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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/feature__track_8cpp_source.html below:

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

67 static const string kBaseKey

=

"GBPlugins.SeqGraphicFeatureTrack"

;

102  if

(iter->second == layout) {

126  if

(iter != sm_LinkedFeatMap.end()) {

136  for

(iter = sm_LinkedFeatMap.begin(); iter != sm_LinkedFeatMap.end(); ++iter) {

137  if

(iter->second == linked_feat) {

154

, m_CompactThreshold(200)

156

, m_Layout(eLayout_Default)

164

, m_HasLinkedFeats(

false

)

172  eIcon_Layout

,

"Layout style"

,

true

,

"track_layout"

));

195

title =

"Other annotations"

;

260  if

(range.

Empty

()) {

290  for

( ; feature_iter; ++feature_iter) {

300

seq_entry.SetAnnot().push_back(pAnnot);

310  LOG_POST

(

Error

<<

"CFeatureTrack::x_OnJobCompleted() notification for job \ 311  does not contain results."

);

419  if

((*iter)->GetType().IsStr() &&

434  if

((*iter)->GetType().IsStr() &&

437  return

(*iter)->GetFieldRef(

kWeightKey

)->GetData().GetInt();

465  config

->m_Colors[

"0"

] =

469  for

(

size_t i

= 1;

i

<

colors

.size(); ++

i

) {

474  if

(subtype != objects::CSeqFeatData::eSubtype_any && subtype != objects::CSeqFeatData::eSubtype_bad) {

476  if

(!descr.empty()) {

481

descr +=

", heatmap"

;

487  if

(subtype != objects::CSeqFeatData::eSubtype_any && subtype != objects::CSeqFeatData::eSubtype_bad) {

498  SetMsg

(

", Distribution histogram"

);

531  bool

set_weight =

false

;

600  if

(objs.empty() && !

result

.m_ExtraObj) {

634  string msg

=

", total "

;

635  const size_t

obj_size = objs.size();

667  dynamic_cast<const CFeatGlyph

*

>

(iter->GetPointer());

707  if

(group && group->GetChildrenNum() > 1) {

711  size_t

num_child = child_objs.size();

712

CLayoutGroup::TObjectList::iterator c_iter = child_objs.begin();

714  while

(c_iter != child_objs.end()) {

717  if

( !c_group && num_child == 2) {

726

feat_group->SetParentFeat(p_feat);

732

feat_group->PushBack(child);

734

c_iter = child_objs.erase(c_iter);

749

feat_group->SetParent(&

m_Group

);

751

feat_group->SetFirstIsParent();

757

CSeqGlyph::TObjects::iterator iter = objs.begin();

758  while

(iter != objs.end()) {

772

feat_group->SetParentFeat(p_feat);

775

group->Remove(c_group);

782

feat_group->SetParent(&

m_Group

);

784

feat_group->SetFirstIsParent();

787

}

else if

(group->GetChildrenNum() > 0) {

803  bool

need_highlight =

false

;

828

need_highlight =

true

;

829

group->SetHighlighted(

true

);

837

feat_group->SetGroup().SetRenderingContext(

m_Context

);

840

need_highlight =

true

;

841

feat_group->SetHighlighted(

true

);

848

need_highlight =

true

;

872  return

need_highlight;

903  dynamic_cast<const CLayoutGroup

*

>

(iter->GetPointer());

924  switch

(iter->second) {

929  label

=

"Show parent, not children"

;

932  label

=

"Show parent, expand children upon a click"

;

935  label

=

"Show parent, merge children"

;

938  label

=

"Merge parent and children"

;

941  label

=

"Show children, not parent"

;

946  if

(!

label

.empty()) {

947

wxMenuItem* item = menu.AppendRadioItem(id_base + iter->second,

ToWxString

(

label

));

955

wxMenuItemList& item_list = menu.GetMenuItems();

956  ITERATE

(wxMenuItemList, iter, item_list) {

974

wxMenuItem* item = menu.AppendRadioItem(id_base + iter->second,

975  ToWxString

(iter->first + (l_default ?

