CAlnMultiDSBuilder Class Reference

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#include <gui/widgets/aln_multiple/alnmulti_ds_builder.hpp>

Collaboration diagram for CAlnMultiDSBuilder:

Public Types
typedef vector< CConstRef< objects::CSeq_annot > >	TAnnotVector
typedef vector< CConstRef< objects::CSeq_align > >	TAlignVector
typedef vector< const objects::CSeq_align * >	TAlnVector
typedef CAlnUserOptions	TOptions

Public Member Functions
	CAlnMultiDSBuilder ()
virtual	~CAlnMultiDSBuilder ()
void	Init (objects::CScope &scope, const objects::CSeq_align &align)
	initial data set from which an alignment will be build More...
void	Init (objects::CScope &scope, const objects::CSeq_annot &annot)
void	Init (objects::CScope &scope, const objects::CBioseq_Handle &handle)
void	Init (objects::CScope &scope, const objects::CBioseq &bioseq)
void	Init (objects::CScope &scope, const objects::CSeq_entry &seq_entry)
void	Init (objects::CScope &scope, TAlignVector &aligns)
void	Init (objects::CScope &scope, TAnnotVector &annots)
void	PreCreateDataSource (bool sparse)
CRef< IAlnMultiDataSource >	CreateDataSource ()
TOptions &	SetOptions ()
void	GetBioseqHandles (vector< CBioseq_Handle > &handles)
bool	GetSyncCreate ()
void	SetSyncCreate (bool sync)
void	SetSelectAnchor (bool select_anchor)
virtual void	SetListener (CDataChangeNotifier::IListener *pListener)
	Subscribe a new listener for data source. More...
virtual CDataChangeNotifier::IListener *	GetListener ()

Public Attributes
CAlnSeqId *	aaa

Protected Types
typedef CAlnSeqIdsExtract< CAlnSeqId >	TIdExtract
typedef vector< CRef< CAnchoredAln > >	TAnchoredAlnVector
typedef CAlnIdMap< TAlnVector, TIdExtract >	TAlnIdMap
typedef CAlnStats< TAlnIdMap >	TAlnStats

Protected Member Functions
void	x_Clear ()
void	x_TestAlignments ()
	Analyzes m_OrigAligns and decides how to build an alignment from it. More...
void	x_GetLinearAlignments (TAlignVector &aligns)
bool	x_IsLinear (const objects::CStd_seg &seg)
	returns true if CStd_seg is linear More...
void	x_PreCreateSparseDataSource ()
CRef< IAlnMultiDataSource >	x_CreateSparseDataSource ()
CRef< IAlnMultiDataSource >	x_CreateAlnVecDataSource ()

Protected Attributes
CAlnSeqId *	d
CRef< objects::CScope >	m_Scope
TAlignVector	m_OrigAligns
CRef< TAlnStats >	m_AlnStats
TAnchoredAlnVector	m_AnchoredAlns
CConstRef< objects::CSeq_id >	m_MasterId
TOptions	m_Options
bool	m_CreateSparse
	control alignment building More...
bool	m_SyncCreate
bool	m_SelectAnchor = false
CDataChangeNotifier::IListener *	m_Listener
	Try to set anchor automatically. More...

Detailed Description

Definition at line 61 of file alnmulti_ds_builder.hpp.

Member Typedef Documentation

TAlignVector

typedef vector< CConstRef<objects::CSeq_align> > CAlnMultiDSBuilder::TAlignVector

Definition at line 67 of file alnmulti_ds_builder.hpp.

TAlnIdMap

typedef CAlnIdMap<TAlnVector, TIdExtract> CAlnMultiDSBuilder::TAlnIdMap

protected

Definition at line 118 of file alnmulti_ds_builder.hpp.

TAlnStats

typedef CAlnStats<TAlnIdMap> CAlnMultiDSBuilder::TAlnStats

protected

Definition at line 119 of file alnmulti_ds_builder.hpp.

TAlnVector

typedef vector<const objects::CSeq_align*> CAlnMultiDSBuilder::TAlnVector

Definition at line 68 of file alnmulti_ds_builder.hpp.

TAnchoredAlnVector

typedef vector<CRef<CAnchoredAln> > CAlnMultiDSBuilder::TAnchoredAlnVector

protected

Definition at line 117 of file alnmulti_ds_builder.hpp.

