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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/dbvar__track_8cpp_source.html below:

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

55 "Variation features"

);

76 string msg

=

"Zoom to see if data exists for this region"

;

81

objs.push_back(comment);

83 config

->m_ShowConnection =

false

;

93 auto

it = settings.

(

"zoom_to_see"

);

103 if

(g1->

() != g2->GetLeft())

104 return

g1->

() < g2->GetLeft();

106 return

g1->

() < g2->GetTop();

112 const string

& annot_name,

126 if

(!title.empty()) {

136

sprintf(buff,

"gi|%d-%08x-%08x-%04x-%08x-%08x"

,

138 type

, checksum, checksum_name);

154 bound

.SetBottom(

.Top() + (

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

179

p_areas->push_back(area);

180 return

&(p_areas->back());

215 LOG_POST

(

<<

"CVarTrackFactory::CreateTracks() subtype "

<< params.

<<

" is not supported!"

);

226 if

(range.

()) {

242 if

( !src_annots.

() ) {

249 if

(iter->first ==

"SNP"

)

257 if

(track_settings.count(

"graph_cache_key"

) > 0) {

260 if

(track_settings.count(

"rmt_type"

) > 0) {

269

feat_track->SetAnnot(iter->first);

270

feat_track->ExcludeAnnotName(

"SNP"

);

271

feat_track->SetFeatSubtype(subtype);

272 if

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

273

feat_track->SetTitle(iter->second);

275

tracks[iter->first] = feat_track.

();

286 if

(params.

!=

"variation"

)

310

config_set->

().push_back(

(settings, track_proxy, is_remote_track));

324 config

->SetLegend_text(

"anchor_5"

);

326 config

->SetLegend_text(

"anchor_4"

);

327 config

->SetSubkey(

"vcf"

);

331 string

hist_t =

"0"

;

336

rendering_str = iter->second;

337 if

(rendering_str ==

"Histogram"

)

338

rendering_str =

"Heatmap"

;

341 if

(

> 0) hist_t = iter->second;

355 "Rendering"

,

"Rendering options"

,

357 "Rendering options for linked features."

);

359

choice->SetValues().push_back(

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

,

364 "The bar on top represents the variant region. Each bar below represents \ 365 the supporting level variants used to define this region.<br>Red: A Deletion or Loss<br> \ 366 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

368

choice->SetValues().push_back(

371 "Show parent, Expand children upon a click"

,

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

,

373 "The bar on top represents the variant region. The bars below appear upon a mouse click and each bar represents \ 374 the supporting level variants used to define this region.<br>Red: A Deletion or Loss<br> \ 375 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

377

choice->SetValues().push_back(

380 "Show parent, Merge children"

,

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

,

382 "The bar on top represents the variant region. The bar below represents \ 383 all of the sample level variants merged onto a single line.<br>Red: A Deletion or Loss<br> \ 384 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

386

choice->SetValues().push_back(

389 "Show children, not parent"

,

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

,

391 "The bar represent supporting variants in this study.<br>Red: A Deletion or Loss<br>\ 392 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

394

choice->SetValues().push_back(

397 "Show parent, not children "

,

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

,

399 "The bar represents the variant region."

));

401

choice->SetValues().push_back(

404 "Display on a single line"

,

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

,

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

));

407

choice->SetValues().push_back(

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

,

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

));

414 config

->SetChoice_list().push_back(choice);

417 "sort_by"

,

"Sort variants by"

,

419 "Sort variants according to a selected criterion."

