRange

TSeqRange CHitMatrixDataSource::m_QueryHitsRange

protected

Definition at line 224 of file dense_ds.hpp.

Referenced by GetQueryHitsRange(), x_CalculateHitsRange(), and x_ClearHits().

◆ m_QueryID

unique_ptr<IHitSeqId> CHitMatrixDataSource::m_QueryID

protected

Definition at line 216 of file dense_ds.hpp.

Referenced by GetQueryId(), SelectIds(), SetParams(), x_ClearHits(), and x_CreateHits().

◆ m_Scope

CRef<objects::CScope> CHitMatrixDataSource::m_Scope

protected

Definition at line 202 of file dense_ds.hpp.

Referenced by GetBioseqHandle(), GetLabel(), GetScope(), Init(), SelectIds(), x_Clear(), and x_CreateIds().

◆ m_ScoreMap

TScoreMap CHitMatrixDataSource::m_ScoreMap

protected

Definition at line 213 of file dense_ds.hpp.

Referenced by GetScoreNames(), GetScoreRange(), x_Clear(), and x_UpdateScoreMap().

◆ m_SeqIds

TIdVector CHitMatrixDataSource::m_SeqIds

protected

Definition at line 211 of file dense_ds.hpp.

Referenced by GetAlignedIds(), GetHitSeqIds(), GetHitSeqIdsForParams(), Init(), SelectDefaultIds(), SelectIds(), SetParams(), x_Clear(), and x_CreateIds().

◆ m_SubjectHandle

objects::CBioseq_Handle CHitMatrixDataSource::m_SubjectHandle

protected

Definition at line 218 of file dense_ds.hpp.

Referenced by GetSubjectHandle(), SelectIds(), and x_ClearHits().

◆ m_SubjectHitsRange

TSeqRange CHitMatrixDataSource::m_SubjectHitsRange

protected

Definition at line 223 of file dense_ds.hpp.

Referenced by GetSubjectHitsRange(), x_CalculateHitsRange(), and x_ClearHits().

◆ m_SubjectID

unique_ptr<IHitSeqId> CHitMatrixDataSource::m_SubjectID

protected

Definition at line 215 of file dense_ds.hpp.

Referenced by GetSubjectId(), SelectIds(), SetParams(), x_ClearHits(), and x_CreateHits().

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

include/gui/widgets/hit_matrix/dense_ds.hpp
src/gui/widgets/hit_matrix/dense_ds.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAlnIdMap

◆ TAlnPtrVector

◆ TAlnStats

◆ TDim

◆ THIdToHandleMap

◆ TIdExtract

◆ TScoreMap

◆ TSeqIdPtr

◆ TSeqIdRefVector

◆ TSeqIdVector

◆ TStd

Constructor & Destructor Documentation

◆ CHitMatrixDataSource()

◆ ~CHitMatrixDataSource()

Member Function Documentation

◆ CanCreateRowBased()

◆ GetAlignedIds()

◆ GetAlignedIdsForParams()

◆ GetBioseqHandle()

◆ GetHits()

◆ GetHitSeqIds()

◆ GetHitSeqIdsForParams()

◆ GetLabel()

◆ GetParams()

◆ GetQueryHandle()

◆ GetQueryHitsRange()

◆ GetQueryId()

◆ GetScope()

◆ GetScoreNames()

◆ GetScoreRange()

◆ GetStdSegRange()

◆ GetSubjectHandle()

◆ GetSubjectHitsRange()

◆ GetSubjectId()

◆ Init()

◆ SelectDefaultIds()

◆ SelectIds()

◆ SetParams()

◆ x_CalculateHitsRange()

◆ x_CanCreateRowBased()

◆ x_Clear()

◆ x_ClearHits()

◆ x_CreateHit()

◆ x_CreateHit_Denseg()

◆ x_CreateHit_Std()

◆ x_CreateHits()

◆ x_CreateHits_Diagonal()

◆ x_CreateIds()

◆ x_GetAlignedSeqIds()

◆ x_GetSeqAlignIds()

◆ x_GoodSeg()

◆ x_TestAndSelectAlign()

◆ x_TestAndSelectAligns()

◆ x_UpdateScoreMap()

Member Data Documentation

◆ m_Aligns

◆ m_AlnIdMap

◆ m_AlnStats

◆ m_CanCreateRowBased

◆ m_HIdToHandleMap

◆ m_Hits

◆ m_Params

◆ m_QueryHandle

◆ m_QueryHitsRange

◆ m_QueryID

◆ m_Scope

◆ m_ScoreMap

◆ m_SeqIds

◆ m_SubjectHandle

◆ m_SubjectHitsRange

◆ m_SubjectID