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CAlignmentTrack Class Reference

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CAlignmentTrack –. More...

#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< stringTHighlights
 
typedef map< string, THighlightsTKeyHighlights
 
- 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, stringTKeyValuePairs
 
- Public Types inherited from CSeqGlyph
enum  ENeighbours { eNghbrs_None = 0x0 , eNghbrs_Left = 0x1 , eNghbrs_Right = 0x2 , eNghbrs_Both = 0x3 }
 
typedef vector< CHTMLActiveAreaTAreaVector
 
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< Uint8TCounter
 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, TListenersTPools
 
typedef list< AutoPtr< SPostRequest > > TPostRequests
 
typedef std::map< CEventHandler *, intTHandlerToCount
 
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 CTrackTypeInfoGetTypeInfo () const override
 
virtual string GetFullTitle () const override
 get a more meaningful title. More...
 
CDataTrack public methods
virtual CRef< CSGGenBankDSGetDataSource () override
 CAlignmentTrack inline methods. More...
 
virtual CConstRef< CSGGenBankDSGetDataSource () 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 CHTMLActiveAreaInitHTMLActiveArea (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 THighlightsGetHighlights () const
 
const TKeyHighlightsGetHighlightsByKey () const
 
CLayoutGroupSetGroup ()
 
const CLayoutGroupGetGroup () const
 
CLayoutGroup::TObjectListSetChildren ()
 
const CLayoutGroup::TObjectListGetChildren () const
 
bool Empty () const
 
void SetLayoutPolicy (ILayoutPolicy *policy)
 Set policy on how to deploy the layout of its children. More...
 
virtual CRef< CSeqGlyphHitTest (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 stringGetProfile () const
 
string GetTitle () const
 get the track title. More...
 
const TTrackErrorStatusGetErrorStatus () 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)
 
CLayoutTrackGetParentTrack ()
 
const CLayoutTrackGetParentTrack () 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 stringGetId () 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 CRenderingContextGetRenderingContext () 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
 
CRgbaColorGetHighlightsColor () 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 TModelPointGetPos () const
 
void GetPosInWorld (TModelPoint &pos) const
 Get top left position in world coordinate. More...
 
const CSeqGlyphGetParent (void) const
 
CSeqGlyphGetParent (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)
 
CSeqGlyphSetParent (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...
 
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 CWeakObject
 CWeakObject (void)
 
virtual ~CWeakObject (void)
 
CPtrToObjectProxyGetPtrProxy (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 TListenersGetListeners (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 stringLayoutValueToStr (ELayout layout)
 
static CAlignmentConfig::ELabelPosition LabelPosStrToValue (const string &pos)
 
static const stringLabelPosValueToStr (CAlignmentConfig::ELabelPosition pos)
 
static CAlignmentConfig::EHideSraAlignments HideFlagStrToValue (const string &hideSra)
 
static const stringHideFlagValueToStr (CAlignmentConfig::EHideSraAlignments hideSra)
 
static CAlignmentConfig::EUnalignedTailsMode UnalignedTailsModeStrToValue (const string &tailsMode)
 
static const stringUnalignedTailsModeValueToStr (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 TSeqRangex_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< CSeqGraphicConfigx_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 SEvtMapGetEventMap () 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< intTSubtypeVec
 

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< CHistParamsx_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 &)
 
CAlignmentTrackoperator= (const CAlignmentTrack &)
 

Private Attributes

wxEvtHandler * m_ContentHandler
 wx-related event handler. More...
 
string m_AnnotName
 
CRef< CSGAlignmentDSm_DS
 
CIRef< ISGDataSourceContextm_DSContext
 
string m_DefaultProfile = "Default"
 
CRef< CAlignmentConfigm_MultiAlignConf
 > Default Settings profile More...
 
CRef< CAlignmentConfigm_PWAlignConf
 
CRef< CAlignmentConfigm_AlignSmearConf
 
CRef< CAlignmentConfigm_MPPWAlignConf
 for linked pairwise aligns More...
 
