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

73 static const string kScale

=

"scale"

;

167  GetChildren

().front()->GetHTMLActiveAreas(p_areas);

170  GetChildren

().front()->GetHTMLActiveAreas(&areas);

171  for

(

auto

& area : areas) {

172

area.m_ParentId =

GetId

();

173

area.m_Descr.clear();

177

&& area.m_Signature !=

"otl"

) {

181

p_areas->insert(p_areas->end(), areas.begin(), areas.end());

188  bound

.SetBottom(

bound

.Top() + (

TVPUnit

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

200  m_Sel

.ResetAnnotsNames();

203  m_Sel

.AddUnnamedAnnots();

231  string

cache_svc = reg.

GetString

(

"Configuration"

,

"service"

,

"NC_SV_Conf_PROD"

);

232  string

cache_name = reg.

GetString

(

"Configuration"

,

"cache"

,

"conf"

);

239  return

cache_instance;

287

}

catch

(exception& e) {

293  bool

parameter_present =

false

, smooth_curve =

false

;

294  string

scale, clip_outliers, outlier_color, sd_thresh, stored_scale, num_bins, neg_color, value_range;

306

hist_settings.

m_Color

= iter->second;

307

parameter_present =

true

;

310

opacity = (opacity <= 0) ? 100 :

min

(opacity, 100);

311

parameter_present =

true

;

314

parameter_present =

true

;

316

hist_settings.

m_Type

= iter->second;

317

parameter_present =

true

;

319

scale = iter->second;

320

parameter_present =

true

;

322

stored_scale = iter->second;

323

parameter_present =

true

;

328

outlier_color = iter->second;

329

parameter_present =

true

;

331

sd_thresh = iter->second;

332

parameter_present =

true

;

334

neg_color = iter->second;

335

parameter_present =

true

;

337

num_bins = iter->second;

338

parameter_present =

true

;

340

value_range = iter->second;

341

parameter_present =

true

;

345

}

catch

(exception& e) {

348

parameter_present =

true

;

351

fit_step = max<int>(fit_step, 1);

352

parameter_present =

true

;

354

}

catch

(std::exception&) {

355  LOG_POST

(

Error

<<

"CGraphTrack::x_LoadSettings: invalid settings " 362  if

(!parameter_present)

378  if

( !hist_settings.

m_Color

.empty() ) {

390  if

(!neg_color.empty())

392  float

alpha = opacity;

402  if

( !hist_settings.

m_Type

.empty() ) {

404

hist_conf->

m_Type

= style;

424  if

(!scale.empty()) {

428  if

(!stored_scale.empty()) {

432  if

(!clip_outliers.empty()) {

436  if

(!outlier_color.empty()) {

440  if

(!sd_thresh.empty()) {

444  if

(!num_bins.empty()) {

449  if

(!value_range.empty()) {

450  string

range_min, range_max;

452  if

(!range_min.empty() && range_min !=

"inf"

) {

455  if

(!range_max.empty() && range_max !=

"inf"

) {

469

}

catch

(std::exception&) {

470  LOG_POST

(

Error

<<

"CGraphTrack::x_LoadSettings: invalid histogram settings"

);

477

vector<string> settings;

513  ERR_POST

(

"CGraphTrack::x_OnJobCompleted() notification for job \ 514  does not contain results."

);

523

vector<string> titles;

536

titles.push_back(title);

543

uo->

SetType

().SetStr(

"YLimits"

);

552

}

catch

(exception& e) {

577  msg

+= (

count

!= 1 ?

