Search Toolkit Book for CAlignmentTrack

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

Inheritance diagram for CAlignmentTrack:

Collaboration diagram for CAlignmentTrack:

Public Types
enum	EJobType { eJob_Align , eJob_AlignFeats , eJob_AlignScore , eJob_AlignStat , eJob_CoverageGraph }

enum	ELayout { eLayout_Adaptive = 0 , eLayout_Packed , eLayout_ExpandedByPos , eLayout_Full , eLayout_Default = eLayout_Adaptive }

enum	EAlignGlyphType { eAlign_Multi , eAlign_PW , eAlign_MatePair , eAlign_Smear , eAlign_Graph , eAlign_Stat , eAlign_Non }

Public Types inherited from CGlyphContainer
typedef vector< CRef< CCommentGlyph > >	TComments

typedef set< string >	THighlights

typedef map< string, THighlights >	TKeyHighlights

Public Types inherited from CLayoutTrack
enum	FTrackAttr { fMovable = 1 << 0 , fCollapsible = 1 << 1 , fFrameVisible = 1 << 2 , fShowTitle = 1 << 3 , fShowAlways = 1 << 4 , fFullTrack = 1 << 5 , fNavigable = 1 << 6 , fShowIcons = 1 << 7 , fDefaultAttr }

typedef vector< CConstRef< CSeqGlyph > >	TLayObjVector

typedef unsigned	TTrackAttrFlags

typedef list< CRef< CLayoutTrack > >	TLayoutTracks

typedef map< string, string >	TKeyValuePairs

Public Types inherited from CSeqGlyph
enum	ENeighbours { eNghbrs_None = 0x0 , eNghbrs_Left = 0x1 , eNghbrs_Right = 0x2 , eNghbrs_Both = 0x3 }

typedef vector< CHTMLActiveArea >	TAreaVector

typedef list< CRef< CSeqGlyph > >	TObjects

typedef list< CConstRef< CSeqGlyph > >	TConstObjects

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 CEventHandler
enum	EDispatch { eDispatch_SelfOnly , eDispatch_AllHandlers , eDispatch_FirstHandler , eDispatch_Default = eDispatch_AllHandlers }
	enum controlling dispatching strategies More...

enum	EPoolName { ePool_Default = 0 , ePool_Parent , ePool_Child , ePool_Sibling , ePool_NextAvailable }
	Identifiers for standard pools. More...

typedef vector< CEventHandler * >	TListeners

typedef map< int, TListeners >	TPools

typedef list< AutoPtr< SPostRequest > >	TPostRequests

typedef std::map< CEventHandler *, int >	THandlerToCount

typedef void(*	FOnPostCallback) ()

Public Member Functions
	CAlignmentTrack (CSGAlignmentDS ds, CRenderingContext r_cntx)

virtual	~CAlignmentTrack ()

void	SetAnnot (const string &annot)

void	SetDSContext (ISGDataSourceContext *ds_ctx)

void	SetAlnType (IAlnExplorer::EAlignType type)

void	SetDefaultProfile (const string &profile)

CLayoutTrack public methods.
virtual const CTrackTypeInfo &	GetTypeInfo () const override

virtual string	GetFullTitle () const override
	get a more meaningful title. More...

CDataTrack public methods
virtual CRef< CSGGenBankDS >	GetDataSource () override
	CAlignmentTrack inline methods. More...

virtual CConstRef< CSGGenBankDS >	GetDataSource () const override

content menu event handlers.
void	OnToggleContent (int id)

void	OnChangeProjectedFeats ()

CGlyphContainer public methods.
virtual void	GetHTMLActiveAreas (TAreaVector *p_areas) const override
	Get html active areas. More...

virtual CHTMLActiveArea *	InitHTMLActiveArea (TAreaVector *p_areas) const override
	Initialize the HTML active area for a track. More...

virtual void	x_UpdateBoundingBox () override
	Update the bounding box assuming children's sizes are fixed if any. More...

Public Member Functions inherited from CDataTrack
	CDataTrack (CRenderingContext *r_cntx)

virtual	~CDataTrack ()

virtual void	DeleteAllJobs ()

virtual bool	AllJobsFinished () const

void	OnAJNotification (CEvent *evt)
	event handlers for job notification event. More...

void	OnAJProgress (CEvent *evt)

void	SetVisRange (const TSeqRange &range)

virtual void	Update (bool layout_only)
	Update content and layout including the bounding box. More...

Public Member Functions inherited from CGlyphContainer
	CGlyphContainer (CRenderingContext *r_cntx)

virtual	~CGlyphContainer ()

void	Add (CSeqGlyph *obj)
	Append a layout object to the end. More...

void	SetObjects (const CLayoutGroup::TObjectList &objs)

virtual void	SetComments (const string &comment_str)
	set comments. More...

virtual void	SetHighlights (const string &hl_str)
	set a list of 'object' need to be highlighted. More...

void	SetCommentGlyphs (const CSeqGlyph::TObjects &objs, CRef< CCommentConfig > config)

void	ResetCommentGlyph ()

void	SetLabelGlyphs (const CSeqGlyph::TObjects &objs, CRef< CCommentConfig > config)

void	ResetLabelGlyph ()

const THighlights &	GetHighlights () const

const TKeyHighlights &	GetHighlightsByKey () const

CLayoutGroup &	SetGroup ()

const CLayoutGroup &	GetGroup () const

CLayoutGroup::TObjectList &	SetChildren ()

const CLayoutGroup::TObjectList &	GetChildren () const

bool	Empty () const

void	SetLayoutPolicy (ILayoutPolicy *policy)
	Set policy on how to deploy the layout of its children. More...

virtual CRef< CSeqGlyph >	HitTest (const TModelPoint &p)
	Hit testing. More...

virtual bool	HitTestHor (TSeqPos x, const CObject *obj)

virtual bool	Intersects (const TModelRect &rect, TConstObjects &objs) const
	Intersect testing. More...

virtual bool	Accept (IGlyphVisitor *visitor)
	Interface for accepting an IGlyphVisitor. More...

Public Member Functions inherited from CLayoutTrack
	CLayoutTrack (CRenderingContext *r_cntx)

virtual	~CLayoutTrack ()

void	LoadProfile (const string &profile_str)
	set track profile and load settings. More...

void	SaveProfile ()

void	SetProfile (const string &preset_style)
	CLayoutTrack inline method implmentation. More...

const string &	GetProfile () const

string	GetTitle () const
	get the track title. More...

const TTrackErrorStatus &	GetErrorStatus () const

void	SetErrorStatus (const TTrackErrorStatus &ErrorStatus)

bool	isInErrorStatus () const

bool	isRmtBased () const

bool	isRemotePath () const

void	MouseOut ()

bool	OnMotion (const TModelPoint &pt)

bool	GetShowTitle () const

void	SetShowTitle (bool flag)

void	SetConfig (CRef< CSeqGraphicConfig > conf)

int	GetIndent () const

void	SetIndent (int indent)

void	SetMsg (const string &msg)

void	SetParentTrack (CLayoutTrack *parent)

CLayoutTrack *	GetParentTrack ()

const CLayoutTrack *	GetParentTrack () const

bool	IsOn () const

bool	IsExpanded () const

bool	IsMovable () const

bool	IsCollapsible () const

void	SetShow (bool shown)
	set the flag only. More...

void	SetExpanded (bool f)

void	SetShowFrame (bool show)

void	MoveTo (TModelUnit y)

void	SetTrackAttr (TTrackAttrFlags flags)

void	SetTitle (const string &label, const string &default_title=NcbiEmptyString)

void	SetIsBlast (bool isBlast)

void	SetHost (ILayoutTrackHost *host)

void	SetOrder (int order)

int	GetOrder () const

void	SetId (const string &id)

const string &	GetId () const

void	CloseMe ()
	close this track. More...

void	ShowMe ()

void	Expand (bool expand)
	Collapse or expand the track. More...

virtual bool	OnLeftDown (const TModelPoint &p)

virtual bool	OnLeftDblClick (const TModelPoint &p)

virtual bool	NeedTooltip (const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const
	Check if need to show tooltip. More...

virtual void	GetTooltip (const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const
	Get the tooltip if available. More...

Public Member Functions inherited from CSeqGlyph
	CSeqGlyph ()

virtual	~CSeqGlyph ()

virtual TSeqRange	GetRange (void) const
	get the total range of this object. More...

virtual bool	SetSelected (bool flag)
	Select or deselect this glyph. More...

virtual void	SetHideLabel (bool)
	Force to hide label. More...

virtual bool	HasSideLabel () const
	Query if there is label and label is on the side. More...

virtual bool	IsClickable () const
	Query if this glyph is clickable. More...

virtual bool	LessBySeqPos (const CSeqGlyph &obj) const
	compare this object to another based on glyph sequence position. More...

bool	LessByPos (const CSeqGlyph &obj) const
	compare this object to another, based on glyph geometry position. More...

bool	LessBySeqSize (const CSeqGlyph &obj) const
	compare this object to another, based on sequence size. More...

bool	LessBySize (const CSeqGlyph &obj) const
	compare this object to another, based on geometry size. More...

void	Draw () const
	render the layout. More...