TAnnotVector

typedef vector< CConstRef<objects::CSeq_annot> > CAlnMultiDSBuilder::TAnnotVector

Definition at line 66 of file alnmulti_ds_builder.hpp.

TIdExtract

typedef CAlnSeqIdsExtract<CAlnSeqId> CAlnMultiDSBuilder::TIdExtract

protected

Definition at line 116 of file alnmulti_ds_builder.hpp.

TOptions

typedef CAlnUserOptions CAlnMultiDSBuilder::TOptions

Definition at line 69 of file alnmulti_ds_builder.hpp.

Constructor & Destructor Documentation

CAlnMultiDSBuilder()

CAlnMultiDSBuilder::CAlnMultiDSBuilder

(

)

Definition at line 58 of file alnmulti_ds_builder.cpp.

~CAlnMultiDSBuilder()

CAlnMultiDSBuilder::~CAlnMultiDSBuilder ( )

virtual

Definition at line 66 of file alnmulti_ds_builder.cpp.

References x_Clear().

Member Function Documentation

CreateDataSource()

CRef< IAlnMultiDataSource > CAlnMultiDSBuilder::CreateDataSource

(

)

Definition at line 175 of file alnmulti_ds_builder.cpp.

References _TRACE, m_CreateSparse, m_OrigAligns, x_CreateAlnVecDataSource(), x_CreateSparseDataSource(), and x_TestAlignments().

Referenced by CAlignMultipleDemoDlg::Init(), CwxDemoAlignTableFrame::InitData(), CMultiAlignView::OnProjectChanged(), CAlignMultipleDemoDlg::OnRebuild(), CUpdateSeqPanel::x_InitAlnMultiDSBuilder(), CAlignSpanView::x_InitWidget(), and CAlnMultiCGIApplication::x_PreProcess().

GetBioseqHandles()

void CAlnMultiDSBuilder::GetBioseqHandles

(

vector< CBioseq_Handle > &

handles

)

Definition at line 189 of file alnmulti_ds_builder.cpp.

References ITERATE, m_AlnStats, and m_Scope.

Referenced by CAlignMultipleDemoDlg::OnRebuild().

GetListener()

virtual CDataChangeNotifier::IListener* CAlnMultiDSBuilder::GetListener ( )

inlinevirtual

Definition at line 98 of file alnmulti_ds_builder.hpp.

References m_Listener.

GetSyncCreate()

bool CAlnMultiDSBuilder::GetSyncCreate ( )

inline

Definition at line 89 of file alnmulti_ds_builder.hpp.

References m_SyncCreate.

Init() [1/7]

void CAlnMultiDSBuilder::Init	(	objects::CScope &	scope,
		const objects::CBioseq &	bioseq
	)

Definition at line 90 of file alnmulti_ds_builder.cpp.

References ExtractSeqAligns(), m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and x_Clear().

Init() [2/7]

void CAlnMultiDSBuilder::Init	(	objects::CScope &	scope,
		const objects::CBioseq_Handle &	handle
	)

Definition at line 112 of file alnmulti_ds_builder.cpp.

References CSeq_annot_Base::C_Data::e_Align, CSeqUtils::GetAnnotSelector(), i, m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and x_Clear().

Init() [3/7]

void CAlnMultiDSBuilder::Init	(	objects::CScope &	scope,
		const objects::CSeq_align &	align
	)

initial data set from which an alignment will be build

Definition at line 72 of file alnmulti_ds_builder.cpp.

References m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and x_Clear().

Referenced by CAlignMultipleDemoDlg::Init(), CwxDemoAlignTableFrame::InitData(), LoadObject(), CAlignMultipleDemoDlg::OnAccClick(), CMultiAlignView::OnProjectChanged(), CUpdateSeqPanel::x_InitAlnMultiDSBuilder(), CAlignSpanView::x_InitWidget(), and CAlnMultiCGIApplication::x_PreProcess().

Init() [4/7]

void CAlnMultiDSBuilder::Init	(	objects::CScope &	scope,
		const objects::CSeq_annot &	annot
	)

Definition at line 81 of file alnmulti_ds_builder.cpp.

References ExtractSeqAligns(), m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and x_Clear().

Init() [5/7]

void CAlnMultiDSBuilder::Init	(	objects::CScope &	scope,
		const objects::CSeq_entry &	seq_entry
	)

Definition at line 98 of file alnmulti_ds_builder.cpp.