"s shown"

:

" shown"

);

597  config

->m_ShowConnection =

false

;

606

group->PushBack(

label

);

614

group->PushBack(*iter);

629

track_proxy =

dynamic_cast<CTrackProxy

*

>

(&**iter);

632  if

((*iter)->GetOrder() == order)

644

wxMenuItem* item = menu.AppendCheckItem(id_base++,

wxT

(

"Fixed scale"

));

648

vector<CRef<CHistogramGlyph>> graphs;

649

vector<wxMenuItem*> settings_menu;

651  if

(!graphs.empty()) {

652

menu.AppendSeparator();

653  for

(

auto

graph : graphs) {

655  static const int

kMaxMenuItemLen = 50;

656  if

(s.Length() > kMaxMenuItemLen) {

657

s.Truncate(kMaxMenuItemLen - 3);

660

settings_menu.push_back(menu.AppendCheckItem(id_base++, s));

665

wxMenuItem* move_item = 0;

667

menu.AppendSeparator();

668

move_item = menu.AppendCheckItem(id_base,

wxT

(

"Remove from parent container"

));

678  for

(

size_t i

= 0;

i

< settings_menu.size() &&

i

< graphs.size(); ++

i

) {

679  if

(!settings_menu[

i

]->IsChecked())

681

graphs[

i

]->RunSettingsDialog();

684  if

(move_item && move_item->IsChecked()) {

691  if

((*iter)->GetOrder() ==

GetOrder

()) {

692

proxy.

Reset

(*iter);

705  if

((*ch_it)->GetOrder() >= new_order) {

706

new_order = (*ch_it)->GetOrder() + 1;

711  if

((*it)->GetOrder() ==

GetOrder

()) {

719

n_proxy->CTempTrackProxy::operator=(*proxy);

720

n_proxy->SetKey(

"graph_track"

);

721

n_proxy->SetOrder(new_order);

722

n_proxy->SetTrack(proxy->

GetTrack

());

723

n_proxy->GetTrack()->SetShowTitle(

true

);

728

annots.push_back(

gt

->GetAnnot());

729

n_proxy->SetAnnots(annots);

739

top_container->

Update

(

true

);

749

vector<int> tracks2remove;

751  if

(!current_track_proxy)

753

tracks2remove.push_back(current_track_proxy->

GetOrder

());

757  if

(!current_track_proxy->

GetId

().empty())

765

subtrack_proxy->

SetOrder

(order++);

766

new_track->

GetChildren

().push_back(subtrack_proxy);

771  if

(!current_track_proxy)

775

subtrack_proxy->

SetOrder

(order++);

776

new_track->

GetChildren

().push_back(subtrack_proxy);

778  if

(!current_track_proxy->

GetId

().empty())

784

tracks2remove.push_back(

gt

->GetOrder());

786  string

track_source =

"graphs:"

;

790

annots.push_back(track_source);

796

*overlay_params = *this_params;

798  ITERATE

(vector<int>, it, tracks2remove) {

822

TAnnotGroup annot_group;

828  string

graph_cache_key;

830  bool

is_cached_bigwig =

false

;

831  if

(!graph_cache_key.empty()) {

840  if

(is_cached_bigwig) {

844  bool

isCoverageCheckFinished{

false

};

864  if

(seqtable_annots.count(*iter) > 0) {

872

isCoverageCheckFinished =

true

;

873

}

NCBI_CATCH

(

"CGraphTrackFactory::CreateTracks()"

);

875  if

(!isCoverageCheckFinished) {

930  ITERATE

(TAnnotGroup, g_iter, annot_group) {

950

track->SetAnnot(iter->first);

952  if

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

953

track->SetTitle(iter->second);

955  if

(!graph_cache_key.empty()) {

997  config

->SetLegend_text(

"anchor_12"

);

1004  bool

smooth_curve =

false

;

1005  string

fit_step =

"4"

;

1009  config

->SetHidden_settings().push_back(

1012  config

->SetHidden_settings().push_back(

1015  config

->SetHidden_settings().push_back(

1018  config

->SetHidden_settings().push_back(

1021  config

->SetHidden_settings().push_back(

1028

value_range = iter->second;

1034  config

->SetHidden_settings().push_back(

1037  config

->SetHidden_settings().push_back(

1042

fit_step = iter->second;

1044

}

catch

(std::exception&) {

1049

scale = stored_scale;

1053  "style"

,

"Display Style"

,

1055  "Display style for graph data"

);

1056

choice->SetValues().push_back(

1060  "Shown as a histogram"

,

1061  "Graph data are shown as a histogram"

));