CRef< CMatePairConfigm_MatePairConf
 
CRef< CBoundaryParamsm_GeneGroupConf
 
CRef< CBoundaryParamsm_FeatGroupConf
 
CRef< CAlnStatConfigm_StatConf
 
CRef< CGeneModelConfigm_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< CColumnLayoutm_Column
 
CRef< CSimpleLayoutm_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< SIconInfoTIcons
 
- 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< CSimpleLayoutm_Simple
 
CRef< CInlineLayoutm_Inline
 
CRef< CLayeredLayoutm_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...
 
ILayoutTrackHostm_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< CSeqGraphicConfigm_gConfig
 global configuration. More...
 
string m_Profile = "Default"
 track setting profile More...
 
- Protected Attributes inherited from CSeqGlyph
CSeqGlyphm_Parent
 parent/child relationships for this feature More...
 
CRenderingContextm_Context
 the rendering context More...
 
unique_ptr< CRgbaColorm_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

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

Enumerator
eIcon_Score 
eIcon_Stat 
eIcon_Tails 

Definition at line 172 of file alignment_track.hpp.

◆ EJobType

Enumerator
eJob_Align 
eJob_AlignFeats 
eJob_AlignScore 
eJob_AlignStat 
eJob_CoverageGraph 

Definition at line 64 of file alignment_track.hpp.

◆ 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 
)

◆ ~CAlignmentTrack()

CAlignmentTrack::~CAlignmentTrack ( )
virtual

◆ 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

◆ 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

◆ 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

◆ LayoutValueToStr()

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

◆ OnChangeProjectedFeats()

void CAlignmentTrack::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

◆ 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

◆ x_GetAlignGlyphType()

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

◆ x_GetGraphParams()

CRef< CHistParams > CAlignmentTrack::x_GetGraphParams ( )
private

◆ x_LayoutToCutoff()

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

◆ x_LayoutToCutoff_SRA()

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

◆ x_LoadAlignedSeqFeats()

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

◆ 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.

References CSGConfigUtils::GetColor(), CSGConfigUtils::GetColorReadView(), CSeqGraphicConfig::GetColorTheme(), CSGConfigUtils::GetFont(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CSeqGraphicConfig::GetLabelPos(), CSGConfigUtils::GetLabelPosReadView(), CException::GetMsg(), CSGConfigUtils::GetReadView(), CSeqGraphicConfig::GetSizeLevel(), CSGConfigUtils::GetSizeReadView(), CRegistryReadView::GetString(), kAlignGlyphKey, kDefProfile, LabelPosStrToValue(), LOG_POST, CAlignmentConfig::m_BarHeight, CAlignmentConfig::m_BG, CAlignmentConfig::m_FG, CAlignmentConfig::m_Gap, CLayoutTrack::m_gConfig, CAlignmentConfig::m_Insertion, CAlignmentConfig::m_Intron, CAlignmentConfig::m_Label, CAlignmentConfig::m_LabelFont, CAlignmentConfig::m_LabelPos, CAlignmentConfig::m_NonConsensus, CAlignmentConfig::m_SeqFont, CAlignmentConfig::m_SeqMismatch, CAlignmentConfig::m_Sequence, CAlignmentConfig::m_ShowIdenticalBases, m_ShowIdenticalBases, CAlignmentConfig::m_ShowLabel, m_ShowLabel, CAlignmentConfig::m_ShowUnalignedTailsForTrans2GenomicAln, m_ShowUnalignedTailsForTrans2GenomicAln, CAlignmentConfig::m_SmearColorMax, CAlignmentConfig::m_SmearColorMin, CAlignmentConfig::m_TailColor, CAlignmentConfig::m_UnalignedFG, CAlignmentConfig::m_UnalignedSequence, CAlignmentConfig::m_UnalignedTailsMode, m_UnalignedTailsMode, registry, CRef< C, Locker >::Reset(), and Warning().

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

◆ x_LoadAlignSmearSettings()

void CAlignmentTrack::x_LoadAlignSmearSettings ( )
inlineprivate

◆ x_LoadMatePairSettings()

void CAlignmentTrack::x_LoadMatePairSettings ( )
private

◆ x_LoadMPPWAlignSettings()

void CAlignmentTrack::x_LoadMPPWAlignSettings ( )
inlineprivate

◆ x_LoadMultiAlignSettings()

void CAlignmentTrack::x_LoadMultiAlignSettings ( )
inlineprivate

◆ 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_stylea preset setting style name
settingsa list of track-specific setting in a form of key-value pair.