References ExtractSeqAligns(), m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and x_Clear().

Init() [6/7]

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

Definition at line 129 of file alnmulti_ds_builder.cpp.

References m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and x_Clear().

Init() [7/7]

void CAlnMultiDSBuilder::Init	(	objects::CScope &	scope,
		TAnnotVector &	annots
	)

PreCreateDataSource()

void CAlnMultiDSBuilder::PreCreateDataSource

(

bool

sparse

)

Definition at line 165 of file alnmulti_ds_builder.cpp.

References m_CreateSparse, and x_PreCreateSparseDataSource().

Referenced by CwxDemoAlignTableFrame::InitData(), CMultiAlignView::OnProjectChanged(), CAlignMultipleDemoDlg::OnRebuild(), CUpdateSeqPanel::x_InitAlnMultiDSBuilder(), and CAlignSpanView::x_InitWidget().

SetListener()

virtual void CAlnMultiDSBuilder::SetListener ( CDataChangeNotifier::IListener *  pListener )

inlinevirtual

Subscribe a new listener for data source.

No ownership transfer for pListener

Definition at line 96 of file alnmulti_ds_builder.hpp.

References m_Listener.

Referenced by CMultiAlignView::OnProjectChanged().

SetOptions()

TOptions& CAlnMultiDSBuilder::SetOptions ( void  )

inline

Definition at line 86 of file alnmulti_ds_builder.hpp.

References m_Options.

Referenced by CMultiAlignView::OnProjectChanged(), and CAlignMultipleDemoDlg::OnRebuild().

SetSelectAnchor()

void CAlnMultiDSBuilder::SetSelectAnchor ( bool  select_anchor )

inline

Definition at line 92 of file alnmulti_ds_builder.hpp.

References m_SelectAnchor.

SetSyncCreate()

void CAlnMultiDSBuilder::SetSyncCreate ( bool  sync )

inline

Definition at line 90 of file alnmulti_ds_builder.hpp.

References m_SyncCreate.

Referenced by CwxDemoAlignTableFrame::InitData(), and CAlignSpanView::x_InitWidget().

x_Clear()

void CAlnMultiDSBuilder::x_Clear ( void  )

protected

Definition at line 154 of file alnmulti_ds_builder.cpp.

References m_AlnStats, m_AnchoredAlns, m_CreateSparse, m_MasterId, m_OrigAligns, m_Scope, CRef< C, Locker >::Reset(), and CConstRef< C, Locker >::Reset().

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

x_CreateAlnVecDataSource()

CRef< IAlnMultiDataSource > CAlnMultiDSBuilder::x_CreateAlnVecDataSource ( )

protected

Definition at line 247 of file alnmulti_ds_builder.cpp.

References CRef< C, Locker >::GetPointer(), m_Listener, m_OrigAligns, m_Scope, m_SelectAnchor, and m_SyncCreate.

Referenced by CreateDataSource().

x_CreateSparseDataSource()

CRef< IAlnMultiDataSource > CAlnMultiDSBuilder::x_CreateSparseDataSource ( )

protected

Definition at line 228 of file alnmulti_ds_builder.cpp.

References _TRACE, CStopWatch::Elapsed(), CConstRef< C, Locker >::GetPointer(), CSparseMultiDataSource::Init(), m_AnchoredAlns, m_Listener, m_MasterId, m_Options, m_OrigAligns, m_Scope, m_SyncCreate, CRef< C, Locker >::Reset(), CDataChangeNotifier::SetListener(), CStopWatch::Start(), and sw.

Referenced by CreateDataSource().

x_GetLinearAlignments()

void CAlnMultiDSBuilder::x_GetLinearAlignments ( TAlignVector &  aligns )

protected

Definition at line 302 of file alnmulti_ds_builder.cpp.

References CSeq_align_Base::GetSegs(), ITERATE, m_OrigAligns, and x_IsLinear().

Referenced by x_TestAlignments().

x_IsLinear()

bool CAlnMultiDSBuilder::x_IsLinear ( const objects::CStd_seg &  seg )

protected

returns true if CStd_seg is linear

Definition at line 341 of file alnmulti_ds_builder.cpp.

