NCBI C++ ToolKit
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CAlignmentTrackFactory Class Reference

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CAlignmentTrackFactory. More...

#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 CTrackTypeInfoGetThisTypeInfo () 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...
CObjectoperator= (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 CTrackTypeInfoGetTypeInfo ()
- 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< Uint8TCounter
 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, stringTAnnotNameTitleMap
 List of annotations with the corresponding titles. More...
typedef map< string, CRef< CAnnotMetaData > > TAnnotMetaDataList
- Public Types inherited from ITrackConfigurable
typedef map< string, stringTKeyValuePairs
- 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


Definition at line 295 of file alignment_track.hpp.

Constructor & Destructor Documentation

◆ CAlignmentTrackFactory()

CAlignmentTrackFactory::CAlignmentTrackFactory ( )

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


Implements ILayoutTrackFactory.

Definition at line 2352 of file alignment_track.cpp.

References CSeqUtils::eAnnot_Other, CSGAlignmentDS::eLoader_Unknown, map_checker< Container >::empty(), IAlnExplorer::fDNA, IAlnExplorer::fHomogenous, IAlnExplorer::fInvalid, CSGAlignmentDS::GetAnnotNames(), CSGGraphDS::GetAnnotNames(), CSeqUtils::GetAnnotSelector(), ISGDataSourceContext::GetDS(), GetMatchedAnnots(), CRef< C, Locker >::GetPointer(), CRenderingContext::GetVisSeqRange(), CSGAlignmentDS::InitAlignType(), map_checker< Container >::insert(), CSGAlignmentDS::IsBamLoader(), CSGAlignmentDS::IsCSRALoader(), CSeqUtils::IsUnnamed(), ITERATE, kReadsProfile, ILayoutTrackFactory::SExtraParams::m_Adaptive, ILayoutTrackFactory::SExtraParams::m_Annots, ILayoutTrackFactory::SExtraParams::m_CoverageGraphCheck, ILayoutTrackFactory::SExtraParams::m_FastConfig, ILayoutTrackFactory::SExtraParams::m_Level, ILayoutTrackFactory::SExtraParams::m_RemotePath, ILayoutTrackFactory::SExtraParams::m_SkipGenuineCheck, ILayoutTrackFactory::SExtraParams::m_SortBy, ILayoutTrackFactory::SExtraParams::m_TrackProfile, CSeqUtils::NameTypeStrToValue(), CSGConfigUtils::ParseProfileString(), s_ParseAlignDataLoader(), s_ParseAlignType(), CSGGenBankDS::SetAdaptive(), CSGAlignmentDS::SetAlnDataLoader(), CSGAlignmentDS::SetAnnotName(), SAnnotSelector::SetCollectNames(), CSGGenBankDS::SetDepth(), CSGAlignmentDS::SetHasCoverageGraph(), CSGAlignmentDS::SetRemotePath(), and CSGAlignmentDS::SetSortBy().

◆ GetExtensionIdentifier()

string CAlignmentTrackFactory::GetExtensionIdentifier ( ) const

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

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

◆ GetSettings()

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

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

Implements ILayoutTrackFactory.

Definition at line 326 of file alignment_track.hpp.

References GetTypeInfo().

Referenced by GetSettings().

◆ GetTypeInfo()

static const CTrackTypeInfo& CAlignmentTrackFactory::GetTypeInfo ( void  )

◆ NeedBackgroundInit()

virtual bool CAlignmentTrackFactory::NeedBackgroundInit ( ) const

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

Implements IIconProvider.

Definition at line 2874 of file alignment_track.cpp.

References CLayoutTrack::RegisterIconImage().

◆ UnderstandLevel()

virtual bool CAlignmentTrackFactory::UnderstandLevel ( ) const

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:
Modified on Sat Dec 09 04:46:22 2023 by rev. 669887