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

=

;

, m_SegMapDS(seg_map_ds)

, m_ColorGapsKey(

)

, m_ShowSegMap(

)

, m_SegMapJobCompleted(

)

title =

;

( !extra.empty() ) {

glyph->SetRenderingContext(r_cntx);

glyph->SetParent(

);

glyph.

(

);

(pp.

() > t_h) {

(pp.

() < t_h)

;

(pp.

() < t_h + t_h - 2.0)

;

show_complement =

(show_complement && pp.

() < t_h + b_h * 2.0 - 2.0) {

((*iter)->NeedTooltip(p, tt, t_title))

;

tt.

(sequence::CDeflineGenerator().GenerateDefline(bsh));

(pp.

() < t_h) {

show_complement =

on_complement =

;

(show_complement && pp.

() > t_h + b_h) {

on_complement =

;

seq_p =

(pp.

());

+=

;

+=

;

(gap->IsSetLength())

(gap->IsSetSeq_data() && gap->GetSeq_data().IsGap() && gap->GetSeq_data().GetGap().IsSetType() && gap->GetSeq_data().GetGap().GetType() ==

)

=

+

;

(gap->IsSetFuzz() && gap->GetFuzz().IsLim() && gap->GetFuzz().GetLim() ==

)

(gap && gap->IsSetSeq_data() && gap->GetSeq_data().IsGap() && gap->GetSeq_data().GetGap().IsSetLinkage_evidence())

(

&ev : gap->GetSeq_data().GetGap().GetLinkage_evidence())

tt.

(

,

, 0);

( !

.empty() ) {

.insert(

.begin() + (seq_p - left + 1),

);

.insert(

.begin() + (seq_p - left),

);

(p_areas ==

)

p_areas->push_back(area);

rsite_areas.reserve(

.size());

(

& rsite :

) {

rsite->GetHTMLActiveAreas(&rsite_areas);

(

&

: rsite_areas) {

p_areas->push_back(

);

show_complement =

().IsNucleotide() && seq_fit;

(show_complement) {

perfLog.

(

,

);

(it.

() == objects::CSeqMap::eSeqGap)

(gap->IsSetSeq_data() && gap->GetSeq_data().IsGap() && gap->GetSeq_data().GetGap().IsSetType() && gap->GetSeq_data().GetGap().GetType() ==

)

(gap->IsSetFuzz() && gap->GetFuzz().IsLim() && gap->GetFuzz().GetLim() ==

)

show_strand)

0,

(seq_str.length()), seq_str);

(

bp = 0; bp != seq_str.length(); bp++) {

bases[0] = seq_str[bp];

(preset_style.empty()) {

(

<<

<< iter->first <<

<< iter->second);

rs_w = view.

(

, 8);

rs_h = view.

(

, 6);

(*s_iter)->SetSiteWidth(rs_w);

(*s_iter)->SetSiteHeight(rs_h);

(*s_iter)->SetSiteColor(rs_color);

(

= 0;

< 5; ++

) {

( !preset_style.empty() ) {

settings[

] = preset_style;

);

(*iter)->Update(

);

(*iter)->Update(

);

((*iter)->HasVisibleRsite())

;

(!params.

.empty())

{

(!src_annots.

()) {

(annots.

()) {

}

(exception& e) {

(annots.

()) {

((is_chromosome && !seg_map_ds->

(1, range)) ||

tracks[annots.

() ?

: annots.

()->first] =

->SetLegend_text(

);

->SetHelp() =

;

(

<<

<< iter->first <<

<< iter->second);

->SetCheck_boxes().push_back(

,

,

,

, show_label));

->SetCheck_boxes().push_back(

,

,

,

, color_gaps));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CAppJobNotification Notification send by CAppJobEventTranslator.

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

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

@ fNoTooltip

do not request and show tooltip

@ fNoPin

tooltip is not pinnable

@ fNoHighlight

no highlighting on mouse over

@ fSequence

sequence track flag

@ fNoSelection

the object can't be selected

int m_Flags

area flags, will need to replace m_Type

string m_ParentId

parent entity idendifier, such as track_id

void PushBack(CSeqGlyph *obj)

Append a layout object to the end.

TObjectList & SetChildren()

virtual void x_UpdateBoundingBox()

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

void SetShowTitle(bool flag)

virtual void GetTooltip(const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const

Get the tooltip if available.

bool m_Expanded

is this track in expanded state

void SetTitle(const string &label, const string &default_title=NcbiEmptyString)

virtual bool OnLeftDblClick(const TModelPoint &p)

bool GetShowTitle() const

ILayoutTrackHost * m_LTHost

Top level host owning the tracks.

const string & GetId() const

const string & GetProfile() const

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.