" (Default)"

:

""

)));

983

wxMenuItemList& item_list = menu.GetMenuItems();

984  ITERATE

(wxMenuItemList, iter, item_list) {

986  if

((*iter)->IsChecked() &&

id

!=

m_Layout

) {

1077  int

w1 = -1, w2 = -1;

1135  if

(range.

Empty

()) {

1151  if

( !src_annots.

empty

() ) {

1163  if

(track_settings.count(

"graph_cache_key"

) > 0) {

1166  if

(track_settings.count(

"rmt_type"

) > 0) {

1178  string

annot(iter->first);

1179

feat_track->SetAnnot(annot);

1180

feat_track->SetFeatSubtype(item.

GetSubtype

());

1181  if

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

1182

feat_track->SetTitle(iter->second);

1205  if

(f_track && tp) {

1232  bool

is_intron_track =

false

;

1239

config_set->

Set

().push_back(

x_GetSettings

(settings, track_proxy, is_intron_track));

1241

config_set->

Set

().push_back(

x_GetSettings

(settings,

nullptr

,

false

));

1253  if

(!

config

->CanGetHelp())

1255  config

->SetLegend_text(

"anchor_1"

);

1260  bool

use_layout_settings =

true

;

1267  bool

has_linked_feats =

true

;

1291  bool

sort_reads =

false

;

1292  bool

sort_strands =

false

;

1300

rendering_str = iter->second;

1301

use_layout_settings =

false

;

1304

has_linked_feats =

true

;

1310

read_range = iter->second;

1318  if

(is_intron_track) {

1319

has_linked_feats =

false

;

1320  config

->SetSubkey(

"intron"

);

1323  if

(use_layout_settings) {

1325  "Layout"

,

"Rendering options"

,

1327  "Rendering style on how to layout features."

);

1329

choice->SetValues().push_back(

1332  "All features on a single line"

,

1333  "Track is displayed, with all features collapsed on a single line."

,

1334  "All the features are packed and shown as a Distribution histogram."

));

1335

choice->SetValues().push_back(

1338  "Pack features if necessary"

,

1341

choice->SetValues().push_back(

1344  "All features are expanded"

,

1345  "Track is displayed with features expanded, and on separate lines if needed."

,

1346  "Always show the individual features and layer the features in a compact form"

));

1347  config

->SetChoice_list().push_back(choice);

1348  if

(has_linked_feats) {

1350  "LinkedFeat"

,

"Feature Linking"

,

1352  "Rendering style on how to render linked features."

);

1353

choice->SetValues().push_back(

1357  "All features, both parent and all child fetaures"

,

1358  "The black bar on top represents the parent feature. Each bar blow represents " 1359  "a child feature."

));

1360

choice->SetValues().push_back(

1363  "Show parent, Merge children"

,

1364  "Show parent on one line and all children merged below it."

,

1365  "The black bar on top represents the parent feature. Each bar blow represents " 1366  "a child feature."

));

1368

choice->SetValues().push_back(

1371  "Show children, not parent"

,

1372  "Show only the chidlren, not parent"

,

1373  "The bar represent children features"

));

1375

choice->SetValues().push_back(

1378  "Show parent, not children "

,

1379  "Show the parent features, not the children"

,

1380  "The black bar represents parent feature."

));

1382

choice->SetValues().push_back(

1385  "Superimpose children on parent"

,

1386  "Render all child features on the parent feature"

,

1387  "The underneath black bar represents parent feature and all the red bars on top represent the children."

));

1389  config

->SetChoice_list().push_back(choice);

1394  "Rendering"

,

"Rendering options"

,

1396  "Rendering options for linked features."

