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NCBI C++ ToolKit: CHitMatrixDataSource Class Reference

Search Toolkit Book for CHitMatrixDataSource

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

CHitMatrixDataSource () CHitMatrixDataSource. More...
virtual ~CHitMatrixDataSource () 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 () 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...
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 virtual ~IHitMatrixDataSource () 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 () virtual void DeleteThis (void) Virtual method "deleting" this object. More...
◆ TAlnIdMap ◆ TAlnPtrVector ◆ TAlnStats ◆ TDim ◆ THIdToHandleMap ◆ TIdExtract ◆ TScoreMap ◆ TSeqIdPtr ◆ TSeqIdRefVector ◆ TSeqIdVector ◆ TStd ◆ CHitMatrixDataSource() CHitMatrixDataSource::CHitMatrixDataSource ( ) ◆ ~CHitMatrixDataSource() CHitMatrixDataSource::~CHitMatrixDataSource ( ) virtual ◆ CanCreateRowBased() bool CHitMatrixDataSource::CanCreateRowBased ( ) const virtual ◆ GetAlignedIds() ◆ GetAlignedIdsForParams() ◆ GetBioseqHandle() ◆ GetHits() ◆ GetHitSeqIds() ◆ GetHitSeqIdsForParams() ◆ GetLabel() ◆ GetParams() void CHitMatrixDataSource::GetParams ( SParams & params ) const virtual ◆ GetQueryHandle() ◆ GetQueryHitsRange() TSeqRange CHitMatrixDataSource::GetQueryHitsRange ( ) virtual ◆ GetQueryId() IHitSeqId & CHitMatrixDataSource::GetQueryId ( void ) const virtual ◆ GetScope() CScope & CHitMatrixDataSource::GetScope ( void ) virtual ◆ GetScoreNames() void CHitMatrixDataSource::GetScoreNames ( vector< string > & names ) const virtual ◆ GetScoreRange() ◆ GetStdSegRange() ◆ GetSubjectHandle() ◆ GetSubjectHitsRange() TSeqRange CHitMatrixDataSource::GetSubjectHitsRange ( ) virtual ◆ GetSubjectId() IHitSeqId & CHitMatrixDataSource::GetSubjectId ( ) const virtual ◆ 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 ◆ SelectIds()

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 ◆ 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 ◆ x_CreateHit_Denseg() void CHitMatrixDataSource::x_CreateHit_Denseg ( const objects::CSeq_align & align, size_t q_index, size_t s_index ) protected ◆ x_CreateHit_Std() void CHitMatrixDataSource::x_CreateHit_Std ( const objects::CSeq_align & align, size_t q_index, size_t s_index ) protected ◆ x_CreateHits() void CHitMatrixDataSource::x_CreateHits ( const objects::CSeq_align & align ) protected ◆ x_CreateHits_Diagonal() void CHitMatrixDataSource::x_CreateHits_Diagonal ( const objects::CSeq_align & align, size_t q_index, size_t s_index ) protected ◆ x_CreateIds()

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() ◆ x_GetSeqAlignIds() void CHitMatrixDataSource::x_GetSeqAlignIds ( const objects::CSeq_align & align, TSeqIdRefVector & ids, bool unique ) const protected ◆ x_GoodSeg() ◆ x_TestAndSelectAlign() void CHitMatrixDataSource::x_TestAndSelectAlign ( const objects::CSeq_align & align ) protected ◆ x_TestAndSelectAligns() void CHitMatrixDataSource::x_TestAndSelectAligns ( TAlignVector & aligns ) protected ◆ 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(), val, and rapidjson::value.

Referenced by Init().

◆ m_Aligns ◆ m_AlnIdMap unique_ptr<TAlnIdMap> CHitMatrixDataSource::m_AlnIdMap protected ◆ m_AlnStats ◆ m_CanCreateRowBased bool CHitMatrixDataSource::m_CanCreateRowBased protected ◆ m_HIdToHandleMap ◆ m_Hits ◆ m_Params SParams CHitMatrixDataSource::m_Params protected ◆ m_QueryHandle objects::CBioseq_Handle CHitMatrixDataSource::m_QueryHandle protected ◆ m_QueryHitsRange TSeqRange CHitMatrixDataSource::m_QueryHitsRange protected ◆ m_QueryID unique_ptr<IHitSeqId> CHitMatrixDataSource::m_QueryID protected ◆ m_Scope CRef<objects::CScope> CHitMatrixDataSource::m_Scope protected ◆ m_ScoreMap ◆ m_SeqIds ◆ m_SubjectHandle objects::CBioseq_Handle CHitMatrixDataSource::m_SubjectHandle protected ◆ m_SubjectHitsRange TSeqRange CHitMatrixDataSource::m_SubjectHitsRange protected ◆ m_SubjectID unique_ptr<IHitSeqId> CHitMatrixDataSource::m_SubjectID protected

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

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