Search Toolkit Book for CAlignmentTrackFactory

#include <gui/widgets/seq_graphic/alignment_track.hpp>

Inheritance diagram for CAlignmentTrackFactory:

Collaboration diagram for CAlignmentTrackFactory:

Public Member Functions
	CAlignmentTrackFactory ()

ILayoutTrackFactory interface implementation
create a layout track based on the input objects and extra parameters.
virtual TTrackMap	CreateTracks (SConstScopedObject &object, ISGDataSourceContext ds_context, CRenderingContext r_cntx, const SExtraParams &params=SExtraParams(), const TAnnotMetaDataList &src_annots=TAnnotMetaDataList()) const override
	CAlignmentTrackFactory. More...

virtual void	GetMatchedAnnots (const TAnnotMetaDataList &src_annots, const ILayoutTrackFactory::SExtraParams &params, TAnnotNameTitleMap &out_annots) const override

virtual bool	UnderstandLevel () const override
	Have any concept of level. More...

virtual bool	NeedBackgroundInit () const override
	Background track initialization. More...

virtual const CTrackTypeInfo &	GetThisTypeInfo () const override

ITrackConfigurable interface implementation
virtual CRef< objects::CTrackConfigSet >	GetSettings (const string &profile, const TKeyValuePairs &settings, const CTempTrackProxy *track_proxy) const override

IIconProvider interface implementation
virtual void	RegisterIconImages () const override

IExtension interface implementation
virtual string	GetExtensionIdentifier () const override
	returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this" More...

virtual string	GetExtensionLabel () const override
	returns a displayable label for this extension ( please capitalize the key words - "My Extension" ) 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

Public Member Functions inherited from ILayoutTrackFactory
virtual void	CloneTrack (const CLayoutTrack , CTempTrackProxy ) const
	duplicate any track setting from a given track instance to a proxy. More...

virtual	~ILayoutTrackFactory ()

virtual bool	SupportsExportToAsn1 () const

Public Member Functions inherited from ITrackConfigurable
virtual	~ITrackConfigurable ()

Public Member Functions inherited from IIconProvider
virtual	~IIconProvider ()

Public Member Functions inherited from IExtension
virtual	~IExtension ()

Static Public Member Functions
static const CTrackTypeInfo &	GetTypeInfo ()

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 Member Functions inherited from ILayoutTrackFactory
static void	GetMatchedAnnots (const TAnnotMetaDataList &src_annots, const vector< string > &target_annots, const string &annot_type, const string &track_type, TAnnotNameTitleMap &out_annots)
	Help function to find matched annotations. More...

static string	MergeAnnotAndFilter (const string &annot, const string &filter)
	create a new name based on annotation name and fitler string. More...

static string	ExtractAnnotName (const string &source)
	extract anntation name from a source string. More...

static string	ExtractFilterName (const string &source)
	extract filter name from a source string. More...

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 ILayoutTrackFactory
typedef map< string, CRef< CLayoutTrack > >	TTrackMap
	the tracks holding a list of annotation name and track pair. More...

typedef map< string, string >	TAnnotNameTitleMap
	List of annotations with the corresponding titles. More...

typedef map< string, CRef< CAnnotMetaData > >	TAnnotMetaDataList

Public Types inherited from ITrackConfigurable
typedef map< string, string >	TKeyValuePairs

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

CAlignmentTrackFactory.

Definition at line 295 of file alignment_track.hpp.

Constructor & Destructor Documentation

◆ CAlignmentTrackFactory()

CAlignmentTrackFactory::CAlignmentTrackFactory ( )

inline

Definition at line 303 of file alignment_track.hpp.

Member Function Documentation

◆ CreateTracks()

ILayoutTrackFactory::TTrackMap CAlignmentTrackFactory::CreateTracks	(	SConstScopedObject &	object,
		ISGDataSourceContext *	ds_context,
		CRenderingContext *	r_cntx,
		const SExtraParams &	params = `SExtraParams()`,
		const TAnnotMetaDataList &	src_annots = `TAnnotMetaDataList()`
	)		const

overridevirtual

CAlignmentTrackFactory.

Implements ILayoutTrackFactory.

Definition at line 2352 of file alignment_track.cpp.

◆ GetExtensionIdentifier()

string CAlignmentTrackFactory::GetExtensionIdentifier ( ) const

overridevirtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 2882 of file alignment_track.cpp.

References CTrackTypeInfo::GetId(), and CAlignmentTrack::m_TypeInfo.

◆ GetExtensionLabel()

string CAlignmentTrackFactory::GetExtensionLabel ( ) const

overridevirtual

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

Implements IExtension.

Definition at line 2888 of file alignment_track.cpp.

References CTrackTypeInfo::GetDescr(), and CAlignmentTrack::m_TypeInfo.

◆ GetMatchedAnnots()

void CAlignmentTrackFactory::GetMatchedAnnots	(	const TAnnotMetaDataList &	src_annots,
		const ILayoutTrackFactory::SExtraParams &	params,
		TAnnotNameTitleMap &	out_annots
	)		const

overridevirtual

Reimplemented from ILayoutTrackFactory.