Referenced by x_GetLinearAlignments().

x_PreCreateSparseDataSource()

void CAlnMultiDSBuilder::x_PreCreateSparseDataSource ( )

protected

Definition at line 201 of file alnmulti_ds_builder.cpp.

References CreateAnchoredAlnVec(), ITERATE, m_AlnStats, m_AnchoredAlns, m_Options, m_OrigAligns, and CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back().

Referenced by PreCreateDataSource().

x_TestAlignments()

void CAlnMultiDSBuilder::x_TestAlignments ( )

protected

Analyzes m_OrigAligns and decides how to build an alignment from it.

Definition at line 257 of file alnmulti_ds_builder.cpp.

References _TRACE, CSeq_id_Handle::GetHandle(), CSeq_id_Handle::GetSeqId(), set< Key, Compare >::insert(), ITERATE, m_MasterId, set< Key, Compare >::size(), and x_GetLinearAlignments().

Referenced by CreateDataSource().

Member Data Documentation

aaa

CAlnSeqId* CAlnMultiDSBuilder::aaa

Definition at line 64 of file alnmulti_ds_builder.hpp.

d

CAlnSeqId* CAlnMultiDSBuilder::d

protected

Definition at line 114 of file alnmulti_ds_builder.hpp.

m_AlnStats

CRef<TAlnStats> CAlnMultiDSBuilder::m_AlnStats

protected

Definition at line 123 of file alnmulti_ds_builder.hpp.

Referenced by GetBioseqHandles(), x_Clear(), and x_PreCreateSparseDataSource().

m_AnchoredAlns

TAnchoredAlnVector CAlnMultiDSBuilder::m_AnchoredAlns

protected

Definition at line 124 of file alnmulti_ds_builder.hpp.

Referenced by x_Clear(), x_CreateSparseDataSource(), and x_PreCreateSparseDataSource().

m_CreateSparse

bool CAlnMultiDSBuilder::m_CreateSparse

protected

control alignment building

Definition at line 128 of file alnmulti_ds_builder.hpp.

Referenced by CreateDataSource(), PreCreateDataSource(), and x_Clear().

m_Listener

CDataChangeNotifier::IListener* CAlnMultiDSBuilder::m_Listener

protected

Try to set anchor automatically.

Definition at line 131 of file alnmulti_ds_builder.hpp.

Referenced by GetListener(), SetListener(), x_CreateAlnVecDataSource(), and x_CreateSparseDataSource().

m_MasterId

CConstRef<objects::CSeq_id> CAlnMultiDSBuilder::m_MasterId

protected

Definition at line 126 of file alnmulti_ds_builder.hpp.

Referenced by x_Clear(), x_CreateSparseDataSource(), and x_TestAlignments().

m_Options

TOptions CAlnMultiDSBuilder::m_Options

protected

Definition at line 127 of file alnmulti_ds_builder.hpp.

Referenced by SetOptions(), x_CreateSparseDataSource(), and x_PreCreateSparseDataSource().

m_OrigAligns

TAlignVector CAlnMultiDSBuilder::m_OrigAligns

protected

Definition at line 122 of file alnmulti_ds_builder.hpp.

Referenced by CreateDataSource(), Init(), x_Clear(), x_CreateAlnVecDataSource(), x_CreateSparseDataSource(), x_GetLinearAlignments(), and x_PreCreateSparseDataSource().

m_Scope

CRef<objects::CScope> CAlnMultiDSBuilder::m_Scope

protected

Definition at line 121 of file alnmulti_ds_builder.hpp.

Referenced by GetBioseqHandles(), Init(), x_Clear(), x_CreateAlnVecDataSource(), and x_CreateSparseDataSource().

m_SelectAnchor

bool CAlnMultiDSBuilder::m_SelectAnchor = false

protected

Definition at line 130 of file alnmulti_ds_builder.hpp.

Referenced by SetSelectAnchor(), and x_CreateAlnVecDataSource().

m_SyncCreate

bool CAlnMultiDSBuilder::m_SyncCreate

protected

Definition at line 129 of file alnmulti_ds_builder.hpp.

Referenced by GetSyncCreate(), SetSyncCreate(), x_CreateAlnVecDataSource(), and x_CreateSparseDataSource().

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

• include/gui/widgets/aln_multiple/alnmulti_ds_builder.hpp
• src/gui/widgets/aln_multiple/alnmulti_ds_builder.cpp