1062

choice->SetValues().push_back(

1066  "Shown as a heat map"

,

1067  "Graph data are shown as a heat map (smear bar)"

));

1068

choice->SetValues().push_back(

1072  "Shown as a line graph"

,

1073  "Graph data are shown as a line graph"

));

1074  config

->SetChoice_list().push_back(choice);

1078  kScale

,

"Linear/Log Scale"

,

1080  "Scale for graph data"

);

1081

choice->SetValues().push_back(

1085  "Shown at linear scale"

,

1086  "Graph data is shown at linear scale"

));

1087

choice->SetValues().push_back(

1091  "Shown at log base 10 scale"

,

1092  "Graph data is shown at logarithmic (base 10) scale"

));

1093

choice->SetValues().push_back(

1097  "Shown at natural logarithm (base e) scale"

,

1098  "Graph data is shown at natural logrithm (base e) scale"

));

1099

choice->SetValues().push_back(

1103  "Shown at log base 2 scale"

,

1104  "Graph data is shown at logarithmic (base 2) scale"

));

1105  config

->SetChoice_list().push_back(choice);

1108  config

->SetCheck_boxes().push_back(

1110  "smooth_curve"

,

"Smooth curve"

,

"Smooth curve"

,

""

, smooth_curve));

1112  bool

range_autoscale =

true

;

1113  string

range_min, range_max;

1114  if

(!value_range.empty()) {

1115  string

r_min, r_max;

1117  if

(!r_min.empty() && r_min !=

"inf"

) {

1118

range_min = (errno) ?

""

: r_min;

1120  if

(!r_max.empty() && r_max !=

"inf"

) {

1121

range_max = (errno) ?

""

: r_max;

1123  config

->SetHidden_settings().push_back(

1129  "Set Value Range (Data outside range will be clipped)"

,

1130  "Set Value Range (Data outside range will be clipped)"

,

1136  auto

condition =

Ref

(

new

objects::CConditional);

1137

condition->SetName(

kScale

);

1142

range_control->SetConditions().push_back(condition);

1145  auto

condition =

Ref

(

new

objects::CConditional);

1146

condition->SetName(

"style"

);

1149

range_control->SetConditions().push_back(condition);

1152  config

->SetRange_controls().push_back(range_control);

1162

legend_item->SetLabel(track_proxy->

GetSource

());

1163

legend_item->SetColor(

"blue"

);

1164

legend_item->SetId(

""

);

1174  color

= iter->second;

1177

opacity = (opacity <= 0) ? 100 :

min

(opacity, 100);

1181

}

catch

(std::exception&) {

1182  LOG_POST

(

Error

<<

"CGraphTrack::GetLegend: invalid settings "

<< iter->second);

1185  bool

color_is_set =

false

;

1187  if

(!

color

.empty()) {

1190

color_is_set =

true

;

1191

}

catch

(exception& e) {

1196  if

(color_is_set ==

false

) {

1212  if

(opacity < 100 && opacity > 0) {

1213  float

alpha = opacity;

1217

legend_item->SetColor(c.

ToString

());

1220

legend_item->SetLabel(

label

);

1221

legend.push_back(legend_item);

1239

axis_max =

max

(hg->

GetMax

(), axis_max);

1240

axis_min =

min

(hg->

GetMin

(), axis_min);

1274  if

(vis_r.

Empty

())

1329  config

->m_ShowConnection =

false

;

1335

group->SetLayoutPolicy(

m_Simple

);

1336

group->SetRenderingContext(

m_Context

);

1338

group->PushBack(

label

);

1339

group->PushBack(hg);

1342

glyphs.push_back(*hist_it);

1345  if

(!glyphs.empty())

1355  if

(

lg

&&

lg

->GetChildrenNum() == 2) {

1360

graphs.push_back(

g

);

1370  if

(!graphs.empty()) {

1395  return

(

gt

!= 0 &&

gt

->GetChildren().size() == 1);

1400

vector<CRef<CGraphTrack>> tracks;

1402  if

(

gt

&&

gt

->GetChildren().size() == 1) {

1403

tracks.push_back(

Ref

(

gt

));

1415  if

(

lg

&&

lg

->GetChildrenNum() == 2) {

1422

graphs.push_back(

Ref

(hg));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Checksum and hash calculation classes.