);

1398

choice->SetValues().push_back(

1402  "All features, both parent and all child fetaures"

,

1403  "The black bar on top represents the variant region. Each bar blow represents \ 1404 the supporting level variants used to define this region.<br>Red: A Deletion or Loss<br> \ 1405 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

1406

choice->SetValues().push_back(

1409  "Show parent, Merge children"

,

1410  "Show parent on one line and all children merged below it."

,

1411  "The black bar on top represents the variant region. The bar blow represents \ 1412 all of the sample level variants merged onto a single line.<br>Red: A Deletion or Loss<br> \ 1413 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

1415

choice->SetValues().push_back(

1418  "Show children, not parent"

,

1419  "Show only the supporting variants (chidlren) not the variant region (parent)"

,

1420  "The bar represent supporting variants in this study.<br>Red: A Deletion or Loss<br>\ 1421 Green: A Gain or Insertion<br>Light Gray: An Inversion"

));

1423

choice->SetValues().push_back(

1426  "Show parent, not children "

,

1427  "Show the variant region (parent) not the supporting variants (children)"

,

1428  "The black bar represents the variant region."

));

1436

choice->SetValues().push_back(

1439  "Display on a single line"

,

1440  "Track is displayed, with all features collapsed on a single line."

,

1441  "All the features are packed into one line."

));

1442

choice->SetValues().push_back(

1446  "Track is displayed, with all features displayed as a histogram."

,

1447  "All the features are packed and shown as a Distribution histogram."

));

1449  config

->SetChoice_list().push_back(choice);

1452  if

(track_proxy && !track_proxy->

GetSortBy

().empty()) {

1453  string

sort_by = track_proxy->

GetSortBy

();

1456  "sort_by"

,

"Sort features by"

,

1458  "Sort features according to a selected criterion."

);

1460

sortby_choice->SetValues().push_back(

1462  ""

,

"No sorting"

,

"Don't sort features"

,

""

));

1465  if

(descr.

m_Name

== sort_by) {

1467  config

->SetLegend_text(

"anchor_3"

);

1472

sortby_choice->SetValues().push_back(

1475  config

->SetChoice_list().push_back(sortby_choice);

1478  if

(is_intron_track) {

1479  config

->SetCheck_boxes().push_back(

1482  "Sort features by number of spliced reads (most reads first)"

,

1483  "Sort features by number of spliced reads (most reads first)"

,

1485  config

->SetCheck_boxes().push_back(

1488  "Sort features by strand"

,

1489  "Sort features by strand"

,

1490  ""

, sort_strands));

1492  string

reads_min, reads_max;

1493  bool

no_range =

true

;

1494  if

(!read_range.empty()) {

1495  string

r_min, r_max;

1497  if

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

"inf"

) {

1500  if

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

"inf"

) {

1507  "Filter by number of spliced reads (data outside the range will be hidden)"

,

1508  "Filter by number of spliced reads (data outside the range will be hidden)"

,

1513  config

->SetRange_controls().push_back(range_control);

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

CAppJobNotification Notification send by CAppJobEventTranslator.

static SSorterDescriptor GetSorterDescr()

CClonePlacementGlyph is similar to CFeatureGlyph, but with different rendering style and settings.

void SetConfig(CConstRef< CClonePlacementParams > conf)

CColumnLayout is for creating layout by sorting glyphs into 'columns'.

void SetMinDist(TSeqPos dist)

CCompactLayout is amed to generate more compact 2D layout policy than layered layout for glyphs with ...

void SetMinDist(TSeqPos dist)

vector< CRgbaColor > TColorCode

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

const TSeqRange & x_GetVisRange() const

virtual void Update(bool layout_only)

Update content and layout including the bounding box.

void SetConfig(CConstRef< CFeatureParams > conf)

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

void GetLabel(string &label, CLabel::ELabelType type) const

retrieve feature label for a given type

CFeatListItem - basic configuration data for one "feature" type.