);

421

sortby_choice->SetValues().push_back(

423 ""

,

"No sorting"

,

"Don't sort variants"

,

""

));

427

sortby_choice->SetValues().push_back(

432

sortby_choice->SetValues().push_back(

437

sortby_choice->SetValues().push_back(

442

sortby_choice->SetValues().push_back(

447

sortby_choice->SetValues().push_back(

451 config

->SetChoice_list().push_back(sortby_choice);

454

txt_box->SetName(

"HistThreshold"

);

455

txt_box->SetValue(hist_t);

456

txt_box->SetDisplay_name(

"Heatmap Threshold"

);

457

txt_box->SetHelp(

"Display a heatmap when there are more features in this track than the value specificed." 458 " 'None' or '0' means threshold is disabled, and the display is up to 'Rendering Options'"

);

459 config

->SetText_boxes().push_back(txt_box);

User-defined methods of the data storage class.

Checksum and hash calculation classes.

CAppJobNotification Notification send by CAppJobEventTranslator.

CChecksum â Checksum calculator.

static SSorterDescriptor GetSorterDescr()

static SSorterDescriptor GetSorterDescr()

static SSorterDescriptor GetSorterDescr()

static SSorterDescriptor GetSorterDescr()

static SSorterDescriptor GetSorterDescr()

static const string & LinkedFeatDisplayValueToStr(ELinkedFeatDisplay linked_feat)

CRef< CSGFeatureDS > m_DS

virtual void x_OnJobCompleted(CAppJobNotification &notify)

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

load the track settings.

virtual void x_UpdateData()

update track content.

const CLayoutGroup::TObjectList & GetChildren() const

CLayoutGroup::TObjectList & SetChildren()

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

string GetTitle() const

get the track title.

TTrackAttrFlags m_Attrs

various track attributes

@ fNavigable

Track has navigation controls.

TModelUnit x_GetTBHeight() const

Get title bar height including margin.

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)

void SetRemoteDataType(const string &data_type)

void SetGraphCacheKey(const string &graph_cache_key)

void SetSortBy(const string &sortby)

void SetFilter(const string &filter)

CSGFeatureDS inline method.

void GetAnnotNames_var(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

objects::CBioseq_Handle & GetBioseqHandle(void)

Get the underlying bioseq handle.

void SetDepth(int depth)

Set the annotation selector resolving depth.

void SetAdaptive(bool flag)

static ESubtype SubtypeNameToValue(CTempString sName)

Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual TModelUnit GetTop() const

virtual TModelUnit GetLeft() const

vector< CHTMLActiveArea > TAreaVector

list< CRef< CSeqGlyph > > TObjects

const string & GetSortBy() const

const string & GetSource() 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::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

virtual string GetExtensionLabel() const

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

CRef< objects::CTrackConfig > x_GetSettings(const TKeyValuePairs &settings, const CTempTrackProxy *track_proxy, bool is_vcf_track) const

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

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

virtual const CTrackTypeInfo & GetThisTypeInfo() const

virtual string GetExtensionIdentifier() const

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

create a layout track based on the input objects and extra parameters.

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

load the track settings.

virtual void x_UpdateData() override

update track content.

static CTrackTypeInfo m_TypeInfo

CVarTrack.

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const override

Initialize the HTML active area for a track.

CVarTrack(CSGFeatureDS *ds, CRenderingContext *r_cntx)

virtual const CTrackTypeInfo & GetTypeInfo() const override

virtual void x_OnJobCompleted(CAppJobNotification &notify) override

static void GetMatchedAnnots(const TAnnotMetaDataList &src_annots, const vector< string > &target_annots, const string &annot_type, const string &track_type, TAnnotNameTitleMap &out_annots)

Help function to find matched annotations.

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

string GenerateSignature(const string &title, const string &annot_name, TGi gi, TSeqRange range)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void AddLine(const char *line, size_t len)

Uint4 GetChecksum(void) const

Return calculated checksum.

#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)

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

static bool IsNAA(const string &annot, bool isStrict=false)

check if a given annotation is a named annotation accession[.version][number] when isSctrict == false...

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

CGlPoint< TModelUnit > TModelPoint

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TGi GetGiForId(const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0)

Given a Seq-id retrieve the corresponding GI.

@ eGetId_ForceGi

return only a gi-based seq-id

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another 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.

@ eNocase

Case insensitive compare.

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)

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