TModelRect	GetModelRect () const
	get the bounding box. More...

bool	IsIn (const TModelPoint &p) const
	Hit test for points in PARENT COORD. More...

bool	IsIn (TModelUnit x, TModelUnit y) const

bool	IsInHor (TModelUnit x) const

void	SetRender (IGlyphRenderer *renderer)
	set customized renderer for this layout objects. More...

void	SetRenderingContext (CRenderingContext *context)
	Set the rendering context. More...

const CRenderingContext *	GetRenderingContext () const
	Get the rendering context. More...

void	SetTearline (size_t Tearline)
	tearline factor – used to limit a list of glyphs More...

size_t	GetTearline () const

void	SetTearlineText (const string &sTearlineText)
	tearline text – if set, is appended to the glyph name (does not naffect processing otherwise) More...

string	GetTearlineText () const

void	SetRowNum (size_t cur_row)

size_t	GetRowNum () const

void	SetVisible (size_t v)

size_t	GetVisible () const

int	GetLevel () const

void	SetLevel (int Level)

virtual string	GetPName () const
	persistent name of the glyph should not depend on the instance of the glyph, but should uniquely reflect its contents so two glyphs having the same contents will have the same name currently used to track isDrawn() status for expandable glyphs default implementation returns an empty string implementations exist for CFeatGlyph (name of the contained feature) and CLayoutGroup (concatenation of all sorted children names) More...

float	GetFadeFactor () const

virtual bool	OnLeftUp (const TModelPoint &)

virtual bool	OnContextMenu (wxContextMenuEvent &event)

bool	IsSelected () const

bool	IsHighlighted () const

CRgbaColor *	GetHighlightsColor () const

virtual TModelUnit	GetHeight () const

virtual TModelUnit	GetWidth () const

virtual TModelUnit	GetLeft () const

virtual TModelUnit	GetTop () const

virtual TModelUnit	GetRight () const

virtual TModelUnit	GetBottom () const

const TModelPoint &	GetPos () const

void	GetPosInWorld (TModelPoint &pos) const
	Get top left position in world coordinate. More...

const CSeqGlyph *	GetParent (void) const

CSeqGlyph *	GetParent (void)

ENeighbours	GetNeighbours () const

void	SetHighlighted (bool flag)

void	SetHighlightsColor (const CRgbaColor &hl_color)

void	SetHighlightsColor (const string &hl_color_str)

virtual void	SetWidth (TModelUnit w)

virtual void	SetHeight (TModelUnit h)

virtual void	SetLeft (TModelUnit l)

virtual void	SetTop (TModelUnit b)

virtual void	SetPos (const TModelPoint &upper_left)

void	SetParent (CSeqGlyph *p)

CSeqGlyph *	SetParent (void)

void	SetNeighbours (ENeighbours neighbours)

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 CEventHandler
	CEventHandler ()
	CEventHandler. More...

virtual	~CEventHandler ()

virtual void	AddListener (CEventHandler *listener, int pool_name=ePool_Default)
	Add a listener. More...

virtual void	RemoveListener (CEventHandler *listener)
	Remove a listener. More...

virtual void	RemoveAllListeners (void)

virtual bool	HasListener (CEventHandler *listener, int pool_name=ePool_Default) const
	returns "true" if the given listener belongs to the specified pool More...

virtual const TListeners *	GetListeners (int pool_name=ePool_Default) const
	returns a set of listeners fro the specified pool More...

virtual bool	OnEvent (CEvent *evt)
	Processes en event. Returns "true" if event has been processed. More...

virtual bool	Dispatch (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Dispatches an event to the listeners (but does not handle it). More...

virtual bool	Send (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Sends an event synchronously. More...

virtual bool	Send (CEvent *evt, int pool_name)

void	Post (CRef< CEvent > evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Handles an event asynchronously (process and/or dispatch). More...

Static Public Member Functions
static methods.
static methods for converting layout str and label position str layout setting and label position setting.
static ELayout	LayoutStrToValue (const string &layout)

static const string &	LayoutValueToStr (ELayout layout)

static CAlignmentConfig::ELabelPosition	LabelPosStrToValue (const string &pos)

static const string &	LabelPosValueToStr (CAlignmentConfig::ELabelPosition pos)

static CAlignmentConfig::EHideSraAlignments	HideFlagStrToValue (const string &hideSra)

static const string &	HideFlagValueToStr (CAlignmentConfig::EHideSraAlignments hideSra)

static CAlignmentConfig::EUnalignedTailsMode	UnalignedTailsModeStrToValue (const string &tailsMode)

static const string &	UnalignedTailsModeValueToStr (CAlignmentConfig::EUnalignedTailsMode tailsMode)

Static Public Member Functions inherited from CLayoutTrack
static void	RegisterIconImage (const TIconAlias &key, const string &img_file)
	register the image for an icon. More...

Static Public Member Functions inherited from CSeqGlyph
static bool	PointInRect (const TModelPoint &p, const TModelRect &rc)

static bool	PointInRect (TModelUnit x, TModelUnit y, const TModelRect &rc)

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 CEventHandler
static bool	HandlePostRequest ()

static void	ClearPostQueue ()
	erases all events from the queue More...

static void	DestroyPostQueue ()

Protected Member Functions
void	x_OnContentIconClicked ()

void	x_OnLayoutIconClicked ()

void	x_OnScoreIconClicked ()

void	x_OnStatIconClicked ()

void	x_OnTailsIconClicked ()

void	x_OnLayoutPolicyChanged ()

void	x_AddAlignmentLayout (const CSGJobResult &result)

void	x_AddAlignFeatLayout (CBatchJobResult &results)

void	x_AddGraphLayout (const CSGJobResult &result)

void	x_AddAlignStatLayout (const CSGJobResult &result)

CLayoutTrack virtual methods overloading.
virtual void	x_LoadSettings (const string &preset_style, const TKeyValuePairs &settings) override
	load the track settings. More...

virtual void	x_SaveSettings (const string &preset_style) override
	save part of settings to a profile string. More...

virtual void	x_OnIconClicked (TIconID id) override
	Mouse left-click event handler on an icon. More...

CDataTrack pure virtual interfaces
virtual void	x_UpdateData () override
	update track content. More...

virtual void	x_OnJobCompleted (CAppJobNotification &notify) override

Protected Member Functions inherited from CDataTrack
	DECLARE_EVENT_MAP ()

virtual void	x_Expand (bool expand)
	Collapse or expand the track. More...

void	x_UpdateLayout ()

const TSeqRange &	x_GetVisRange () const

virtual bool	x_IsJobNeeded (CAppJobDispatcher::TJobID id) const

virtual void	x_OnJobFailed (CAppJobNotification &notify)

virtual void	x_OnAllJobsFinished ()

Protected Member Functions inherited from CGlyphContainer
virtual string	x_GetHistMsg () const
	Histogram configuration (linear, log, etc) is also on the title bar but multiple track types can have histograms, so we use virtual functinons. More...

virtual void	x_RenderContent () const
	The content rendering must be implemented in the derived layout tracks. More...

virtual bool	x_Empty () const

virtual void	x_ClearContent ()

Protected Member Functions inherited from CLayoutTrack
virtual void	x_Draw () const
	The default renderer for this layout object. More...

virtual bool	x_ShowTitle () const
	Need to preserve title space and show the title. More...

TModelUnit	x_GetTBHeight () const
	Get title bar height including margin. More...

CConstRef< CSeqGraphicConfig >	x_GetGlobalConfig () const
	Method for getting global configuration from rendering context. More...

void	x_OnLayoutChanged ()
	update the layout. More...

virtual void	x_GetTBRect (TModelRect &rc) const
	Get title bar rectange exclude top margin. More...

virtual void	x_RenderProgressBar () const
	Method for rendering the job loading or layout generating progress. More...

virtual void	x_RenderTitleBar () const
	Method for rendering the track title bar. More...

virtual void	x_RenderIcon (TIconID id, bool highlighted, bool lite_version=false) const
	Render track icons. More...

virtual int	x_GetIconState (TIconID id) const
	Get current status for a given button. More...

void	x_RegisterIcon (const SIconInfo &icon)
	register track icons. More...

void	x_DeregisterIcon (TIconID id)
	deregister an icon if already registered. More...

void	x_EnableIcon (TIconID id, bool enabled)
	Enable/disable an existing icon. More...

void	x_ShowIcon (TIconID id, bool shown)
	Show/hide an existing icon. More...

int	x_HitIconTest (const TModelPoint &p) const
	hit any icon?. More...

bool	x_HitTitleBar (const TModelPoint &p) const
	hit the title bar?. More...

void	x_SetStatus (const string &msg, int progress)

void	x_SetStartStatus ()

void	x_SetFinishStatus ()

bool	x_IsNCBITrack () const
	Indicates whether the track is NCBI track. More...

