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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vcf__track_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/seq_graphic/vcf_track.cpp Source File

79 if

(iter->second == layout) {

114 static size_t

s_MaxFeatures(5 * 1000 * 1000);

117 if

(

nullptr

!= vcf_ds) {

120

extra.

(

"VCF-records-in-range"

, nFeats);

123 if

(nFeats > s_MaxFeatures) {

126 " records. Please reduce the range and try again."

;

135 string msg

=

"Zoom to see if data exists for this region"

;

140

objs.push_back(comment);

142 config

->m_ShowConnection =

false

;

152 auto

it = settings.

(

"zoom_to_see"

);

167 if

(

nullptr

!= vcf_ds) {

183 LOG_POST

(

<<

"CVcfTrack::x_OnJobCompleted() notification for job \ 184 does not contain results."

);

188 const size_t

obj_size = objs.size();

209 string msg

=

", total "

;

239 bound

.SetBottom(

.Top() + (

)tb_height + (tb_height > 0.0 ? 2 : 0));

250

p_areas->push_back(area);

251 return

&(p_areas->back());

284 if

(range.

()) {

290 if

( !src_annots.

() ) {

302

feat_track->SetAnnot(iter->first);

303 if

( !iter->second.empty() ) {

304

feat_track->SetTitle(iter->second);

306

tracks[iter->first] = feat_track.

();

320 for

(

auto

&

i

: src_annots) {

323 i

.first,

i

.second->m_Title));

339 for

(

auto

&

i

: src_annots) {

340 if

(!

->HasNonAsnData(

i

.first))

370 config

->SetLegend_text(

"anchor_5"

);

373 string

hist_t =

"0"

;

374 bool

show_only_pathogenic {

false

};

379

rendering_str = iter->second;

380 if

(rendering_str ==

"Histogram"

)

381

rendering_str =

"Heatmap"

;

384 if

(

> 0) hist_t = iter->second;

401 "Rendering"

,

"Rendering options"

,

403 "Rendering options for linked features."

);

405

choice->SetValues().push_back(

409 "All features, both parent and all child features"

,

410 "The bar on top represents the variant region. Each bar below represents \ 411 the supporting level variants used to define this region.<br>Red: A Deletion or Loss<br> \ 412 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

414

choice->SetValues().push_back(

417 "Show parent, Expand children upon a click"

,

418 "Show parent on one line and expand all children upon a mouse click."

,

419 "The bar on top represents the variant region. The bars below appear upon a mouse click and each bar represents \ 420 the supporting level variants used to define this region.<br>Red: A Deletion or Loss<br> \ 421 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

423

choice->SetValues().push_back(

426 "Show parent, Merge children"

,

427 "Show parent on one line and all children merged below it."

,

428 "The bar on top represents the variant region. The bar below represents \ 429 all of the sample level variants merged onto a single line.<br>Red: A Deletion or Loss<br> \ 430 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

432

choice->SetValues().push_back(

435 "Show children, not parent"

,

436 "Show only the supporting variants (chidlren) not the variant region (parent)"

,

437 "The bar represent supporting variants in this study.<br>Red: A Deletion or Loss<br>\ 438 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

440

choice->SetValues().push_back(

443 "Show parent, not children "

,

444 "Show the variant region (parent) not the supporting variants (children)"

,

445 "The bar represents the variant region."

));

447

choice->SetValues().push_back(

450 "Display on a single line"

,

451 "Track is displayed, with all features collapsed on a single line."

,

452 "All the features are packed into one line."

));

453

choice->SetValues().push_back(

457 "Track is displayed, with all features displayed as a heatmap."

,

458 "All the features are packed and shown as a heatmap."

));

460 config

->SetChoice_list().push_back(choice);

464

txt_box->SetName(

"HistThreshold"

);

465

txt_box->SetValue(hist_t);

466

txt_box->SetDisplay_name(

"Heatmap Threshold"

);

467

txt_box->SetHelp(

"Display a heatmap when there are more features in this track than the value specificed." 468 " 'None' or '0' means threshold is disabled, and the display is up to 'Rendering Options'"

);

469 config

->SetText_boxes().push_back(txt_box);

471 config

->SetCheck_boxes().push_back(

473 "ShowOnlyPathogenic"

,

474 "Show only pathogenic/likely pathogenic"

,

475 "Show only pathogenic/likely pathogenic"

,

476 ""

, show_only_pathogenic,

true

));

User-defined methods of the data storage class.

static const map< string, CAlignmentTrack::ELayout > sm_LayoutMap

Checksum and hash calculation classes.

CAppJobNotification Notification send by CAppJobEventTranslator.

static const string & LinkedFeatDisplayValueToStr(ELinkedFeatDisplay linked_feat)

CRef< CSGFeatureDS > m_DS

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

load the track settings.

void x_AdjustFeatureLayout()

virtual void x_UpdateData()

update track content.