Reimplemented from CLayoutTrack.

Definition at line 559 of file alignment_track.cpp.

References _ASSERT, CUser_field_Base::C_Data::e_Str, CAlignmentConfig::eHide_None, CSGAlignmentDS::EnablePileUpCache(), NStr::EqualNocase(), CAlnStatConfig::eStat_A, CAlnStatConfig::eStat_C, CAlnStatConfig::eStat_G, CAlnStatConfig::eStat_Gap, CAlnStatConfig::eStat_Match, CAlnStatConfig::eStat_Mismatch, CAlnStatConfig::eStat_T, CAlnStatConfig::eStat_Total, CAlignmentConfig::eTails_Hide, f(), NStr::fConvErr_NoThrow, IAlnExplorer::fMixed, IAlnExplorer::fProtein, NStr::fSplit_Tokenize, CRegistryReadView::GetBool(), CSeqGraphicConfig::GetCgiMode(), CSGConfigUtils::GetColor(), CSGConfigUtils::GetColorReadView(), CSeqGraphicConfig::GetColorTheme(), CRegistryReadView::GetField(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CException::GetMsg(), CLayoutTrack::GetProfile(), CSGConfigUtils::GetReadView(), CRegistryReadView::GetReal(), CSeqGraphicConfig::GetShowComments(), CSeqGraphicConfig::GetSizeLevel(), CSGConfigUtils::GetSizeReadView(), CRegistryReadView::GetString(), CSGAlignmentDS::HasCoverageGraph(), HideFlagStrToValue(), CSGAlignmentDS::IsValidDNAScoringMethod(), CSGAlignmentDS::IsValidProteinScoringMethod(), ITERATE, kBaseKey, kDefProfile, kGeneModelBaseKey, LayoutStrToValue(), CGeneModelConfig::LoadSettings(), LOG_POST, m_AlignSmearConf, m_AlignSmearProfile, m_AlnType, CAlnStatConfig::m_Colors, m_Column, m_CompactEnabled, m_CompactThreshold, m_DefaultProfile, CAlnStatConfig::m_Display, m_DS, m_ExtremeCompactThreshold, CHistParams::m_fgColor, CLayoutTrack::m_gConfig, m_GeneModelConfig, CHistParams::m_Height, m_HideSraAlignments, m_IsDefaultLayout, CGlyphContainer::m_Layered, m_Layout, m_MatePairConf, m_MatePairProfile, m_MaxAlignCost, m_MaxAlignShownAdaptive, m_MaxAlignShownFull, m_MinAlignCost, m_MinPileUpCost, m_MPPWAlignConf, m_MultiAlignConf, m_MultiAlignProfile, m_ProjectedFeats, m_PWAlignProfile, CHistParams::m_Scale, m_ShowAlignedSeqFeats, m_ShowAlnStat, m_ShowIdenticalBases, m_ShowLabel, m_ShowSecondPassAlignments, m_ShowUnalignedTailsForTrans2GenomicAln, m_StatConf, CAlnStatConfig::m_StatZoomLevel, m_UnalignedTailsMode, registry, CRef< C, Locker >::Reset(), CHistParams::ScaleStrToValue(), CSGAlignmentDS::SetCgiMode(), CSGAlignmentDS::SetDNAScoringMethod(), CSGAlignmentDS::SetEnableColoration(), CSGAlignmentDS::SetHideSra(), CSGAlignmentDS::SetLinkMatePairs(), CSGAlignmentDS::SetMemoryLimit(), CLayoutTrack::SetProfile(), CSGAlignmentDS::SetProteinScoringMethod(), CAlnStatConfig::SetShowLabel(), CSGAlignmentDS::SetShowSecondPassAlignments(), CSGAlignmentDS::SetSortBy(), CSGAlignmentDS::SetUnalignedTailsMode(), CColumnLayout::SetVertSpace(), CLayeredLayout::SetVertSpace(), CAlnStatConfig::ShowAGTC(), NStr::Split(), str(), NStr::StringToBool(), NStr::StringToInt(), NStr::StringToUInt8_DataSize(), NStr::TruncateSpacesInPlace(), UnalignedTailsModeStrToValue(), Warning(), CLayoutTrack::x_GetGlobalConfig(), x_GetGraphParams(), x_LoadAlignSmearSettings(), x_LoadMatePairSettings(), x_LoadMPPWAlignSettings(), x_LoadMultiAlignSettings(), x_LoadPWAlignSettings(), and x_OnLayoutPolicyChanged().