CAppJobNotification Notification send by CAppJobEventTranslator.

CChecksum – Checksum calculator.

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

virtual void Update(bool layout_only)

Update content and layout including the bounding box.

virtual void x_UpdateBoundingBox()

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

virtual void x_RenderContent() const

The content rendering must be implemented in the derived layout tracks.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

void Add(CSeqGlyph *obj)

Append a layout object to the end.

void SetObjects(const CLayoutGroup::TObjectList &objs)

CLayoutGroup & SetGroup()

const CLayoutGroup::TObjectList & GetChildren() const

const CLayoutGroup & GetGroup() const

CLayoutGroup::TObjectList & SetChildren()

CRef< CLayeredLayout > m_Layered

CRef< CSimpleLayout > m_Simple

void SetLayoutPolicy(ILayoutPolicy *policy)

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

virtual string GetExtensionIdentifier() const

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

virtual string GetExtensionLabel() const

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

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 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 const CTrackTypeInfo & GetThisTypeInfo() const

virtual CRef< CSGGenBankDS > GetDataSource()

Method for accessing the data source.

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

load the track settings.

objects::SAnnotSelector m_Sel

void SetAnnot(const string &annot)

virtual void x_UpdateBoundingBox()

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

bool CreateOverlay(vector< CRef< CGraphTrack >> &tracks)

virtual bool Drop(CRef< CLayoutTrack > &track)

static const string kOverlayed

static CNetICacheClient & s_GetICacheInstance()

void x_OnSettingsIconClicked()

bool m_FixedScale

Dynamic or fixed graph scale.

static string x_LayoutValueToStr(ELayout layout)

static ELayout x_LayoutStrToValue(const string &layout)

virtual void x_OnJobCompleted(CAppJobNotification &notify)

CGraphTrack(CSGGraphDS *ds, CRenderingContext *r_cntx)

static CNetICacheClient s_InitICache()

virtual void x_OnLayoutChanged()

update the layout.

CRef< CHistogramGlyph > m_Grid

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

virtual void x_RenderContent() const

The content rendering must be implemented in the derived layout tracks.

void SetLayout(ELayout layout)

CSGGraphDS::TAxisLimits m_YLimits

Graph y limits stored when FixedScale is set.

virtual const CTrackTypeInfo & GetTypeInfo() const

virtual bool CanDrop(CRef< CLayoutTrack > &track)

virtual void x_UpdateData()

update track content.

virtual void GetLegend(const CTempTrackProxy *track_proxy, objects::CTrackConfig::TLegend &legend) const

static CTrackTypeInfo m_TypeInfo

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

void x_CollectAllGraphs(vector< CRef< CHistogramGlyph >> &graphs) const

virtual void x_SaveSettings(const string &preset_style)

save part of settings to a profile string.

string m_Descr

description that can be used as label or tooltip

@ fNoNavigation

track title won't show navigation controls

int m_Flags

area flags, will need to replace m_Type

void AddSettings(const string &name, CRef< CHistParams > hist_params)

Add a new settings for a given name.

bool HasSettings(const string &name) const

Check if there is settings for a given name.

CRef< CHistParams > GetDefHistParams() const

CRef< CHistParams > GetHistParams(TFeatSubtype subtype) const

Get histogram settings using feature subtype.

CRgbaColor m_SmearColorMin

static EType TypeStrToValue(const string &type)

int m_SDeviationThreshold

EScale m_StoredScale

stored scale of the underlying data (e.g. as reported by TMS)

CRgbaColor m_OutlierColor

static EScale ScaleStrToValue(const string &scale)

static const string & TypeValueToStr(CHistParams::EType type)

static const string & ScaleValueToStr(CHistParams::EScale scale)

EScale m_Scale

requested scale

CRange< float > m_ValueRange

CRgbaColor m_SmearColorMax

const string & GetAnnotName() const

void SetAxisMin(TDataType min)

TDataType GetAxisMin() const

void SetShowTitle(bool f)

void SetAnnotName(const string &name)

void SetAxisMax(TDataType max)

void SetFixedScale(bool value)

const string & GetTitle() const

TDataType GetAxisMax() const

Get the axis limits (max/min).