Protected Member Functions inherited from CSeqGlyph
virtual void	x_DrawHighlight () const

void	x_DrawInnerLabelColumns (TModelUnit base, const string &label, const CRgbaColor &color, const CGlTextureFont &font, bool side_label_visible) const

void	x_DrawInnerLabels (TModelUnit base, const string &label, const CRgbaColor &color, const CGlTextureFont &font, bool side_label_visible, bool inside_only, vector< TModelRange > labels_ranges=nullptr, TSeqRange interval=nullptr, bool XOR_mode=false) const

void	x_DrawTruncatedLabel (const string &label, const CGlTextureFont &font, TModelUnit width, TModelUnit x, TModelUnit y, vector< TModelRange > *labels_ranges=nullptr) const

void	x_DrawException () const
	Draw a shading background to indicate exception. More...

void	x_Parent2Local (TModelPoint &pnt) const
	Transform the coordiante from parent coord. to local coord. More...

void	x_Parent2Local (TModelUnit &, TModelUnit &y) const
	Transform the coordiante from parent coord. to local coord. More...

void	x_Parent2Local (TModelRect &rect) const
	Transform the coordiante from parent coord. to local coord. More...

void	x_World2Local (TModelPoint &p) const
	Transform the coordiante from world coord. to local coord. More...

void	x_World2Local (TModelUnit &x, TModelUnit &y) const

void	x_Local2World (TModelPoint &p) const
	Transform the coordiantes from local coord. to world coord. More...

void	x_Local2World (TModelUnit &x, TModelUnit &y) const

void	x_InitHTMLActiveArea (CHTMLActiveArea &area) const
	initialize the basic information for a given active area. More...

bool	x_Visible_V () const
	is this glyph visible in vertical direction? More...

template<class T >
bool	x_IntersectVisible (const CRange< T > &SeqRange, T &from, T &to) const

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 Member Functions inherited from CEventHandler
virtual const SEvtMap *	GetEventMap () const

void	x_DeclareDead ()
	Removes itself unavailable for async event delivery. More...

void	x_AddListenerToPool (CEventHandler *listener, int pool_name)

Private Types
enum	EAlignIconID { eIcon_Score = eIcon_MaxTrackIconID + 1 , eIcon_Stat = eIcon_MaxTrackIconID + 2 , eIcon_Tails = eIcon_MaxTrackIconID + 3 }

typedef vector< int >	TSubtypeVec

Private Member Functions
void	x_AddAlignFeat_Recursive (CLayoutGroup::TObjectList &objs)

void	x_LoadAlignedSeqFeats (vector< CRef< CAlignGlyph > > &aligns, CAlignGlyph *aln)

EAlignGlyphType	x_GetAlignGlyphType (const CSeqGlyph *glyph) const

void	x_SaveConfiguration (const string &preset_style) const
	save all track settings to the configuration file. More...

void	x_LoadAlignmentSettings (const string &key, CRef< CAlignmentConfig > &conf)
	common function for loading settings for multialign, pairwise aligns, and align smear. More...

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

void	x_LoadMultiAlignSettings ()

void	x_SaveMultiAlignSettings () const

void	x_LoadPWAlignSettings ()

void	x_SavePWAlignSettings () const

void	x_LoadAlignSmearSettings ()

void	x_SaveAlignSmearSettings () const

void	x_LoadMPPWAlignSettings ()

void	x_LoadMatePairSettings ()

void	x_SaveMatePairSettings () const

void	x_SetMsg ()

CRef< CHistParams >	x_GetGraphParams ()

int	x_LayoutToCutoff (CAlignmentTrack::ELayout layout)
	CAlignmentTrack. More...

int	x_LayoutToCutoff_SRA (CAlignmentTrack::ELayout layout)

prohibited copy constructor and assignment operator.
	CAlignmentTrack (const CAlignmentTrack &)

CAlignmentTrack &	operator= (const CAlignmentTrack &)

Private Attributes
wxEvtHandler *	m_ContentHandler
	wx-related event handler. More...

string	m_AnnotName

CRef< CSGAlignmentDS >	m_DS

CIRef< ISGDataSourceContext >	m_DSContext

string	m_DefaultProfile = "Default"

CRef< CAlignmentConfig >	m_MultiAlignConf
	> Default Settings profile More...

CRef< CAlignmentConfig >	m_PWAlignConf

CRef< CAlignmentConfig >	m_AlignSmearConf

CRef< CAlignmentConfig >	m_MPPWAlignConf
	for linked pairwise aligns More...

CRef< CMatePairConfig >	m_MatePairConf

CRef< CBoundaryParams >	m_GeneGroupConf

CRef< CBoundaryParams >	m_FeatGroupConf

CRef< CAlnStatConfig >	m_StatConf

CRef< CGeneModelConfig >	m_GeneModelConfig

ELayout	m_Layout = eLayout_Adaptive

bool	m_IsDefaultLayout = true

bool	m_ShowAlignedSeqFeats

bool	m_ShowLabel

bool	m_ShowUnalignedTailsForTrans2GenomicAln

bool	m_ShowAlnStat

bool	m_ShowIdenticalBases

double	m_MinPileUpCost = 3.

double	m_MinAlignCost = 1.5
	MinPileUpCost - Show Coverage Graph if cost is higher than MinPileUpCost. More...

double	m_MaxAlignCost = 15
	MinAlignCost - Show Alignment Graph if cost is higher than MinAlignCost. More...

int	m_MaxAlignShownFull = 250000
	MaxAlignCost Show PileUp Graph is cost is higher than MaxAlignCost. More...

int	m_MaxAlignShownAdaptive = 7500

CAlignmentConfig::EHideSraAlignments	m_HideSraAlignments

CAlignmentConfig::EUnalignedTailsMode	m_UnalignedTailsMode

bool	m_ShowSecondPassAlignments = true

bool	m_CompactEnabled

size_t	m_CompactThreshold
	Alignment number threshold between compact mode and non-compact mode. More...

size_t	m_ExtremeCompactThreshold
	Alignment number threshold between compact mode and extreme compact mode. More...

TSubtypeVec	m_ProjectedFeats

string	m_MultiAlignProfile

string	m_PWAlignProfile

string	m_AlignSmearProfile

string	m_MatePairProfile

IAlnExplorer::EAlignType	m_AlnType

size_t	m_ObjNum

CRef< CColumnLayout >	m_Column

CRef< CSimpleLayout >	m_GeneModelLayout

vector< CRef< CAlnStatGlyph > >	m_StatGlyph

Static Private Attributes
static CTrackTypeInfo	m_TypeInfo

Friends
class	CAlignmentTrackFactory

Additional Inherited Members
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 Types inherited from CLayoutTrack
enum	EIconID { eIcon_Close = 0 , eIcon_Expand , eIcon_Content , eIcon_Layout , eIcon_Settings , eIcon_Help , eIcon_MaxTrackIconID = 100 }
	Icon id used in layout track. More...

typedef int	TIconID
	use int as TIconID instead of EIconID. More...

typedef string	TIconAlias
	the icon alias used as a key More...

typedef vector< SIconInfo >	TIcons

Static Protected Member Functions inherited from CLayoutTrack
static void	RegisterCommonIconImages ()
	register images for the common icons. More...

static bool	InitIconTextures ()
	initialize OpenGL ttexture objects for icons. More...

Protected Attributes inherited from CGlyphContainer
CLayoutGroup	m_Group

CRef< CSimpleLayout >	m_Simple

CRef< CInlineLayout >	m_Inline

CRef< CLayeredLayout >	m_Layered

Protected Attributes inherited from CLayoutTrack
int	m_Order
	track order number More...

string	m_Id
	track identifier More...

bool	m_On
	is this track shown More...

bool	m_ShowFrame
	need to draw frame, not title More...

bool	m_Expanded
	is this track in expanded state More...

TIcons	m_Icons
	registered icon info More...

int	m_HighlightedIcon
	the highlighted icon index More...

TTrackAttrFlags	m_Attrs
	various track attributes More...

ILayoutTrackHost *	m_LTHost
	Top level host owning the tracks. More...

string	m_Title
	track title More...

bool	m_isBlast {false}
	true if the track is known to be generated and uploaded by BLAST More...

string	m_DefaultTitle
	Default track title. More...

string	m_Msg
	special message need to show on title bar More...

int	m_Progress
	any job progress index (0 - 100) More...

int	m_IndentLevel
	track hierachy indentation level. More...

TTrackErrorStatus	m_ErrorStatus

CRef< CSeqGraphicConfig >	m_gConfig
	global configuration. More...

string	m_Profile = "Default"
	track setting profile More...

Protected Attributes inherited from CSeqGlyph
CSeqGlyph *	m_Parent
	parent/child relationships for this feature More...

CRenderingContext *	m_Context
	the rendering context More...

unique_ptr< CRgbaColor >	m_HighlightsColor
	Highlight color. More...

ENeighbours	m_Neighbours
	Indicates whether the glyph has neighbours. More...

Protected Attributes inherited from CEventHandler
TPools	m_Pools

Static Protected Attributes inherited from CEventHandler
static const SEvtMap	sm_EvtMap

Detailed Description

CAlignmentTrack –.

Definition at line 58 of file alignment_track.hpp.

Member Typedef Documentation

◆ TSubtypeVec

typedef vector<int> CAlignmentTrack::TSubtypeVec

private

Definition at line 272 of file alignment_track.hpp.