CConfigurableItems - a static list of items that can be configured.

string GetStoragekey(int type, int subtype) const

Get the key used to store this type of feature.

bool GetItemByKey(const string &key, CFeatListItem &config_item) const

string GetDescription(int type, int subtype) const

Get the displayable description of this type of feature.

bool NeedFiltering() const

bool Pass(const objects::CMappedFeat *feat)

void Init(const string &filter)

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

virtual void CloneTrack(const CLayoutTrack *track, CTempTrackProxy *track_proxy) const

duplicate any track setting from a given track instance to a proxy.

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

virtual string GetExtensionLabel() const

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

virtual string GetExtensionIdentifier() const

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

CFeatureTrack::ELayout m_DefaultLayout

ELinkedFeatDisplay m_DefaultLinkedFeat

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

static const string & LinkedFeatDisplayValueToStr(ELinkedFeatDisplay linked_feat)

virtual void x_SaveSettings(const string &)

save part of settings to a profile string.

int m_FeatLimits

maximal number of features shown in on track.

int GetFeatSubtype() const

virtual void x_LoadFeatures(const TSeqRange &range, int feat_limit)

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

void x_CountFeats_recursive(const CSeqGlyph::TObjects &objs, int &count, bool is_overview)

virtual void x_OnLayoutPolicyChanged()

CRef< CLayeredLayout > m_GroupLayered

void GenerateAsn1(objects::CSeq_entry &seq_entry, TSeqRange range)

CRef< CColumnLayout > m_Column

CSeqGraphicConfig::TFeatSubtype m_Subtype

static ELayout LayoutStrToValue(const string &layout)

int m_MaxAdaptiveHeight

Maximal feature group pixel height in adaptive mode.

CRef< CSGFeatureDS > m_DS

objects::SAnnotSelector m_FeatSel

bool x_NeedHighlight(const CSeqGlyph::TObjects &objs) const

virtual void x_OnJobCompleted(CAppJobNotification &notify)

void x_RegroupFeats(CSeqGlyph::TObjects &objs, ELinkedFeatDisplay link_mode)

rearrange the child features if necessary.

static const string & LayoutValueToStr(ELayout layout)

virtual string GetFullTitle() const

get a more meaningful title.

void x_SortFeaturesByWeight(CSeqGlyph::TObjects &objs) const

virtual void x_ParseSettings(const TKeyValuePairs &settings)

CRef< CLayeredLayout > m_LinkedGroup

CRef< CCompactLayout > m_Compact

void x_AddFeaturesLayout(const CSGJobResult &result)

bool x_HasLinkedFeats() const

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

load the track settings.

CRef< CSimpleLayout > m_GroupSimple

void SetAnnot(const string &annot)

int m_MaxRow

Maximal number of feature rows in one feature track.

void x_AddHistogram(CHistogramGlyph *hist, int layout=-1)

size_t m_HistThreshold

An independent histogram threshold used by SViewer.

void x_AdjustFeatureLayout()

void x_ExtracGlyphs_Recursive(CSeqGlyph::TObjects &objs, CLinkedFeatsGroup *feat_group)

CFeatureTrack(CSGFeatureDS *ds, CRenderingContext *r_cntx)

CRef< CBoundaryParams > m_GroupConfig

virtual void x_UpdateData()

update track content.

static CTrackTypeInfo m_TypeInfo

void SetFeatSubtype(int subtype)

@ eLayout_ExpandedColumn

show all features with column layout

@ eLayout_AdaptiveInline

adaptively switch between packed and inline

@ eLayout_Packed

pack all feature into a histogram

@ eLayout_ExpandedLayered

show all features with layered layout

@ eLayout_OneLine

pack all feature into one line

@ eLayout_AdaptiveLayered

adaptively switch between packed and layered

@ eLayout_ExpandedByPos

show all features, one per row sorted by pos

@ eLayout_ExpandedBySize

one feature per row sorted by size

bool x_InitGlyphs_Recursive(CSeqGlyph::TObjects &objs, int curr_level, bool compact_mode)

initialize all children.