TDataType GetMax() const

Get the actually density max/min values.

void SetRenderingMode(ERenderingMode mode)

void SetDesc(const string &desc)

void DrawGrid(bool include_background) const

void SetConfig(const CSeqGraphicConfig &config)

CLayoutGroup is a container of CSeqGlyphs (layout objects).

TObjectList & SetChildren()

const TObjectList & GetChildren() const

CLayoutGroup inline methods.

ILayoutPolicy::TObjectList TObjectList

bool m_Expanded

is this track in expanded state

@ eIcon_Settings

icon id for track settings

ILayoutTrackHost * m_LTHost

Top level host owning the tracks.

string m_Title

track title

bool m_On

is this track shown

CLayoutTrack * GetParentTrack()

void x_OnLayoutChanged()

update the layout.

const string & GetId() const

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

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.

void SetProfile(const string &preset_style)

CLayoutTrack inline method implmentation.

CRef< CSeqGraphicConfig > m_gConfig

global configuration.

int TIconID

use int as TIconID instead of EIconID.

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

void x_RegisterIcon(const SIconInfo &icon)

register track icons.

static CNcbiApplication * Instance(void)

Singleton method.

Client to NetCache server (implements ICache interface)

COverlayLayout is the layout policy that arranges glyphs over the top of each other.

Note about the "buf_size" parameter for streams in this API.

@ fOwnReader

Own the underlying reader.

@ fOwnWriter

Own the underlying writer.

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

const TSeqRange & GetVisSeqRange() const

TModelRange IntersectVisible(const CSeqGlyph *obj) const

class CRgbaColor provides a simple abstraction for managing colors.

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

virtual bool AllJobsFinished() const

void SetJobListener(CEventHandler *listener)

Set JobDispatcher listener.

virtual void ClearJobID(TJobID job_id)

void SetDepth(int depth)

Set the annotation selector resolving depth.

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

void SetAdaptive(bool flag)

void LoadSeqGraphs(const string &annotName, objects::SAnnotSelector &sel, CRenderingContext &ctx, bool fixed_scale, const TAxisLimits &y_limits, CConstRef< CSeqGraphicConfig > config)

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

void SetSeqTable(bool f)

inline methods

void SetGraphCacheKey(const string &graph_cache_key)

void GetAnnotNames(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names, bool seq_table=false) const

CSGJobResult – the data structure holding the seqgraphic job results.

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual void SetHeight(TModelUnit h)

void SetParent(CSeqGlyph *p)

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

virtual void Update(bool)

Update content and layout including the bounding box.

virtual void SetTop(TModelUnit b)

virtual TModelUnit GetWidth() const

virtual TModelUnit GetLeft() const

vector< CHTMLActiveArea > TAreaVector

list< CRef< CSeqGlyph > > TObjects

void SetRenderingContext(CRenderingContext *context)

Set the rendering context.

CRef< CHistParamsManager > GetHistParamsManager() const

Get histogram config manager.

list< CRef< CTempTrackProxy > > TTrackProxies

const string & GetKey() const

const TAnnots & GetAnnots() const

const string & GetId() const

const string & GetTrackProfile() const

const TTrackProxies & GetChildren() const

void SetOrder(int order)

CTempTrackProxy class implementation.

TSubTracks & SetSubTracks()

const string & GetStoredScale() const

void SetAnnots(const TAnnots &annots)

const CLayoutTrack * GetTrack() const

const TSubTracks & GetSubTracks() 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::CHiddenSetting > CreateHiddenSetting(const string &name, const string &value)

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::CRangeControl > CreateRangeControl(const string &name, const string &disp_name, const string &help, const string &value_min, const string &value_max, bool autoscale=true, bool inverse=false, bool optional=false)

static void DecodeValueRange(const string &value_range, string &range_min, string &range_max, bool &range_auto)

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

CTrackContainer - a track container in the form of layout track.

const TTrackProxies & GetSubtrackProxies() const

CTrackContainer inline methods.

void AddTrackProxy(CTempTrackProxy *proxy, bool upgateMsg=true)

Add a track proxy.