@ eLayout_AdaptiveInline

adaptively switch between packed and inline

@ eLayout_ExpandedLayered

show all features with layered layout

@ eLayout_AdaptiveLayered

adaptively switch between packed and layered

int m_CompactThreshold

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

void SetObjects(const CLayoutGroup::TObjectList &objs)

const CLayoutGroup::TObjectList & GetChildren() const

CRef< CLayeredLayout > m_Layered

void SetLayoutPolicy(ILayoutPolicy *policy)

Set policy on how to deploy the layout of its children.

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

@ fNoNavigation

track title won't show navigation controls

@ fNoPin

tooltip is not pinnable

@ fNoSelection

the object can't be selected

int m_Flags

area flags, will need to replace m_Type

void SetConfig(const CSeqGraphicConfig &config)

TTrackAttrFlags m_Attrs

various track attributes

@ fNavigable

Track has navigation controls.

TModelUnit x_GetTBHeight() const

Get title bar height including margin.

void SetMsg(const string &msg)

CConstRef< CSeqGraphicConfig > x_GetGlobalConfig() const

Method for getting global configuration from rendering context.

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

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

const TSeqRange & GetVisSeqRange() const

static void ParseProfileString(const string &profile_str, TKeyValuePairs &settings)

virtual bool AllJobsFinished() const

virtual void ClearJobID(TJobID job_id)

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

CSGJobResult â the data structure holding the seqgraphic job results.

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

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual void SetHideLabel(bool)

Force to hide label.

vector< CHTMLActiveArea > TAreaVector

list< CRef< CSeqGlyph > > TObjects

void SetRenderingContext(CRenderingContext *context)

Set the rendering context.

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

const string & GetSortBy() const

static CRef< objects::CChoice > CreateChoice(const string &name, const string &disp_name, const string &curr_val, const string &help, bool optional=false)

static CRef< objects::CCheckBox > CreateCheckBox(const string &name, const string &disp_n, const string &help_text, const string &legend_txt, bool value, bool optional=false)

static CRef< objects::CChoiceItem > CreateChoiceItem(const string &name, const string &disp_name, const string &help, const string &legend_txt, bool optional=false)

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

void ShowOnlyPathogenic(bool show=true)

size_t GetFeaturesCountInRange(const string &annot_name, const TSeqRange &range)

void SetConfig(CConstRef< CFeatureParams > conf)

virtual string GetExtensionLabel() const override

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

virtual string GetExtensionIdentifier() const override

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual TTrackMap CreateTracks(SConstScopedObject &object, ISGDataSourceContext *ds_context, CRenderingContext *r_cntx, const SExtraParams &params=SExtraParams(), const TAnnotMetaDataList &src_annots=TAnnotMetaDataList()) const override

CVcfTrackFactory.

virtual const CTrackTypeInfo & GetThisTypeInfo() const override

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

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

CVcfTrack(CSGFeatureDS *ds, CRenderingContext *r_cntx)

virtual bool CheckRange(TSeqRange range, string &sMsg, size_t &nFeats) override

virtual void x_UpdateData() override

update track content.

virtual void x_OnJobCompleted(CAppJobNotification &notify) override

virtual const CTrackTypeInfo & GetTypeInfo() const override

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const override

Initialize the HTML active area for a track.

bool m_ShowOnlyPathogenic

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

load the track settings.

static CTrackTypeInfo m_TypeInfo

virtual void x_ParseSettings(const TKeyValuePairs &settings) override

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

virtual CIRef< ISGDataSource > GetDS(const string &type, SConstScopedObject &object)=0

Get a seqgraphic data source instance of the specified type.

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

CGlPoint< TModelUnit > TModelPoint

CRef< CObject > GetResult() const

returns non-null pointer only if Completed or Running and has temporary results available

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StringToBool(const CTempString str)

Convert string to bool.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fWithCommas

Use commas as thousands separator.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

Tdata & Set(void)

Assign a value to data member.

constexpr bool empty(list< Ts... >) noexcept

T bound(T x_, T xlo_, T xhi_)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

static const TLayoutStr s_LayoutStrs[]

SStaticPair< const char *, CFeatureTrack::ELayout > TLayoutStr

CVcfTrack.

static CFeatureTrack::ELayout s_LayoutStrToValue(const string &layout)

const string & s_LayoutValueToStr(CFeatureTrack::ELayout layout)

DEFINE_STATIC_ARRAY_MAP(TLayoutMap, sm_LayoutMap, s_LayoutStrs)

CStaticArrayMap< string, CFeatureTrack::ELayout > TLayoutMap

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