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

void AddParameter(const std::string &name, const std::string &value)

void Post(CRequestStatus::ECode status=CRequestStatus::e200_Ok)

static string GetSeqLocSignature(const objects::CSeq_loc &loc, objects::CScope *scope)

void GetLabel(string *label) const

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

bool GetBool(const string &key, bool default_val=false) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

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

void TextOut(const CGlTextureFont *font, const char *text, TModelUnit x, TModelUnit y, bool center, bool adjust_flip=true) const

const TSeqRange & GetVisSeqRange() const

const TModelRange & GetVisibleRange() const

TSeqPos GetVisSeqTo() const

void DrawQuad(const TModelRect &rc, bool border=false) const

const TModelUnit & GetScale() const

bool WillSeqLetterFit() const

is it enougth space to sequence letters.

TSeqPos GetVisSeqFrom() const

void Draw3DQuad(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, const CRgbaColor &color, bool border=false) const

void Draw5Prime(TModelUnit x, TModelUnit y, bool direct, TModelUnit size_h, TModelUnit size_v) const

class CRgbaColor provides a simple abstraction for managing colors.

A glyph representing a list of restriction sites stored in one seq-feat.

static CRegistryReadView GetSizeReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static void GetFont(const CRegistryReadView &view, const string &face_key, const string &size_key, CGlTextureFont &f)

static string ComposeProfileString(const TKeyValuePairs &settings)

static CRegistryReadView GetColorReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

Create a read view specifically for 'Color' section.

static CRegistryReadView GetReadView(const CGuiRegistry &reg, const string &base_key, const string &curr_key, const string &def_key1="", const string &def_key2="", const string &def_key3="")

read/readwrite view creation helper methods.

static CRegistryWriteView GetWriteView(CGuiRegistry &reg, const string &base_key, const string &curr_key, const string &def_key1="", const string &def_key2="", const string &def_key3="")

static CRegistryWriteView GetColorRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static CRegistryWriteView GetSizeRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

static void SetColor(CRegistryWriteView &view, const string &key, const CRgbaColor &color)

static void GetColor(const CRegistryReadView &view, const string &key, CRgbaColor &color)

static void SetFont(CRegistryWriteView &view, const string &face_key, const string &size_key, const CGlTextureFont &f)

void SetJobListener(CEventHandler *listener)

Set JobDispatcher listener.

virtual void ClearJobID(TJobID job_id)

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

CSGJobResult – the data structure holding the seqgraphic job results.

void SetAnnot(const string &annot)

CSGFeatureDS inline methods.

const string & GetAnnot() const

static bool GetEnabled()

Indicates if the segment map is enabled.

void LoadSegmentSmear(const TSeqRange &range, TModelUnit scale, const objects::CSeqVector *seq_vec=nullptr)

Used in sequence track for showing segment color.

bool HasSegmentMap(int level, const TSeqRange &range) const

Query if there is segment maps for given level.

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

objects::CScope & GetScope(void) const

Get the scope from the handle.

TSeqPos GetSequenceLength() const

const objects::CSeqVector & GetSeqVector(void) const

objects::CBioseq_Handle GetBioseqHandle(void) const

Get the underlying bioseq handle.

void GetSequence(TSeqPos from, TSeqPos to, string &buffer) const

retrieve a string representing the IUPAC characters for the sequence [from to].

string GetAcc_Best() const

this is more suitable for display purposes since the returned string will not always be good to recon...

objects::CSeq_id_Handle GetBestIdHandle() const

static bool IsChromosome(const objects::CBioseq_Handle &handle, objects::CScope &scope)

void SetColorCode(const TColorCode &colors)

CSegmentSmearGlyph inline methods.

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)

bool IsIn(const TModelPoint &p) const

Hit test for points in PARENT COORD.