CTrackProxy * AddNewTrack(const string &track_key, const CTrackProxy::TAnnots &annots, const string &disp_name, const string &name="", const string &filter="", const string &sub_key="")

Add a new empty track proxy.

virtual void RemoveTrack(int order, bool immediately=true)

completely remove a track from the hierachical tree.

void MoveTrack(int from, int to)

CTempTrackProxy::TTrackProxies TTrackProxies

CTrackProxy data structure contains information about the position of a track in its parent scope,...

virtual CRef< CTempTrackProxy > Clone() const

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

Writer-based output stream.

map< string, string > TAnnotNameTitleMap

List of annotations with the corresponding titles.

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.

virtual void LTH_PopupMenu(wxMenu *menu)=0

show track-specific context menu.

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.

iterator_bool insert(const value_type &val)

container_type::value_type value_type

static const string kSeqGraph

static const string kScale

static const string kNumBins

static const string kSDeviationThreshold

CTrackProxy * s_FindTrackProxy(CTrackContainer &p_track, int order)

static const string kOutlierColor

static const string kClipOutliers

static string s_GetCacheKey(const string &annot_name)

static const CGraphTrack::ELayout kDefaultLayout

static const string kSeqTable

CGraphTrackFactory methods.

static const string kTrackTitle

CGraphTrack.

static const bool kDefaultFixedScale

static const string kNegColor

static const string kValueRange

static const string kStoredScale

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

#define VECTOR_ERASE(Var, Cont)

Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

string GetHexSum(void) const

Return string with checksum in hexadecimal form.

void AddLine(const char *line, size_t len)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#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_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

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

request an annotation selector for a given type

static TAnnotNameType NameTypeStrToValue(const string &type)

static bool isRmtAnnotName(const string &sAnnotname)

check if a given annotation was created by a remote file pipeline

@ eAnnot_Unnamed

unnamed annotation

string ToString(bool printAlpha=true, bool uchars=true) const

Return a string representation of the current color.

CRef< CObject > GetResult() const

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

static bool GetKey(const TTrackSettings &TrackSettings, const string &key, string &value)

returns a specified key; if it does not exist, returns false

void FromString(const string &str)

Assign color values encoded in a string.

void Lighten(float scale)

@ eSerial_AsnBinary

ASN.1 binary.

IReader * GetReadStream(const string &key, int version, const string &subkey, size_t *blob_size_ptr, const CNamedParameterList *optional=NULL)

Read a lengthy blob via the IReader interface.

virtual bool HasBlobs(const string &key, const string &subkey)

Check if any BLOB exists (any version)

virtual IWriter * GetWriteStream(const string &key, int version, const string &subkey, unsigned int time_to_live=0, const string &owner=kEmptyStr)

Return sequential stream interface to write BLOB data.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

static position_type GetEmptyFrom(void)

TThisType & Set(position_type from, position_type to)

static position_type GetEmptyTo(void)

static TThisType GetWhole(void)

virtual string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

#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 StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

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

Convert string to int.

static const string BoolToString(bool value)

Convert bool to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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.

@ fConvErr_NoThrow

Do not throw an exception on error.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TData & GetData(void) const

Get the Data member data.

TReal GetReal(void) const

Get the variant data.

void SetType(TType &value)

Assign a value to Type data member.

list< CRef< CLegendItem > > TLegend

Tdata & Set(void)

Assign a value to data member.

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

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

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

NetCache ICache client specs.

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

Reader-writer based streams.

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

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

A help struct for storing information about a icon.

SCustomizedHistSettings()

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

void UseDefaultMarginWidth(wxMenu &menu)

Using default menu item margin width.

wxString ToWxString(const string &s)


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