Search Toolkit Book for IAlnMultiDataSource

IAlnMultiDataSource - interface to a data source representing an abstract multiple alignment. More...

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

Inheritance diagram for IAlnMultiDataSource:

Collaboration diagram for IAlnMultiDataSource:

Public Types
typedef IAlnExplorer::TNumrow	TNumrow

typedef IAlnExplorer::TResidue	TResidue

typedef IAlnExplorer::ESearchDirection	TSearchDirection

typedef CRangeCollection< TSeqPos >	TRangeColl

using	TStatGraphs = map< char, vector< unsigned > >

Public Types inherited from CDataChangeNotifier
enum	EUpdateType { eChanged , eProgressReport , eError }

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
virtual bool	IsEmpty () const =0

virtual void	SetGapChar (TResidue gap_char)=0

virtual IAlnExplorer::EAlignType	GetAlignType () const =0

virtual TNumrow	GetNumRows (void) const =0
	number of rows in alignment More...

virtual TSeqPos	GetAlnStart (void) const =0

virtual TSeqPos	GetAlnStop (void) const =0

virtual TSeqPos	GetSeqStart (TNumrow row) const =0

virtual TSeqPos	GetSeqStop (TNumrow row) const =0

virtual int	GetConsensusRow () const =0
	returns index of the Consensus row or -1 if it doesn't exist More...

virtual bool	CanCreateConsensus ()=0

virtual void	CreateConsensus ()=0

virtual void	SetCreateConsensus (bool b)=0

virtual const IAlignRowHandle *	GetRowHandle (TNumrow row) const =0

virtual bool	IsSetAnchor (void) const =0
	Anchoring methods. More...

virtual TNumrow	GetAnchor (void) const =0

virtual bool	CanChangeAnchor (void) const =0

virtual bool	SetAnchor (TNumrow anchor)=0

virtual bool	UnsetAnchor (void)=0

virtual bool	CanGetId (TNumrow row) const =0

virtual const objects::CSeq_id &	GetSeqId (TNumrow row) const =0

virtual bool	IsPositiveStrand (TNumrow row) const =0

virtual bool	IsNegativeStrand (TNumrow row) const =0

virtual TSignedSeqPos	GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual TSignedSeqPos	GetAlnPosFromSeqPos (TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual string &	GetAlnSeqString (TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

virtual IAlnSegmentIterator *	CreateSegmentIterator (TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

virtual void	GetAlnFromSeq (TNumrow row, const TRangeColl &seq_coll, TRangeColl &aln_coll) const =0

virtual void	GetSeqFromAln (TNumrow row, const TRangeColl &aln_coll, TRangeColl &seq_coll) const =0

virtual bool	IsDataReadSync () const

void	CollectAlignStats (const TSignedSeqRange &range, TStatGraphs &graphs, bool translate_sequence=false) const

Public Member Functions inherited from CDataChangeNotifier
	CDataChangeNotifier ()
	CUIDataSource. More...

virtual	~CDataChangeNotifier ()

virtual void	SetListener (IListener *pListener)
	Subscribe a new listener. More...

virtual IListener *	GetListener ()

virtual void	NotifyListener (CUpdate &update)

Public Member Functions inherited from CObjectEx
	CObjectEx (void)

virtual	~CObjectEx (void)

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 CWeakObject
	CWeakObject (void)

virtual	~CWeakObject (void)

CPtrToObjectProxy *	GetPtrProxy (void) const
	Get pointer to proxy object containing pointer to this object. More...

Public Member Functions inherited from IScoringAlignment
virtual	~IScoringAlignment ()

virtual TSeqPos	GetBaseWidth (IAlnExplorer::TNumrow) const =0

virtual int	GetGenCode (IAlnExplorer::TNumrow row) const =0

virtual bool	IsMixedAlign () const
	New interfaces to handle alignemnt with mixed type (protein-to-genomic) To make them backward compatible, they have default implementation. 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...

Protected Member Functions inherited from CWeakObject
void	CleanWeakRefs (void) const
	Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More...

Protected Attributes inherited from CDataChangeNotifier
IListener *	m_Listener

Detailed Description

IAlnMultiDataSource - interface to a data source representing an abstract multiple alignment.