Definition at line 2491 of file alignment_track.cpp.

References ILayoutTrackFactory::GetMatchedAnnots(), and ILayoutTrackFactory::SExtraParams::m_Annots.

Referenced by CreateTracks().

◆ GetSettings()

CRef< CTrackConfigSet > CAlignmentTrackFactory::GetSettings	(	const string &	profile,
		const TKeyValuePairs &	settings,
		const CTempTrackProxy *	track_proxy
	)		const

overridevirtual

Implements ITrackConfigurable.

Definition at line 2514 of file alignment_track.cpp.

References CONFIG_ALL, CONFIG_NUC, CONFIG_PROT, CONFIG_SRA, CTrackConfigUtils::CreateCheckBox(), CTrackConfigUtils::CreateChoice(), CTrackConfigUtils::CreateChoiceItem(), CAlnStatGlyph::CreateDisplayOptions(), CTrackConfigUtils::CreateHiddenSetting(), CAlignmentConfig::eHide_BadReads, CAlignmentConfig::eHide_Both, CAlignmentConfig::eHide_Duplicates, CAlignmentConfig::eHide_None, CAlignmentTrack::eLayout_Adaptive, CAlignmentTrack::eLayout_ExpandedByPos, CAlignmentTrack::eLayout_Full, CAlignmentTrack::eLayout_Packed, NStr::EqualNocase(), CAlignmentConfig::eTails_Hide, CAlignmentConfig::eTails_ShowGlyph, CAlignmentConfig::eTails_ShowSequence, IAlnExplorer::fHomogenous, NStr::FindNoCase(), IAlnExplorer::fInvalid, IAlnExplorer::fMixed, IAlnExplorer::fProtein, CRegistryReadView::GetBool(), CTrackTypeInfo::GetDescr(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CSGConfigUtils::GetReadView(), CSGAlnQualityScore::GetScoreName(), CTempTrackProxy::GetSortBy(), CRegistryReadView::GetString(), GetThisTypeInfo(), CTempTrackProxy::GetTrack(), CAlignmentTrack::HideFlagValueToStr(), ITERATE, kBaseKey, kDefaultScoringMethod, kDefaultSraFilter, kDefaultUnalignedTailsMode, kDefProfile, kEmptyStr, label, CAlignmentTrack::LayoutStrToValue(), CAlignmentTrack::LayoutValueToStr(), LOG_POST, CAlignmentTrack::m_AlnType, registry, s_LayoutToDisplayName(), CTrackConfigSet_Base::Set(), CAlignSorterFactory::SetTrackSetting(), NStr::StringToBool(), NStr::StringToInt(), CAlignmentTrack::UnalignedTailsModeValueToStr(), and Warning().

◆ GetThisTypeInfo()

virtual const CTrackTypeInfo& CAlignmentTrackFactory::GetThisTypeInfo ( ) const

inlineoverridevirtual

Implements ILayoutTrackFactory.

Definition at line 326 of file alignment_track.hpp.

References GetTypeInfo().

Referenced by GetSettings().

◆ GetTypeInfo()

static const CTrackTypeInfo& CAlignmentTrackFactory::GetTypeInfo ( void )

inlinestatic

Definition at line 330 of file alignment_track.hpp.

References CAlignmentTrack::m_TypeInfo.

Referenced by CTrackConfigManager::CreateTrackConfig(), and GetThisTypeInfo().

◆ NeedBackgroundInit()

virtual bool CAlignmentTrackFactory::NeedBackgroundInit ( ) const

inlineoverridevirtual

Background track initialization.

Since some of track initializations will be time consumming, but others are not, we need to know if there is a need to do background track initialization.

Implements ILayoutTrackFactory.

Definition at line 323 of file alignment_track.hpp.

◆ RegisterIconImages()

void CAlignmentTrackFactory::RegisterIconImages ( ) const

overridevirtual

Implements IIconProvider.

Definition at line 2874 of file alignment_track.cpp.

References CLayoutTrack::RegisterIconImage().

◆ UnderstandLevel()

virtual bool CAlignmentTrackFactory::UnderstandLevel ( ) const

inlineoverridevirtual

Have any concept of level.

Feature retrieving level (adaptive or exact level) for annotation selector.

Implements ILayoutTrackFactory.

Definition at line 320 of file alignment_track.hpp.

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

include/gui/widgets/seq_graphic/alignment_track.hpp
src/gui/widgets/seq_graphic/alignment_track.cpp

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CAlignmentTrackFactory()

Member Function Documentation

◆ CreateTracks()

◆ GetExtensionIdentifier()

◆ GetExtensionLabel()

◆ GetMatchedAnnots()

◆ GetSettings()

◆ GetThisTypeInfo()

◆ GetTypeInfo()

◆ NeedBackgroundInit()

◆ RegisterIconImages()

◆ UnderstandLevel()