Member Enumeration Documentation

◆ EAlignGlyphType

enum CAlignmentTrack::EAlignGlyphType

Enumerator
eAlign_Multi
eAlign_PW
eAlign_MatePair
eAlign_Smear
eAlign_Graph
eAlign_Stat
eAlign_Non

Definition at line 80 of file alignment_track.hpp.

◆ EAlignIconID

enum CAlignmentTrack::EAlignIconID

private

Enumerator
eIcon_Score
eIcon_Stat
eIcon_Tails

Definition at line 172 of file alignment_track.hpp.

◆ EJobType

enum CAlignmentTrack::EJobType

Enumerator
eJob_Align
eJob_AlignFeats
eJob_AlignScore
eJob_AlignStat
eJob_CoverageGraph

Definition at line 64 of file alignment_track.hpp.

◆ ELayout

enum CAlignmentTrack::ELayout

Enumerator
eLayout_Adaptive	adaptive using loading costs to switch between rendering modes
eLayout_Packed	smear/pack all alignments into one smear bar
eLayout_ExpandedByPos	one alignment per row sorted by pos
eLayout_Full	one alignment per row sorted by pos
eLayout_Default

Definition at line 72 of file alignment_track.hpp.

Constructor & Destructor Documentation

◆ CAlignmentTrack() [1/2]

CAlignmentTrack::CAlignmentTrack	(	CSGAlignmentDS *	ds,
		CRenderingContext *	r_cntx
	)

Definition at line 371 of file alignment_track.cpp.

References CLayoutTrack::eIcon_Content, CLayoutTrack::eIcon_Layout, eIcon_Score, eIcon_Stat, eIcon_Tails, m_Column, m_DS, m_GeneModelLayout, CGlyphContainer::m_Simple, CSGGenBankDS::SetJobListener(), CGlyphContainer::SetLayoutPolicy(), CColumnLayout::SetLimitRowPerGroup(), CColumnLayout::SetVertSpace(), CSimpleLayout::SetVertSpace(), and CLayoutTrack::x_RegisterIcon().

◆ ~CAlignmentTrack()

CAlignmentTrack::~CAlignmentTrack ( )

virtual

Definition at line 416 of file alignment_track.cpp.

References CLayoutGroup::Clear(), CSGAlignmentDS::ClearCache(), CSGAlignmentDS::DeleteAllJobs(), ERR_POST, Error(), CSeqGraphicConfig::GetCgiMode(), m_DS, CLayoutTrack::m_gConfig, CSGAlignmentDS::NeedReleaseMemory(), CSGAlignmentDS::ReleaseMemory(), and CGlyphContainer::SetGroup().

◆ CAlignmentTrack() [2/2]

CAlignmentTrack::CAlignmentTrack ( const CAlignmentTrack & )

private

Member Function Documentation

◆ GetDataSource() [1/2]

CConstRef< CSGGenBankDS > CAlignmentTrack::GetDataSource ( void ) const

inlineoverridevirtual

Implements CDataTrack.

Definition at line 365 of file alignment_track.hpp.

References CRef< C, Locker >::GetPointer(), and m_DS.

◆ GetDataSource() [2/2]

CRef< CSGGenBankDS > CAlignmentTrack::GetDataSource ( void )

inlineoverridevirtual

CAlignmentTrack inline methods.

Implements CDataTrack.

Definition at line 359 of file alignment_track.hpp.

References CRef< C, Locker >::GetPointer(), and m_DS.

◆ GetFullTitle()

string CAlignmentTrack::GetFullTitle ( ) const

overridevirtual

get a more meaningful title.

This allows a concrete track to compose a more meaningful title in a more complex way.

Reimplemented from CLayoutTrack.

Definition at line 440 of file alignment_track.cpp.

References CLayoutTrack::GetTitle(), CSeqUtils::IsUnnamed(), and m_AnnotName.

◆ GetHTMLActiveAreas()

void CAlignmentTrack::GetHTMLActiveAreas ( TAreaVector * ) const

overridevirtual

Get html active areas.

This function is for CGI mode only. By default, it does nothing.

Reimplemented from CGlyphContainer.

Definition at line 2291 of file alignment_track.cpp.

References CHTMLActiveArea::fComment, CHTMLActiveArea::fDrawBackground, CHTMLActiveArea::fNoHighlight, CHTMLActiveArea::fNoSelection, CHTMLActiveArea::fTooltipEmbedded, CGlyphContainer::GetHTMLActiveAreas(), CLayoutTrack::GetId(), CHTMLActiveArea::m_Bounds, CHTMLActiveArea::m_Flags, CHTMLActiveArea::m_ID, CHTMLActiveArea::m_ParentId, CHTMLActiveArea::m_PositiveStrand, CHTMLActiveArea::m_SeqRange, m_ShowSecondPassAlignments, msg(), CRange_Base::SetFrom(), CGlRect< T >::SetLeft(), CGlRect< T >::SetRight(), CRange_Base::SetTo(), CGlRect< T >::SetTop(), CGlRect< T >::Top(), CLayoutTrack::x_GetTBHeight(), and CSeqGlyph::x_InitHTMLActiveArea().

◆ GetTypeInfo()

const CTrackTypeInfo & CAlignmentTrack::GetTypeInfo ( void ) const

overridevirtual

Reimplemented from CGlyphContainer.

Definition at line 434 of file alignment_track.cpp.

References m_TypeInfo.

◆ HideFlagStrToValue()

CAlignmentConfig::EHideSraAlignments CAlignmentTrack::HideFlagStrToValue ( const string & hideSra )

static

Definition at line 309 of file alignment_track.cpp.

References CAlignmentConfig::eHide_None.

Referenced by x_LoadSettings().

◆ HideFlagValueToStr()

const string & CAlignmentTrack::HideFlagValueToStr ( CAlignmentConfig::EHideSraAlignments hideSra )

static

Definition at line 318 of file alignment_track.cpp.

References kEmptyStr.

Referenced by CAlignmentTrackFactory::GetSettings(), x_SaveConfiguration(), and x_SaveSettings().

◆ InitHTMLActiveArea()

CHTMLActiveArea * CAlignmentTrack::InitHTMLActiveArea ( TAreaVector * p_areas ) const

overridevirtual

Initialize the HTML active area for a track.

Returns: retrun the newly added HTML active area for this track if further initializatin is required.

Reimplemented from CLayoutTrack.

Definition at line 2320 of file alignment_track.cpp.

References CLayoutTrack::GetId(), CLayoutTrack::InitHTMLActiveArea(), CSeqUtils::IsAlignDb(), and m_AnnotName.

◆ LabelPosStrToValue()

CAlignmentConfig::ELabelPosition CAlignmentTrack::LabelPosStrToValue ( const string & pos )

static

Definition at line 276 of file alignment_track.cpp.

References NCBI_THROW.

Referenced by x_LoadAlignmentSettings().

◆ LabelPosValueToStr()

const string & CAlignmentTrack::LabelPosValueToStr ( CAlignmentConfig::ELabelPosition pos )

static

Definition at line 287 of file alignment_track.cpp.

References kEmptyStr.

Referenced by x_SaveAlignmentSettings().

◆ LayoutStrToValue()

CAlignmentTrack::ELayout CAlignmentTrack::LayoutStrToValue ( const string & layout )

static

Definition at line 241 of file alignment_track.cpp.

References eLayout_Adaptive, eLayout_Default, NStr::FindNoCase(), LOG_POST, sm_LayoutMap, and Warning().

Referenced by CAlignmentTrackFactory::GetSettings(), and x_LoadSettings().

◆ LayoutValueToStr()

const string & CAlignmentTrack::LayoutValueToStr ( CAlignmentTrack::ELayout layout )

static

Definition at line 253 of file alignment_track.cpp.

References kEmptyStr, and sm_LayoutMap.

Referenced by CAlignmentTrackFactory::GetSettings(), x_SaveConfiguration(), and x_SaveSettings().

◆ OnChangeProjectedFeats()

void CAlignmentTrack::OnChangeProjectedFeats ( )

Definition at line 530 of file alignment_track.cpp.

References CSeqFeatData::GetFeatList(), CFeatList::GetItemBySubtype(), CFeatureCheckDialog::GetSelected(), set< Key, Compare >::insert(), ITERATE, CLayoutTrack::m_LTHost, m_ProjectedFeats, NULL, IGlyphDialogHost::PostDialogShow(), IGlyphDialogHost::PreDialogShow(), CFeatureCheckDialog::SetSelected(), CFeatureCheckDialog::ShowModal(), and x_UpdateData().

Referenced by CAlnContentEvtHandler::x_OnChangeProjectedFeats().

◆ OnToggleContent()

void CAlignmentTrack::OnToggleContent ( int id )

◆ operator=()

CAlignmentTrack& CAlignmentTrack::operator= ( const CAlignmentTrack & )

private

◆ SetAlnType()

void CAlignmentTrack::SetAlnType ( IAlnExplorer::EAlignType type )

inline

Definition at line 375 of file alignment_track.hpp.

References m_AlnType, and type.

◆ SetAnnot()

void CAlignmentTrack::SetAnnot ( const string & annot )

Definition at line 455 of file alignment_track.cpp.

References m_AnnotName.

◆ SetDefaultProfile()

void CAlignmentTrack::SetDefaultProfile ( const string & profile )

inline

Definition at line 429 of file alignment_track.hpp.

