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NCBI C++ ToolKit: include/gui/widgets/seq_graphic/alignment_track.hpp Source File

eLayout_Default = eLayout_Adaptive

ELayout LayoutStrToValue(

& layout);

& LayoutValueToStr(ELayout layout);

SetAnnot(

& annot);

OnToggleContent(

);

OnChangeProjectedFeats();

SetDefaultProfile(

& profile);

(

& preset_style)

;

x_OnContentIconClicked();

x_OnLayoutIconClicked();

x_OnScoreIconClicked();

x_OnStatIconClicked();

x_OnTailsIconClicked();

x_OnLayoutPolicyChanged();

eIcon_Score = eIcon_MaxTrackIconID + 1,

eIcon_Stat = eIcon_MaxTrackIconID + 2,

eIcon_Tails = eIcon_MaxTrackIconID + 3

x_SaveConfiguration(

& preset_style)

;

x_LoadAlignmentSettings(

&

,

x_SaveAlignmentSettings(

&

,

x_LoadMultiAlignSettings();

x_SaveMultiAlignSettings()

;

x_LoadPWAlignSettings();

x_SavePWAlignSettings()

;

x_LoadAlignSmearSettings();

x_SaveAlignSmearSettings()

;

x_LoadMPPWAlignSettings();

x_LoadMatePairSettings();

x_SaveMatePairSettings()

;

m_DefaultProfile =

;

m_IsDefaultLayout =

;

m_MinPileUpCost = 3.;

m_MinAlignCost = 1.5;

m_MaxAlignCost = 15;

m_MaxAlignShownFull = 250000;

m_MaxAlignShownAdaptive = 7500;

m_ShowSecondPassAlignments =

;

TTrackMap CreateTracks(

SExtraParams& params = SExtraParams(),

TAnnotMetaDataList& src_annots = TAnnotMetaDataList())

;

GetMatchedAnnots(

TAnnotMetaDataList& src_annots,

TAnnotNameTitleMap& out_annots)

;

GetSettings(

& profile,

TKeyValuePairs& settings,

RegisterIconImages()

;

GetExtensionIdentifier()

;

GetExtensionLabel()

;

bool m_ShowUnalignedTailsForTrans2GenomicAln

EUnalignedTailsMode m_UnalignedTailsMode

virtual const CTrackTypeInfo & GetThisTypeInfo() const override

virtual bool NeedBackgroundInit() const override

Background track initialization.

static const CTrackTypeInfo & GetTypeInfo()

virtual bool UnderstandLevel() const override

Have any concept of level.

static CTrackTypeInfo m_TypeInfo

CRef< CSGAlignmentDS > m_DS

size_t m_CompactThreshold

Alignment number threshold between compact mode and non-compact mode.

CRef< CAlnStatConfig > m_StatConf

void x_LoadAlignmentSettings(const string &key, CRef< CAlignmentConfig > &conf)

common function for loading settings for multialign, pairwise aligns, and align smear.

CAlignmentTrack(const CAlignmentTrack &)

bool m_ShowUnalignedTailsForTrans2GenomicAln

vector< CRef< CAlnStatGlyph > > m_StatGlyph

void SetDSContext(ISGDataSourceContext *ds_ctx)

CAlignmentConfig::EHideSraAlignments m_HideSraAlignments

void x_LoadMPPWAlignSettings()

size_t m_ExtremeCompactThreshold

Alignment number threshold between compact mode and extreme compact mode.

void x_SavePWAlignSettings() const

virtual CRef< CSGGenBankDS > GetDataSource() override

CAlignmentTrack inline methods.

vector< int > TSubtypeVec

CRef< CSimpleLayout > m_GeneModelLayout

CRef< CColumnLayout > m_Column

void SetDefaultProfile(const string &profile)

CRef< CBoundaryParams > m_GeneGroupConf

void x_LoadAlignSmearSettings()

CRef< CAlignmentConfig > m_MultiAlignConf

> Default Settings profile

CIRef< ISGDataSourceContext > m_DSContext

void x_SaveMultiAlignSettings() const

void SetAlnType(IAlnExplorer::EAlignType type)

string m_MultiAlignProfile

IAlnExplorer::EAlignType m_AlnType

bool m_ShowAlignedSeqFeats

CRef< CAlignmentConfig > m_MPPWAlignConf

for linked pairwise aligns

CAlignmentConfig::EUnalignedTailsMode m_UnalignedTailsMode

TSubtypeVec m_ProjectedFeats

CAlignmentTrack & operator=(const CAlignmentTrack &)

string m_AlignSmearProfile

CRef< CAlignmentConfig > m_AlignSmearConf

CRef< CGeneModelConfig > m_GeneModelConfig

void x_SaveAlignSmearSettings() const

bool m_ShowIdenticalBases

void x_LoadMultiAlignSettings()

CRef< CMatePairConfig > m_MatePairConf

@ eLayout_Full

one alignment per row sorted by pos

@ eLayout_ExpandedByPos

one alignment per row sorted by pos

@ eLayout_Packed

smear/pack all alignments into one smear bar

CRef< CBoundaryParams > m_FeatGroupConf

void x_LoadPWAlignSettings()

CRef< CAlignmentConfig > m_PWAlignConf

void x_SaveAlignmentSettings(const string &key, CConstRef< CAlignmentConfig > conf) const

wxEvtHandler * m_ContentHandler

wx-related event handler.

CAppJobNotification Notification send by CAppJobEventTranslator.

CBatchJobResult – the data structure holding the seqgraphic job results for a batch job processing.

CDataTrack - a abstract base class for layout tracks which need to deal with background data retrieva...

virtual CRef< CSGGenBankDS > GetDataSource()=0

Method for accessing the data source.

virtual void x_UpdateData()=0

update track content.

virtual void x_OnJobCompleted(CAppJobNotification &notify)=0

virtual void x_UpdateBoundingBox()

Update the bounding box assuming children's sizes are fixed if any.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

virtual const CTrackTypeInfo & GetTypeInfo() const

ILayoutPolicy::TObjectList TObjectList

virtual void x_SaveSettings(const string &preset_style)

save the track settings to a profile string.

virtual void x_LoadSettings(const string &preset_style, const TKeyValuePairs &settings)

load the track settings.

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

virtual string GetFullTitle() const

get a more meaningful title.

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...

CSGJobResult – the data structure holding the seqgraphic job results.

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

CTrackTypeInfo - holds description of a layout track type.

IExtension IExtension interface represents an abstract pluggable component.

IIconProvider interface for tracks providing track icons.

ISGDSManager is seqgraphic data source manage that serves as an data source context.

ITrackConfigurable interface for tracks that are configurable.

map< string, string > TKeyValuePairs

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

const struct ncbi::grid::netcache::search::fields::KEY key

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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