ELinkedFeatDisplay m_LinkedFeat

void x_OnContentIconClicked()

static ELinkedFeatDisplay LinkedFeatDisplayStrToValue(const string &linked_feat)

virtual const CTrackTypeInfo & GetTypeInfo() const

void ExcludeAnnotName(const string &annot)

void x_OnLayoutIconClicked()

int m_CompactThreshold

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

void x_InitLayoutPolicy(CLayoutGroup &group, ELinkedFeatDisplay link_mode)

static SSorterDescriptor GetSorterDescr()

void Add(CSeqGlyph *obj)

Append a layout object to the end.

void SetObjects(const CLayoutGroup::TObjectList &objs)

const THighlights & GetHighlights() const

CLayoutGroup & SetGroup()

CRef< CInlineLayout > m_Inline

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.

static CGuiRegistry & GetInstance()

access the application-wide singleton

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

Add a new settings for a given name.

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

Add a temporary 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.

const string & GetAnnotName() const

void SetDialogHost(IGlyphDialogHost *host)

void SetSubtype(objects::CSeqFeatData::ESubtype subtype)

void SetDesc(const string &desc)

void SetConfig(const CSeqGraphicConfig &config)

CLayeredLayout is a standard 2D layout policy.

void SetMinDist(TSeqPos dist)

void SetLimitRowPerGroup(bool f)

void SetSorted(bool flag)

CLayoutGroup is a container of CSeqGlyphs (layout objects).

void SetLinkedFeat(ELinkedFeatDisplay LinkedFeat)

TObjectList & SetChildren()

const TObjectList & GetChildren() const

CLayoutGroup inline methods.

ILayoutPolicy::TObjectList TObjectList

@ eIcon_Content

icon id for setting content

@ eIcon_Layout

icon id for setting layout style

ILayoutTrackHost * m_LTHost

Top level host owning the tracks.

string GetTitle() const

get the track title.

TTrackAttrFlags m_Attrs

various track attributes

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

@ fNavigable

Track has navigation controls.

void SetMsg(const string &msg)

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.

void x_RegisterIcon(const SIconInfo &icon)

register track icons.

CLinkedFeatsGroup is a container class contains related features.

void PushBack(CSeqGlyph *obj)

CTitleGroup is a layout group with a title.

void SetTitleFont(CGlTextureFont *font)

void SetBackgroundColor(const CRgbaColor &color)

void SetRepeatDist(int dist)

void SetRepeatTitle(bool f)

void SetTitleColor(const CRgbaColor &color)

void SetIndent(int indent)

void SetShowTitle(bool f)

class CRegistryReadView provides a nested hierarchical view at a particular key.

int GetInt(const string &key, int default_val=0) const

access a named key at this level, with no recursion

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

const TSeqRange & GetVisSeqRange() const

const TModelUnit & GetScale() const

TModelUnit ScreenToSeq(const TModelUnit &size) const

convert from screen pixels to sequence positions

bool IsOverviewMode() const

bool WillSeqLetterFit() const

is it enougth space to sequence letters.

class CRgbaColor provides a simple abstraction for managing colors.

static string ComposeProfileString(const TKeyValuePairs &settings)

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

void SetRemoteDataType(const string &data_type)

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

void SetGraphCacheKey(const string &graph_cache_key)

void SetSortBy(const string &sortby)

void SetFilter(const string &filter)

CSGFeatureDS inline method.

virtual void LoadFeatures(objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TJobToken token=-1, int max_feat=-1, ELinkedFeatDisplay LinkedFeatDisplay=ELinkedFeatDisplay::eLFD_Default, const string &extra_filter="")

const string & GetFilter() const

virtual bool AllJobsFinished() const

void SetJobListener(CEventHandler *listener)

Set JobDispatcher listener.

objects::CBioseq_Handle & GetBioseqHandle(void)

Get the underlying bioseq handle.