References m_DefaultProfile.

◆ SetDSContext()

void CAlignmentTrack::SetDSContext ( ISGDataSourceContext * ds_ctx )

inline

Definition at line 371 of file alignment_track.hpp.

References m_DSContext, and CRef< C, Locker >::Reset().

◆ UnalignedTailsModeStrToValue()

CAlignmentConfig::EUnalignedTailsMode CAlignmentTrack::UnalignedTailsModeStrToValue ( const string & tailsMode )

static

Definition at line 340 of file alignment_track.cpp.

References CAlignmentConfig::eTails_ShowGlyph.

Referenced by x_LoadSettings().

◆ UnalignedTailsModeValueToStr()

const string & CAlignmentTrack::UnalignedTailsModeValueToStr ( CAlignmentConfig::EUnalignedTailsMode tailsMode )

static

Definition at line 349 of file alignment_track.cpp.

References kEmptyStr.

Referenced by CAlignmentTrackFactory::GetSettings(), x_SaveConfiguration(), and x_SaveSettings().

◆ x_AddAlignFeat_Recursive()

void CAlignmentTrack::x_AddAlignFeat_Recursive ( CLayoutGroup::TObjectList & objs )

private

◆ x_AddAlignFeatLayout()

void CAlignmentTrack::x_AddAlignFeatLayout ( CBatchJobResult & results )

protected

◆ x_AddAlignmentLayout()

void CAlignmentTrack::x_AddAlignmentLayout ( const CSGJobResult & result )

protected

Definition at line 1352 of file alignment_track.cpp.

References _ASSERT, CSGAlignmentDS::CalcAlnStat(), CSGAlignmentDS::CalculateAlignmentScore(), CLayoutGroup::Clear(), CSeqUtils::CreateCoverageAnnotName(), eAlign_Graph, eAlign_MatePair, eAlign_Multi, eAlign_PW, eAlign_Smear, CAlignmentConfig::eCompact, CAlignmentConfig::eExtremeCompact, eJob_AlignFeats, eJob_AlignScore, eJob_AlignStat, CSGAlignmentDS::EnablePileUpCache(), CAlignmentConfig::eNormal, IAlnExplorer::fDNA, IAlnExplorer::fInvalid, CLayoutTrack::fNavigable, CAlignGlyph::GetAlignMgr(), CSGAlignmentDS::GetAlignType(), CSeqGraphicConfig::GetBGCommentColor(), CSeqGraphicConfig::GetCgiMode(), CLayoutGroup::GetChild(), CLayoutGroup::GetChildren(), CSeqGraphicConfig::GetCommentFont(), CSeqGraphicConfig::GetCommentRepeatDist(), CSGAlignmentDS::GetEnableColoration(), CSeqGraphicConfig::GetFGCommentColor(), CLayoutTrack::GetIndent(), CRef< C, Locker >::GetPointer(), CSeqGraphicConfig::GetRepeatComment(), CRenderingContext::GetScale(), CSeqGraphicConfig::GetShowComments(), CRenderingContext::GetVisSeqRange(), CSGAlignmentDS::HasCoverageGraph(), CSeqUtils::IsAlignDb(), IAlnGraphicDataSource::IsColoringAvailable(), CRenderingContext::IsOverviewMode(), CAlignGlyph::IsSimplified(), CSGAlignmentDS::LoadAlignFeats(), m_AlignSmearConf, m_AlnType, m_AnnotName, CLayoutTrack::m_Attrs, m_Column, m_CompactEnabled, CAlignmentConfig::m_CompactMode, m_CompactThreshold, CSeqGlyph::m_Context, m_DS, m_ExtremeCompactThreshold, CLayoutTrack::m_gConfig, CGlyphContainer::m_Layered, CLayoutTrack::m_LTHost, m_MatePairConf, m_MPPWAlignConf, m_MultiAlignConf, m_ObjNum, m_ProjectedFeats, m_PWAlignConf, m_ShowAlignedSeqFeats, m_ShowAlnStat, CAlignmentConfig::m_ShowIdenticalBases, m_ShowIdenticalBases, CAlignmentConfig::m_ShowLabel, m_ShowLabel, m_StatConf, m_StatGlyph, max(), NON_CONST_ITERATE, NULL, CLayoutGroup::PushBack(), CLayoutGroup::Remove(), result, CRenderingContext::ScreenToSeq(), CLayoutGroup::Set(), CHistogramGlyph::SetAnnotName(), CNamedGroup::SetBackgroundColor(), CLayoutGroup::SetChildren(), CAlignSmearGlyph::SetConfig(), CMatePairGlyph::SetConfig(), CAlignGlyph::SetConfig(), CHistogramGlyph::SetConfig(), CHistogramGlyph::SetDialogHost(), CGlyphContainer::SetGroup(), CNamedGroup::SetIndent(), CColumnLayout::SetMinDist(), CLayoutTrack::SetMsg(), CNamedGroup::SetRepeatDist(), CNamedGroup::SetRepeatTitle(), CMatePairGlyph::SetSeqAligns(), CAlignGlyph::SetShowScore(), CNamedGroup::SetShowTitle(), CNamedGroup::SetTitleColor(), CNamedGroup::SetTitleFont(), CColumnLayout::SetVertSpace(), CLayeredLayout::SetVertSpace(), CAlnStatConfig::ShowAGTC(), tmp, CRenderingContext::WillSeqLetterFit(), x_GetAlignGlyphType(), x_LoadAlignedSeqFeats(), x_LoadAlignSmearSettings(), x_LoadMatePairSettings(), x_LoadMPPWAlignSettings(), x_LoadMultiAlignSettings(), x_OnLayoutPolicyChanged(), x_SetMsg(), and CDataTrack::x_UpdateLayout().

Referenced by x_OnJobCompleted().

◆ x_AddAlignStatLayout()

void CAlignmentTrack::x_AddAlignStatLayout ( const CSGJobResult & result )

protected

◆ x_AddGraphLayout()

void CAlignmentTrack::x_AddGraphLayout ( const CSGJobResult & result )

protected

Definition at line 1671 of file alignment_track.cpp.

References CLayoutGroup::Clear(), CSeqUtils::CreateCoverageAnnotName(), m_AnnotName, CLayoutTrack::m_gConfig, CLayoutTrack::m_LTHost, m_StatGlyph, result, CLayoutGroup::Set(), CHistogramGlyph::SetAnnotName(), CGlyphContainer::SetChildren(), CHistogramGlyph::SetConfig(), CHistogramGlyph::SetDialogHost(), CGlyphContainer::SetGroup(), CLayoutTrack::SetMsg(), and CDataTrack::x_UpdateLayout().

Referenced by x_OnJobCompleted().

◆ x_GetAlignGlyphType()

CAlignmentTrack::EAlignGlyphType CAlignmentTrack::x_GetAlignGlyphType ( const CSeqGlyph * glyph ) const

private

Definition at line 1984 of file alignment_track.cpp.

References _ASSERT, eAlign_Graph, eAlign_MatePair, eAlign_Multi, eAlign_Non, eAlign_PW, eAlign_Smear, CAlignGlyph::GetAlignMgr(), IScoringAlignment::GetAnchor(), IScoringAlignment::GetNumRows(), IAlnGraphicDataSource::GetSeqId(), CSeq_id::Match(), and row.

Referenced by x_AddAlignmentLayout().

◆ x_GetGraphParams()

CRef< CHistParams > CAlignmentTrack::x_GetGraphParams ( )

private

Definition at line 1697 of file alignment_track.cpp.

References _ASSERT, CSeqUtils::CreateCoverageAnnotName(), CAlnStatConfig::eStat_Match, CSeqGraphicConfig::GetHistParamsManager(), m_AnnotName, CAlnStatConfig::m_Colors, CHistParams::m_fgColor, CLayoutTrack::m_gConfig, CHistParams::m_NeedRulerLabels, m_StatConf, and CRef< C, Locker >::Reset().

Referenced by x_AddAlignStatLayout(), x_LoadSettings(), and x_OnStatIconClicked().

◆ x_LayoutToCutoff()

int CAlignmentTrack::x_LayoutToCutoff ( CAlignmentTrack::ELayout layout )

private

CAlignmentTrack.

Definition at line 174 of file alignment_track.cpp.

References eLayout_Adaptive, eLayout_ExpandedByPos, eLayout_Full, and eLayout_Packed.

Referenced by x_UpdateData().

◆ x_LayoutToCutoff_SRA()

int CAlignmentTrack::x_LayoutToCutoff_SRA ( CAlignmentTrack::ELayout layout )

private

Definition at line 192 of file alignment_track.cpp.

References eLayout_Adaptive, eLayout_ExpandedByPos, eLayout_Full, eLayout_Packed, m_MaxAlignShownAdaptive, and m_MaxAlignShownFull.

◆ x_LoadAlignedSeqFeats()

void CAlignmentTrack::x_LoadAlignedSeqFeats	(	vector< CRef< CAlignGlyph > > &	aligns,
		CAlignGlyph *	aln
	)

private

Definition at line 1902 of file alignment_track.cpp.