Definition at line 196 of file alnmulti_ds.hpp.

Member Typedef Documentation

◆ TNumrow

typedef IAlnExplorer::TNumrow IAlnMultiDataSource::TNumrow

Definition at line 201 of file alnmulti_ds.hpp.

◆ TRangeColl

typedef CRangeCollection<TSeqPos> IAlnMultiDataSource::TRangeColl

Definition at line 204 of file alnmulti_ds.hpp.

◆ TResidue

typedef IAlnExplorer::TResidue IAlnMultiDataSource::TResidue

Definition at line 202 of file alnmulti_ds.hpp.

◆ TSearchDirection

typedef IAlnExplorer::ESearchDirection IAlnMultiDataSource::TSearchDirection

Definition at line 203 of file alnmulti_ds.hpp.

◆ TStatGraphs

using IAlnMultiDataSource::TStatGraphs = map<char, vector<unsigned> >

Definition at line 268 of file alnmulti_ds.hpp.

Member Function Documentation

◆ CanChangeAnchor()

virtual bool IAlnMultiDataSource::CanChangeAnchor ( void ) const

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiModel::CanChangeMasterRow(), and CUpdateSeqAlignWidget::OnDSChanged().

◆ CanCreateConsensus()

virtual bool IAlnMultiDataSource::CanCreateConsensus ( )

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiWidget::x_UpdateOnStylesChanged().

◆ CanGetId()

virtual bool IAlnMultiDataSource::CanGetId ( TNumrow row ) const

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiCGIApplication::x_PreProcess(), and CAlnSpanVertModel::x_UpdateLocs().

◆ CollectAlignStats()

void IAlnMultiDataSource::CollectAlignStats	(	const TSignedSeqRange &	range,
		TStatGraphs &	graphs,
		bool	translate_sequence = `false`
	)		const

◆ CreateConsensus()

virtual void IAlnMultiDataSource::CreateConsensus ( )

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiModel::CreateConsensus().

◆ CreateSegmentIterator()

virtual IAlnSegmentIterator* IAlnMultiDataSource::CreateSegmentIterator	(	TNumrow	row,
		const IAlnExplorer::TSignedRange &	range,
		IAlnSegmentIterator::EFlags	flags
	)		const

pure virtual

Implements IScoringAlignment.

Implemented in CAlnVecMultiDataSource, and CSparseMultiDataSource.

Referenced by CollectAlignStats(), and CAlnSpanVertModel::x_PopulateRows().

◆ GetAlignType()

virtual IAlnExplorer::EAlignType IAlnMultiDataSource::GetAlignType ( ) const

pure virtual

Implements IScoringAlignment.

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CollectAlignStats(), CAlnMultiModel::GetDefaultMethod(), CAlnMultiWidget::OnShowMethodDlg(), CAlnMultiWidget::OnUpdateShowMethodDlg(), CAlnMultiWidget::SaveSettings(), CUpdateSeqAlignWidget::SaveSettingsV(), CAlnMultiModel::SetDefaultMethod(), CAlnSpanVertModel::x_CreateRows(), CAlnMultiWidget::x_GetDefMethodName(), CAlnMultiWidget::x_GetScoringMRUListName(), and CAlnSpanVertModel::x_PopulateRows().

◆ GetAlnFromSeq()

virtual void IAlnMultiDataSource::GetAlnFromSeq	(	TNumrow	row,
		const TRangeColl &	seq_coll,
		TRangeColl &	aln_coll
	)		const

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

◆ GetAlnPosFromSeqPos()

virtual TSignedSeqPos IAlnMultiDataSource::GetAlnPosFromSeqPos	(	TNumrow	row,
		TSeqPos	seq_pos,
		IAlnExplorer::ESearchDirection	dir = `IAlnExplorer::eNone`,
		bool	try_reverse_dir = `true`
	)		const

pure virtual

Implemented in CAlnVecMultiDataSource, and CSparseMultiDataSource.

Referenced by CAlignMarkHandler::x_AlnRangeFromSeqRange(), CAlignMarkHandler::x_HitTest(), and CAlnMultiWidget::x_UpdateOnSwitchMaster().