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)

CSGJobResult – the data structure holding the seqgraphic job results.

static E_Choice GetTypeFromSubtype(ESubtype subtype)

static const CFeatList * GetFeatList()

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

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

void SetHighlightsColor(const CRgbaColor &hl_color)

CRenderingContext * m_Context

the rendering context

virtual void SetHideLabel(bool)

Force to hide label.

void SetParent(CSeqGlyph *p)

virtual TModelUnit GetHeight() const

unique_ptr< CRgbaColor > m_HighlightsColor

Highlight color.

void SetHighlighted(bool flag)

list< CRef< CSeqGlyph > > TObjects

void SetRenderingContext(CRenderingContext *context)

Set the rendering context.

CRef< CHistParamsManager > GetHistParamsManager() const

Get histogram config manager.

const string & GetCurrTheme() const

CRef< CGlTextureFont > GetCommentFont() const

bool GetRepeatComment() const

CConstRef< CCustomFeatureColor > GetCustomFeatColors() const

CConstRef< CFeatureParams > GetFeatParams(TFeatSubtype subtype) const

Get feature settings using a feature subtype.

int GetHistogramCutoff() const

int GetObjectSpace() const

const CRgbaColor & GetFGCommentColor() const

const CRgbaColor & GetBGCommentColor() const

CConstRef< CClonePlacementParams > GetClonePlacementParams() const

bool GetShowComments() const

int GetCommentRepeatDist() const

namespace ncbi::objects::

CSimpleLayout is the simpliest layout policy that simply stack a set of glyphs one on top of the othe...

@ eSort_BySeqPos

seq start position

@ eSort_BySeqSize

sequence length

void SetSortingType(TSortingMethod meth)

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

TBase::const_iterator const_iterator

const string & GetSubkey() const

const string & GetSortBy() const

void SetKey(const string &key)

void SetSubkey(const string &sub_key)

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)

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

const string & GetDB() const

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

IGlyphDialogHost An interface used for handling issues related to any dialog pops up that requires so...

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 Colors colors

static const TLayoutStr s_LayoutStrs[]

bool s_IsSetWeight(const CSeq_feat &feat)

SStaticPair< const char *, ELinkedFeatDisplay > TLinkedFeatStr

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

CFeatureTrack.

static bool s_FeatByWeight(const CRef< CSeqGlyph > &g1, const CRef< CSeqGlyph > &g2)

CStaticArrayMap< string, ELinkedFeatDisplay > TLinkedFeatMap

DEFINE_STATIC_ARRAY_MAP(TLayoutMap, sm_LayoutMap, s_LayoutStrs)

static const string kDispSettings

CStaticArrayMap< string, CFeatureTrack::ELayout > TLayoutMap

static const string kWeightKey

static const TLinkedFeatStr s_LinkedFeatStrs[]

static const string kBaseKey

int s_GetWeight(const CSeq_feat &feat)

static const char * pack(const char *fmt,...)

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

#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_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)

static bool isRmtPipelineFileType(const string &sFileType)

check if a file type is one of remote file types

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

request an annotation selector for a given type

static bool IsUnnamed(const string &annot)

check if a given annotation is a unnamed annotation.

static TAnnotNameType NameTypeStrToValue(const string &type)

static bool isRmtAnnotName(const string &sAnnotname)

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

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

@ eAnnot_Unnamed

unnamed annotation

CRef< CObject > GetResult() const

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

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.

#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 string & ToLower(string &str)

Convert string to lower case – string& version.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

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.

const TExts & GetExts(void) const

Get the Exts member data.

list< CRef< CUser_object > > TExts

E_Choice

Choice variants.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_feat > > TFtable

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

const struct ncbi::grid::netcache::search::fields::SUBKEY subkey

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.

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

void UseDefaultMarginWidth(wxMenu &menu)

Using default menu item margin width.

wxString ToWxString(const string &s)


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