References CAlignGlyph::GetLocation(), CSeq_loc::GetTotalRange(), CRenderingContext::GetVisSeqRange(), CSeqGlyph::m_Context, compile_time_bits::range(), and CRenderingContext::SeqToScreen().

Referenced by x_AddAlignmentLayout().

◆ x_LoadAlignmentSettings()

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

private

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

Definition at line 2062 of file alignment_track.cpp.

Referenced by x_LoadAlignSmearSettings(), x_LoadMPPWAlignSettings(), x_LoadMultiAlignSettings(), and x_LoadPWAlignSettings().

◆ x_LoadAlignSmearSettings()

void CAlignmentTrack::x_LoadAlignSmearSettings ( )

inlineprivate

Definition at line 407 of file alignment_track.hpp.

References m_AlignSmearConf, m_AlignSmearProfile, and x_LoadAlignmentSettings().

Referenced by x_AddAlignmentLayout(), and x_LoadSettings().

◆ x_LoadMatePairSettings()

void CAlignmentTrack::x_LoadMatePairSettings ( )

private

Definition at line 2165 of file alignment_track.cpp.

Referenced by x_AddAlignmentLayout(), and x_LoadSettings().

◆ x_LoadMPPWAlignSettings()

void CAlignmentTrack::x_LoadMPPWAlignSettings ( )

inlineprivate

Definition at line 420 of file alignment_track.hpp.

References CAlignmentConfig::eTails_ShowGlyph, m_MPPWAlignConf, m_PWAlignProfile, CAlignmentConfig::m_ShowLabel, CAlignmentConfig::m_ShowUnalignedTailsForTrans2GenomicAln, CAlignmentConfig::m_UnalignedTailsMode, and x_LoadAlignmentSettings().

Referenced by x_AddAlignmentLayout(), and x_LoadSettings().

◆ x_LoadMultiAlignSettings()

void CAlignmentTrack::x_LoadMultiAlignSettings ( )

inlineprivate

Definition at line 379 of file alignment_track.hpp.

References CAlignmentConfig::eTails_ShowGlyph, m_MultiAlignConf, m_MultiAlignProfile, CAlignmentConfig::m_ShowUnalignedTailsForTrans2GenomicAln, CAlignmentConfig::m_UnalignedTailsMode, and x_LoadAlignmentSettings().

Referenced by x_AddAlignmentLayout(), and x_LoadSettings().

◆ x_LoadPWAlignSettings()

void CAlignmentTrack::x_LoadPWAlignSettings ( )

inlineprivate

Definition at line 394 of file alignment_track.hpp.

References m_PWAlignConf, m_PWAlignProfile, and x_LoadAlignmentSettings().

Referenced by x_LoadSettings().

◆ x_LoadSettings()

void CAlignmentTrack::x_LoadSettings	(	const string &	preset_style,
		const TKeyValuePairs &	settings
	)

overrideprotectedvirtual

load the track settings.

By default, it does nothing.

Parameters

preset_style	a preset setting style name
settings	a list of track-specific setting in a form of key-value pair.

Reimplemented from CLayoutTrack.

Definition at line 559 of file alignment_track.cpp.

◆ x_OnContentIconClicked()

void CAlignmentTrack::x_OnContentIconClicked ( )

protected

◆ x_OnIconClicked()

void CAlignmentTrack::x_OnIconClicked ( TIconID id )

overrideprotectedvirtual

Mouse left-click event handler on an icon.

In this class, only clicks on close and expand icons are handled. Any other icons are very likely track-specific, so they need to be handled in the derived tracks.

Reimplemented from CLayoutTrack.

Definition at line 853 of file alignment_track.cpp.

References CLayoutTrack::eIcon_Content, CLayoutTrack::eIcon_Layout, eIcon_Score, eIcon_Stat, eIcon_Tails, x_OnContentIconClicked(), CLayoutTrack::x_OnIconClicked(), x_OnLayoutIconClicked(), x_OnScoreIconClicked(), x_OnStatIconClicked(), and x_OnTailsIconClicked().

◆ x_OnJobCompleted()

void CAlignmentTrack::x_OnJobCompleted ( CAppJobNotification & notify )

overrideprotectedvirtual

◆ x_OnLayoutIconClicked()

void CAlignmentTrack::x_OnLayoutIconClicked ( )

protected

Definition at line 1089 of file alignment_track.cpp.

References eLayout_Default, ITERATE, ILayoutTrackHost::LTH_PopupMenu(), m_CompactEnabled, m_IsDefaultLayout, m_Layout, CLayoutTrack::m_LTHost, max(), sm_LayoutDispMap, ToWxString(), UseDefaultMarginWidth(), wxT, x_OnLayoutPolicyChanged(), and x_UpdateData().

Referenced by x_OnIconClicked().

◆ x_OnLayoutPolicyChanged()

void CAlignmentTrack::x_OnLayoutPolicyChanged ( )

protected

◆ x_OnScoreIconClicked()

void CAlignmentTrack::x_OnScoreIconClicked ( )

protected

◆ x_OnStatIconClicked()

void CAlignmentTrack::x_OnStatIconClicked ( )

protected

Definition at line 1204 of file alignment_track.cpp.

Referenced by x_OnIconClicked().

◆ x_OnTailsIconClicked()

void CAlignmentTrack::x_OnTailsIconClicked ( )

protected

◆ x_SaveAlignmentSettings()

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

private

Definition at line 2116 of file alignment_track.cpp.

Referenced by x_SaveAlignSmearSettings(), x_SaveMultiAlignSettings(), and x_SavePWAlignSettings().

◆ x_SaveAlignSmearSettings()

void CAlignmentTrack::x_SaveAlignSmearSettings ( ) const

inlineprivate

Definition at line 413 of file alignment_track.hpp.

References m_AlignSmearConf, m_AlignSmearProfile, and x_SaveAlignmentSettings().

Referenced by x_SaveConfiguration().

◆ x_SaveConfiguration()

void CAlignmentTrack::x_SaveConfiguration ( const string & preset_style ) const

private

save all track settings to the configuration file.

this is not used currently.

Definition at line 2032 of file alignment_track.cpp.

References CSGAlignmentDS::GetDNAScoringMethod(), CSGAlignmentDS::GetEnableColoration(), CGuiRegistry::GetInstance(), CSGAlignmentDS::GetLinkMatePairs(), CSGAlignmentDS::GetProteinScoringMethod(), CSGConfigUtils::GetWriteView(), HideFlagValueToStr(), kBaseKey, kDefProfile, LayoutValueToStr(), m_AlignSmearProfile, m_DS, m_HideSraAlignments, m_Layout, m_MatePairProfile, m_MultiAlignProfile, m_PWAlignProfile, m_ShowAlignedSeqFeats, m_ShowIdenticalBases, m_ShowLabel, m_ShowSecondPassAlignments, m_ShowUnalignedTailsForTrans2GenomicAln, m_UnalignedTailsMode, registry, CRegistryWriteView::Set(), UnalignedTailsModeValueToStr(), x_SaveAlignSmearSettings(), x_SaveMatePairSettings(), x_SaveMultiAlignSettings(), and x_SavePWAlignSettings().

◆ x_SaveMatePairSettings()

void CAlignmentTrack::x_SaveMatePairSettings ( ) const

private

Definition at line 2208 of file alignment_track.cpp.

Referenced by x_SaveConfiguration().

◆ x_SaveMultiAlignSettings()

void CAlignmentTrack::x_SaveMultiAlignSettings ( ) const

inlineprivate

Definition at line 387 of file alignment_track.hpp.

References m_MultiAlignConf, m_MultiAlignProfile, and x_SaveAlignmentSettings().

Referenced by x_SaveConfiguration().

◆ x_SavePWAlignSettings()

void CAlignmentTrack::x_SavePWAlignSettings ( ) const

inlineprivate

Definition at line 400 of file alignment_track.hpp.

References m_PWAlignConf, m_PWAlignProfile, and x_SaveAlignmentSettings().

Referenced by x_SaveConfiguration().

◆ x_SaveSettings()

void CAlignmentTrack::x_SaveSettings ( const string & preset_style )

overrideprotectedvirtual

save part of settings to a profile string.

Only the potential settings changed by users will be saved.

Reimplemented from CLayoutTrack.

Definition at line 816 of file alignment_track.cpp.

References NStr::BoolToString(), CSGConfigUtils::ComposeProfileString(), CSGAlignmentDS::GetDNAScoringMethod(), CSGAlignmentDS::GetEnableColoration(), CSGAlignmentDS::GetLinkMatePairs(), CSGAlignmentDS::GetProteinScoringMethod(), CSGAlignmentDS::GetSortBy(), HideFlagValueToStr(), NStr::IntToString(), ITERATE, kEmptyStr, LayoutValueToStr(), m_CompactEnabled, CAlnStatConfig::m_Display, m_DS, m_HideSraAlignments, m_Layout, m_ProjectedFeats, m_ShowAlignedSeqFeats, m_ShowAlnStat, m_ShowIdenticalBases, m_ShowLabel, m_ShowUnalignedTailsForTrans2GenomicAln, m_StatConf, CAlnStatConfig::m_StatZoomLevel, m_UnalignedTailsMode, CLayoutTrack::SetProfile(), and UnalignedTailsModeValueToStr().