◆ 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

◆ x_OnLayoutPolicyChanged()

void CAlignmentTrack::x_OnLayoutPolicyChanged ( )
protected

◆ x_OnScoreIconClicked()

void CAlignmentTrack::x_OnScoreIconClicked ( )
protected

◆ x_OnStatIconClicked()

void CAlignmentTrack::x_OnStatIconClicked ( )
protected

◆ x_OnTailsIconClicked()

void CAlignmentTrack::x_OnTailsIconClicked ( )
protected

◆ x_SaveAlignmentSettings()

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

◆ x_SaveAlignSmearSettings()

void CAlignmentTrack::x_SaveAlignSmearSettings ( ) const
inlineprivate

◆ x_SaveConfiguration()

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

◆ x_SaveMatePairSettings()

void CAlignmentTrack::x_SaveMatePairSettings ( ) const
private

◆ x_SaveMultiAlignSettings()

void CAlignmentTrack::x_SaveMultiAlignSettings ( ) const
inlineprivate

◆ 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

◆ x_SetMsg()

void CAlignmentTrack::x_SetMsg ( )
private

◆ x_UpdateBoundingBox()

void CAlignmentTrack::x_UpdateBoundingBox ( )
overridevirtual

◆ x_UpdateData()

void CAlignmentTrack::x_UpdateData ( )
overrideprotectedvirtual

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

◆ m_AlignSmearProfile

string CAlignmentTrack::m_AlignSmearProfile
private

◆ m_AlnType

IAlnExplorer::EAlignType CAlignmentTrack::m_AlnType
private

◆ m_AnnotName

string CAlignmentTrack::m_AnnotName
private

◆ m_Column

CRef<CColumnLayout> CAlignmentTrack::m_Column
private

◆ m_CompactEnabled

bool CAlignmentTrack::m_CompactEnabled
private

◆ 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

◆ 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

◆ 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

◆ m_MatePairConf

CRef<CMatePairConfig> CAlignmentTrack::m_MatePairConf
private

◆ m_MatePairProfile

string CAlignmentTrack::m_MatePairProfile
private

◆ 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

◆ 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

◆ m_PWAlignConf

CRef<CAlignmentConfig> CAlignmentTrack::m_PWAlignConf
private

◆ m_PWAlignProfile

string CAlignmentTrack::m_PWAlignProfile
private

◆ m_ShowAlignedSeqFeats

bool CAlignmentTrack::m_ShowAlignedSeqFeats
private

◆ m_ShowAlnStat

bool CAlignmentTrack::m_ShowAlnStat
private

◆ m_ShowIdenticalBases

bool CAlignmentTrack::m_ShowIdenticalBases
private

◆ m_ShowLabel

bool CAlignmentTrack::m_ShowLabel
private

◆ m_ShowSecondPassAlignments

bool CAlignmentTrack::m_ShowSecondPassAlignments = true
private

◆ m_ShowUnalignedTailsForTrans2GenomicAln

bool CAlignmentTrack::m_ShowUnalignedTailsForTrans2GenomicAln
private

◆ m_StatConf

CRef<CAlnStatConfig> CAlignmentTrack::m_StatConf
private

◆ m_StatGlyph

vector<CRef<CAlnStatGlyph> > CAlignmentTrack::m_StatGlyph
private

◆ m_TypeInfo

CTrackTypeInfo CAlignmentTrack::m_TypeInfo
staticprivate

◆ m_UnalignedTailsMode

CAlignmentConfig::EUnalignedTailsMode CAlignmentTrack::m_UnalignedTailsMode
private

The documentation for this class was generated from the following files:
Modified on Sat May 25 14:20:15 2024 by modify_doxy.py rev. 669887