◆ GetAlnSeqString()

virtual string& IAlnMultiDataSource::GetAlnSeqString	(	TNumrow	row,
		string &	buffer,
		const IAlnExplorer::TSignedRange &	aln_range
	)		const

pure virtual

Implements IScoringAlignment.

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CollectAlignStats().

◆ GetAlnStart()

virtual TSeqPos IAlnMultiDataSource::GetAlnStart ( void ) const

pure virtual

Implements IScoringAlignment.

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiModel::SetPortLimits(), CAlnSpanVertModel::x_CreateRows(), and CAlnMultiCGIApplication::x_PreProcess().

◆ GetAlnStop()

virtual TSeqPos IAlnMultiDataSource::GetAlnStop ( void ) const

pure virtual

Implements IScoringAlignment.

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiModel::SetPortLimits(), CAlnSpanVertModel::x_CreateRows(), and CAlnMultiCGIApplication::x_PreProcess().

◆ GetAnchor()

virtual TNumrow IAlnMultiDataSource::GetAnchor ( void ) const

pure virtual

Implements IScoringAlignment.

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CollectAlignStats(), CAlnMultiModel::CreateRows(), CAlnMultiModel::SetVisible(), and CAlnMultiWidget::x_UpdateOnSwitchMaster().

◆ GetConsensusRow()

virtual int IAlnMultiDataSource::GetConsensusRow ( ) const

pure virtual

returns index of the Consensus row or -1 if it doesn't exist

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CollectAlignStats(), CAlnMultiModel::CreateRows(), CAlnMultiWidget::OnMakeConsensusRowMaster(), CAlnMultiModel::SetVisible(), CAlnMultiWidget::x_UpdateOnDataChanged(), and CAlnMultiWidget::x_UpdateOnStylesChanged().

◆ GetNumRows()

virtual TNumrow IAlnMultiDataSource::GetNumRows ( void ) const

pure virtual

number of rows in alignment

Implements IScoringAlignment.

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CollectAlignStats(), CwxExportAlnmultiImgDlg::Create(), CAlnMultiModel::CreateRows(), CAlnMultiWidget::SetSelectedIds(), CUpdateSeqAlignWidget::x_FindAnchorRow(), CAlnMultiWidget::x_GetMatchingHiddenRows(), CAlnSpanVertModel::x_Init(), CAlnMultiCGIApplication::x_PreProcess(), and CAlnMultiWidget::x_UpdateOnDataChanged().

◆ GetRowHandle()

virtual const IAlignRowHandle* IAlnMultiDataSource::GetRowHandle ( TNumrow row ) const

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiModel::CreateRows(), CAlnMultiModel::SetMasterRow(), CAlnMultiModel::x_CreateRow(), CAlnSpanVertModel::x_Init(), CAlnSpanVertModel::x_PopulateRows(), and CAlnSpanVertModel::x_UpdateMetaData().

◆ GetSeqFromAln()

virtual void IAlnMultiDataSource::GetSeqFromAln	(	TNumrow	row,
		const TRangeColl &	aln_coll,
		TRangeColl &	seq_coll
	)		const

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

◆ GetSeqId()

virtual const objects::CSeq_id& IAlnMultiDataSource::GetSeqId ( TNumrow row ) const

pure virtual

Implemented in CSparseMultiDataSource, and CAlnVecMultiDataSource.

Referenced by CAlnMultiWidget::GetMarks(), CAlnMultiWidget::GetSelectedIds(), CAlnMultiWidget::SetSelectedIds(), CUpdateSeqAlignWidget::x_FindAnchorRow(), CAlnMultiCGIApplication::x_PreProcess(), and CAlnSpanVertModel::x_UpdateLocs().

◆ GetSeqPosFromAlnPos()

virtual TSignedSeqPos IAlnMultiDataSource::GetSeqPosFromAlnPos	(	TNumrow	for_row,
		TSeqPos	aln_pos,
		IAlnExplorer::ESearchDirection	dir = `IAlnExplorer::eNone`,
		bool	try_reverse_dir = `true`
	)		const