◆ x_SetMsg()

void CAlignmentTrack::x_SetMsg ( )

private

Definition at line 2250 of file alignment_track.cpp.

References NStr::fWithCommas, m_ObjNum, msg(), CLayoutTrack::SetMsg(), and NStr::SizetToString().

Referenced by x_AddAlignFeatLayout(), x_AddAlignmentLayout(), x_AddAlignStatLayout(), and x_OnJobCompleted().

◆ x_UpdateBoundingBox()

void CAlignmentTrack::x_UpdateBoundingBox ( )

overridevirtual

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

Reimplemented from CGlyphContainer.

Definition at line 2331 of file alignment_track.cpp.

References CSeqGraphicConfig::GetCgiMode(), GetGl(), CSeqGlyph::GetHeight(), CSeqGlyph::GetTop(), CLayoutTrack::m_gConfig, CGlyphContainer::m_Group, m_ShowSecondPassAlignments, CSeqGlyph::SetHeight(), CSeqGlyph::SetTop(), and CGlyphContainer::x_UpdateBoundingBox().

◆ x_UpdateData()

void CAlignmentTrack::x_UpdateData ( )

overrideprotectedvirtual

update track content.

Implements CDataTrack.

Definition at line 878 of file alignment_track.cpp.

References CSGAlignmentDS::CalcAlnStat(), CSGAlignmentDS::CanShowRange(), CLayoutGroup::Clear(), CSGAlignmentDS::DeleteAllJobs(), eJob_Align, eJob_AlignStat, eJob_CoverageGraph, eLayout_Adaptive, eLayout_ExpandedByPos, eLayout_Full, eLayout_Packed, IAlnExplorer::fDNA, CSGAlignmentDS::GetAlignmentCost(), CLayoutGroup::GetChild(), CSGAlignmentDS::GetGraphCost(), COpenRange< Position >::GetLength(), CRef< C, Locker >::GetPointer(), CRenderingContext::GetScale(), CRenderingContext::GetVisSeqRange(), CSGAlignmentDS::HasCoverageGraph(), CSGAlignmentDS::IsRangeCached(), kMinCoverageZoomLevel, kShowPileUpRange, CSGAlignmentDS::LoadAlignments(), CSGAlignmentDS::LoadCoverageGraph(), m_AlnType, CSeqGlyph::m_Context, m_DS, m_Layout, m_MaxAlignCost, m_MaxAlignShownFull, m_MinAlignCost, m_MinPileUpCost, m_ShowAlnStat, m_StatConf, m_StatGlyph, CSGAlignmentDS::NeedReleaseMemory(), CSGAlignmentDS::ReleaseMemory(), CLayoutGroup::Remove(), CGlyphContainer::SetGroup(), CAlnStatConfig::ShowAGTC(), x_LayoutToCutoff(), and CLayoutTrack::x_SetStartStatus().

Referenced by OnChangeProjectedFeats(), OnToggleContent(), x_OnLayoutIconClicked(), x_OnScoreIconClicked(), x_OnStatIconClicked(), and x_OnTailsIconClicked().

Friends And Related Function Documentation

◆ CAlignmentTrackFactory

friend class CAlignmentTrackFactory

friend

Definition at line 61 of file alignment_track.hpp.

Member Data Documentation

◆ m_AlignSmearConf

CRef<CAlignmentConfig> CAlignmentTrack::m_AlignSmearConf

private

Definition at line 231 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadAlignSmearSettings(), x_LoadSettings(), x_OnTailsIconClicked(), and x_SaveAlignSmearSettings().

◆ m_AlignSmearProfile

string CAlignmentTrack::m_AlignSmearProfile

private

Definition at line 277 of file alignment_track.hpp.

Referenced by x_LoadAlignSmearSettings(), x_LoadSettings(), x_SaveAlignSmearSettings(), and x_SaveConfiguration().

◆ m_AlnType

IAlnExplorer::EAlignType CAlignmentTrack::m_AlnType

private

Definition at line 281 of file alignment_track.hpp.

Referenced by CAlignmentTrackFactory::GetSettings(), SetAlnType(), x_AddAlignmentLayout(), x_LoadSettings(), x_OnScoreIconClicked(), and x_UpdateData().

◆ m_AnnotName

string CAlignmentTrack::m_AnnotName

private

Definition at line 223 of file alignment_track.hpp.

Referenced by GetFullTitle(), InitHTMLActiveArea(), SetAnnot(), x_AddAlignmentLayout(), x_AddGraphLayout(), and x_GetGraphParams().

◆ m_Column

CRef<CColumnLayout> CAlignmentTrack::m_Column

private

Definition at line 284 of file alignment_track.hpp.

Referenced by CAlignmentTrack(), x_AddAlignFeatLayout(), x_AddAlignmentLayout(), x_LoadSettings(), and x_OnLayoutPolicyChanged().

◆ m_CompactEnabled

bool CAlignmentTrack::m_CompactEnabled

private

Definition at line 263 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), x_LoadSettings(), x_OnLayoutIconClicked(), and x_SaveSettings().

◆ m_CompactThreshold

size_t CAlignmentTrack::m_CompactThreshold

private

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

Maximal number of alignments shown in the non-compact mode

Definition at line 267 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), and x_LoadSettings().

◆ m_ContentHandler

wxEvtHandler* CAlignmentTrack::m_ContentHandler

private

wx-related event handler.

Definition at line 221 of file alignment_track.hpp.

Referenced by x_OnContentIconClicked().

◆ m_DefaultProfile

string CAlignmentTrack::m_DefaultProfile = "Default"

private

Definition at line 227 of file alignment_track.hpp.

Referenced by SetDefaultProfile(), and x_LoadSettings().

◆ m_DS

CRef<CSGAlignmentDS> CAlignmentTrack::m_DS

private

Definition at line 224 of file alignment_track.hpp.

Referenced by CAlignmentTrack(), GetDataSource(), OnToggleContent(), x_AddAlignFeatLayout(), x_AddAlignmentLayout(), x_LoadSettings(), x_OnContentIconClicked(), x_OnJobCompleted(), x_OnLayoutPolicyChanged(), x_OnScoreIconClicked(), x_OnTailsIconClicked(), x_SaveConfiguration(), x_SaveSettings(), x_UpdateData(), and ~CAlignmentTrack().

◆ m_DSContext

CIRef<ISGDataSourceContext> CAlignmentTrack::m_DSContext

private

Definition at line 225 of file alignment_track.hpp.

Referenced by SetDSContext().

◆ m_ExtremeCompactThreshold

size_t CAlignmentTrack::m_ExtremeCompactThreshold

private

Alignment number threshold between compact mode and extreme compact mode.

Maximal number of alignments shown in the compact mode

Definition at line 270 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), and x_LoadSettings().

◆ m_FeatGroupConf

CRef<CBoundaryParams> CAlignmentTrack::m_FeatGroupConf

private

Definition at line 235 of file alignment_track.hpp.

Referenced by x_AddAlignFeatLayout().

◆ m_GeneGroupConf

CRef<CBoundaryParams> CAlignmentTrack::m_GeneGroupConf

private

Definition at line 234 of file alignment_track.hpp.

Referenced by x_AddAlignFeat_Recursive().

◆ m_GeneModelConfig

CRef<CGeneModelConfig> CAlignmentTrack::m_GeneModelConfig

private

Definition at line 237 of file alignment_track.hpp.

Referenced by x_AddAlignFeat_Recursive(), and x_LoadSettings().

◆ m_GeneModelLayout

CRef<CSimpleLayout> CAlignmentTrack::m_GeneModelLayout

private

Definition at line 285 of file alignment_track.hpp.

Referenced by CAlignmentTrack(), x_AddAlignFeat_Recursive(), x_AddAlignFeatLayout(), and x_OnLayoutPolicyChanged().

◆ m_HideSraAlignments

CAlignmentConfig::EHideSraAlignments CAlignmentTrack::m_HideSraAlignments

private

Definition at line 256 of file alignment_track.hpp.

Referenced by x_LoadSettings(), x_SaveConfiguration(), and x_SaveSettings().

◆ m_IsDefaultLayout

bool CAlignmentTrack::m_IsDefaultLayout = true

private

Definition at line 240 of file alignment_track.hpp.

Referenced by x_LoadSettings(), and x_OnLayoutIconClicked().

◆ m_Layout

ELayout CAlignmentTrack::m_Layout = eLayout_Adaptive

private

Definition at line 239 of file alignment_track.hpp.

Referenced by x_LoadSettings(), x_OnLayoutIconClicked(), x_OnLayoutPolicyChanged(), x_SaveConfiguration(), x_SaveSettings(), and x_UpdateData().

◆ m_MatePairConf

CRef<CMatePairConfig> CAlignmentTrack::m_MatePairConf

private

Definition at line 233 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadMatePairSettings(), x_LoadSettings(), and x_SaveMatePairSettings().

◆ m_MatePairProfile

string CAlignmentTrack::m_MatePairProfile

private

Definition at line 278 of file alignment_track.hpp.

Referenced by x_LoadMatePairSettings(), x_LoadSettings(), x_SaveConfiguration(), and x_SaveMatePairSettings().

◆ m_MaxAlignCost

double CAlignmentTrack::m_MaxAlignCost = 15

private

MinAlignCost - Show Alignment Graph if cost is higher than MinAlignCost.

Definition at line 249 of file alignment_track.hpp.

Referenced by x_LoadSettings(), and x_UpdateData().

◆ m_MaxAlignShownAdaptive

int CAlignmentTrack::m_MaxAlignShownAdaptive = 7500

private

Definition at line 252 of file alignment_track.hpp.

Referenced by x_LayoutToCutoff_SRA(), and x_LoadSettings().

◆ m_MaxAlignShownFull

int CAlignmentTrack::m_MaxAlignShownFull = 250000

private

MaxAlignCost Show PileUp Graph is cost is higher than MaxAlignCost.

Definition at line 251 of file alignment_track.hpp.

Referenced by x_LayoutToCutoff_SRA(), x_LoadSettings(), and x_UpdateData().

◆ m_MinAlignCost

double CAlignmentTrack::m_MinAlignCost = 1.5

private

MinPileUpCost - Show Coverage Graph if cost is higher than MinPileUpCost.

Definition at line 248 of file alignment_track.hpp.

Referenced by x_LoadSettings(), and x_UpdateData().

◆ m_MinPileUpCost

double CAlignmentTrack::m_MinPileUpCost = 3.

private

Definition at line 247 of file alignment_track.hpp.

Referenced by x_LoadSettings(), and x_UpdateData().

◆ m_MPPWAlignConf

CRef<CAlignmentConfig> CAlignmentTrack::m_MPPWAlignConf

private

for linked pairwise aligns

Definition at line 232 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), x_LoadMPPWAlignSettings(), and x_LoadSettings().

◆ m_MultiAlignConf

CRef<CAlignmentConfig> CAlignmentTrack::m_MultiAlignConf

private

> Default Settings profile

Definition at line 229 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadMultiAlignSettings(), x_LoadSettings(), and x_SaveMultiAlignSettings().

◆ m_MultiAlignProfile

string CAlignmentTrack::m_MultiAlignProfile

private

Definition at line 275 of file alignment_track.hpp.

Referenced by x_LoadMultiAlignSettings(), x_LoadSettings(), x_SaveConfiguration(), and x_SaveMultiAlignSettings().

◆ m_ObjNum

size_t CAlignmentTrack::m_ObjNum

private

Definition at line 282 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), and x_SetMsg().

◆ m_ProjectedFeats

TSubtypeVec CAlignmentTrack::m_ProjectedFeats

private

Definition at line 273 of file alignment_track.hpp.

Referenced by OnChangeProjectedFeats(), x_AddAlignmentLayout(), x_LoadSettings(), and x_SaveSettings().

◆ m_PWAlignConf

CRef<CAlignmentConfig> CAlignmentTrack::m_PWAlignConf

private

Definition at line 230 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadPWAlignSettings(), x_OnTailsIconClicked(), and x_SavePWAlignSettings().

◆ m_PWAlignProfile

string CAlignmentTrack::m_PWAlignProfile

private

Definition at line 276 of file alignment_track.hpp.

Referenced by x_LoadMPPWAlignSettings(), x_LoadPWAlignSettings(), x_LoadSettings(), x_SaveConfiguration(), and x_SavePWAlignSettings().

◆ m_ShowAlignedSeqFeats

bool CAlignmentTrack::m_ShowAlignedSeqFeats

private

Definition at line 241 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadSettings(), x_OnContentIconClicked(), x_SaveConfiguration(), and x_SaveSettings().

◆ m_ShowAlnStat

bool CAlignmentTrack::m_ShowAlnStat

private

Definition at line 244 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadSettings(), x_OnContentIconClicked(), x_OnStatIconClicked(), x_SaveSettings(), and x_UpdateData().

◆ m_ShowIdenticalBases

bool CAlignmentTrack::m_ShowIdenticalBases

private

Definition at line 245 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadAlignmentSettings(), x_LoadSettings(), x_OnContentIconClicked(), x_SaveConfiguration(), and x_SaveSettings().

◆ m_ShowLabel

bool CAlignmentTrack::m_ShowLabel

private

Definition at line 242 of file alignment_track.hpp.

Referenced by OnToggleContent(), x_AddAlignmentLayout(), x_LoadAlignmentSettings(), x_LoadMatePairSettings(), x_LoadSettings(), x_OnContentIconClicked(), x_SaveConfiguration(), and x_SaveSettings().

◆ m_ShowSecondPassAlignments

bool CAlignmentTrack::m_ShowSecondPassAlignments = true

private

Definition at line 260 of file alignment_track.hpp.

Referenced by GetHTMLActiveAreas(), x_LoadSettings(), x_SaveConfiguration(), and x_UpdateBoundingBox().

◆ m_ShowUnalignedTailsForTrans2GenomicAln

bool CAlignmentTrack::m_ShowUnalignedTailsForTrans2GenomicAln

private

Definition at line 243 of file alignment_track.hpp.

Referenced by x_LoadAlignmentSettings(), x_LoadSettings(), x_OnTailsIconClicked(), x_SaveConfiguration(), and x_SaveSettings().

◆ m_StatConf

CRef<CAlnStatConfig> CAlignmentTrack::m_StatConf

private

Definition at line 236 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), x_AddAlignStatLayout(), x_GetGraphParams(), x_LoadSettings(), x_OnStatIconClicked(), x_SaveSettings(), and x_UpdateData().

◆ m_StatGlyph

vector<CRef<CAlnStatGlyph> > CAlignmentTrack::m_StatGlyph

private

Definition at line 286 of file alignment_track.hpp.

Referenced by x_AddAlignmentLayout(), x_AddAlignStatLayout(), x_AddGraphLayout(), x_OnLayoutPolicyChanged(), and x_UpdateData().

◆ m_TypeInfo

CTrackTypeInfo CAlignmentTrack::m_TypeInfo

staticprivate

Definition at line 288 of file alignment_track.hpp.

Referenced by CAlignmentTrackFactory::GetExtensionIdentifier(), CAlignmentTrackFactory::GetExtensionLabel(), CAlignmentTrackFactory::GetTypeInfo(), and GetTypeInfo().

◆ m_UnalignedTailsMode

CAlignmentConfig::EUnalignedTailsMode CAlignmentTrack::m_UnalignedTailsMode

private

Definition at line 258 of file alignment_track.hpp.

Referenced by x_LoadAlignmentSettings(), x_LoadSettings(), x_OnTailsIconClicked(), x_SaveConfiguration(), and x_SaveSettings().

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 Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TSubtypeVec

Member Enumeration Documentation

◆ EAlignGlyphType

◆ EAlignIconID

◆ EJobType

◆ ELayout

Constructor & Destructor Documentation

◆ CAlignmentTrack() [1/2]

◆ ~CAlignmentTrack()

◆ CAlignmentTrack() [2/2]

Member Function Documentation

◆ GetDataSource() [1/2]

◆ GetDataSource() [2/2]

◆ GetFullTitle()

◆ GetHTMLActiveAreas()

◆ GetTypeInfo()

◆ HideFlagStrToValue()

◆ HideFlagValueToStr()

◆ InitHTMLActiveArea()

◆ LabelPosStrToValue()

◆ LabelPosValueToStr()

◆ LayoutStrToValue()

◆ LayoutValueToStr()

◆ OnChangeProjectedFeats()

◆ OnToggleContent()

◆ operator=()

◆ SetAlnType()

◆ SetAnnot()

◆ SetDefaultProfile()

◆ SetDSContext()

◆ UnalignedTailsModeStrToValue()

◆ UnalignedTailsModeValueToStr()

◆ x_AddAlignFeat_Recursive()

◆ x_AddAlignFeatLayout()

◆ x_AddAlignmentLayout()

◆ x_AddAlignStatLayout()

◆ x_AddGraphLayout()

◆ x_GetAlignGlyphType()

◆ x_GetGraphParams()

◆ x_LayoutToCutoff()

◆ x_LayoutToCutoff_SRA()

◆ x_LoadAlignedSeqFeats()

◆ x_LoadAlignmentSettings()

◆ x_LoadAlignSmearSettings()

◆ x_LoadMatePairSettings()

◆ x_LoadMPPWAlignSettings()

◆ x_LoadMultiAlignSettings()

◆ x_LoadPWAlignSettings()

◆ x_LoadSettings()

◆ x_OnContentIconClicked()

◆ x_OnIconClicked()

◆ x_OnJobCompleted()

◆ x_OnLayoutIconClicked()

◆ x_OnLayoutPolicyChanged()

◆ x_OnScoreIconClicked()

◆ x_OnStatIconClicked()

◆ x_OnTailsIconClicked()

◆ x_SaveAlignmentSettings()

◆ x_SaveAlignSmearSettings()

◆ x_SaveConfiguration()

◆ x_SaveMatePairSettings()

◆ x_SaveMultiAlignSettings()

◆ x_SavePWAlignSettings()

◆ x_SaveSettings()

◆ x_SetMsg()

◆ x_UpdateBoundingBox()

◆ x_UpdateData()

Friends And Related Function Documentation