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetHeight() const

virtual void SetTop(TModelUnit b)

void Draw() const

render the layout.

vector< CHTMLActiveArea > TAreaVector

void x_World2Local(TModelPoint &p) const

Transform the coordiante from world coord. to local coord.

list< CRef< CSeqGlyph > > TObjects

void SetRenderingContext(CRenderingContext *context)

Set the rendering context.

const string & GetSizeLevel() const

int GetObjectSpace() const

bool GetShowComments() const

const string & GetColorTheme() const

static SIZE_TYPE Complement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

namespace ncbi::objects::

virtual string GetExtensionLabel() const

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

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

virtual const CTrackTypeInfo & GetThisTypeInfo() const

virtual CRef< objects::CTrackConfigSet > GetSettings(const string &profile, const TKeyValuePairs &settings, const CTempTrackProxy *track_proxy) 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 input object and extra parameters.

virtual string GetExtensionIdentifier() const

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

CSequenceTrack – the layout track for holding and visualizing a molecule sequence superimposed by com...

vector< CRef< CRsitesGlyph > > TRsites

list of restriction sites

CRgbaColor m_SeqBarColor

sequence bar color.

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

load the track settings.

CRef< CGlTextureFont > m_SeqFont

font

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

access our core component - we wrap an object(s) of some sort.

virtual CRef< CSeqGlyph > HitTest(const TModelPoint &p)

Hit testing.

virtual bool x_Empty() const

bool m_SegMapJobCompleted

virtual const IObjectBasedGlyph::TIntervals & GetIntervals(void) const

access sub-intervals (if any).

const objects::CSeqVector & GetSeqVector() const

virtual CHTMLActiveArea * InitHTMLActiveArea(TAreaVector *p_areas) const

Initialize the HTML active area for a track.

virtual bool HasObject(CConstRef< CObject > obj) const

check if the wrapped object(s) is the one.

bool x_HasVisibleRsite() const

virtual void x_SaveSettings(const string &preset_style)

save part of settings to a profile string.

virtual void x_OnJobCompleted(CAppJobNotification &notify)

TModelUnit x_GetBarHeight() const

Get the sequence bar height.

virtual bool NeedTooltip(const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const

Check if need to show tooltip.

virtual string GetSignature() const

return signature for this glyph.

CRgbaColor m_StrandColor

sequence strand color.

virtual const CTrackTypeInfo & GetTypeInfo() const

void x_RenderGaps(const TModelRect &rcm, TSeqPos from, TSeqPos to, bool show3d) const

bool m_ShowSegMap

superimpose segment map.

CSegmentSmearGlyph::TColorCode m_SegMapColors

color codes for segment map.

TModelUnit x_GetGapsBarHeight() const

Get the height of the gaps bar, drown on top of the segment map.

CRef< CSGSequenceDS > m_SeqDS

CRgbaColor m_SeqColor

sequence text color.

CRef< objects::CSeq_loc > m_Location

bool x_ShowSegMap() const

virtual void x_RenderContent() const

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

virtual void x_UpdateData()

update track content.

CRef< CSGSegmentMapDS > m_SegMapDS

void x_SaveConfiguration(const string &preset_style) const

save all track settings to the configuration file.

virtual bool OnLeftDblClick(const TModelPoint &p)

CSequenceTrack(CSGSequenceDS *seq_ds, CRenderingContext *r_cntx, CSGSegmentMapDS *seg_map_ds=NULL)

virtual CRef< CSGGenBankDS > GetDataSource()

Method for accessing the data source.

virtual void x_UpdateBoundingBox()

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

void x_RenderSequence(const TModelRect &rcm, bool seq_fit, bool direct, bool show_strand) const

Render a sequence bar and the sequence if fits.

static CTrackTypeInfo m_TypeInfo

virtual void GetTooltip(const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const

Get the tooltip if available.

virtual void GetObjects(vector< CConstRef< CObject > > &objs) const

retrieve CObjects corresponding to this CSeqGlyph.

virtual const objects::CSeq_loc & GetLocation(void) const

access the position of this object.

bool m_ShowLabel

show sequence label.

const CLayoutTrack * GetTrack() const

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)

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

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_ZoomOnRange(const TSeqRange &range)=0

notifies the host we need to zoom on to a range.

vector< TSeqRange > TIntervals

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 begin() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

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)

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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

request an annotation selector for a given type

void Offset(T d_x, T d_y)

IRender & GetGl()

convenience function for getting current render manager

virtual TModelUnit TextHeight(const CGlTextureFont *font) const =0

virtual void ColorC(const CRgbaColor &c)=0

Set current color (glColor{3,4}{f,d}{v,})

virtual void AddRow(const string &sContents="", unsigned colspan=2)=0

add a row with a cell, spanning across all columns

CRef< CObject > GetResult() const

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

CRgbaColor GetGreyscale() const

Returns the greyscale equivalent of the current color.

virtual bool IsEmpty() const =0

Indicates if the tooltip is empty.

#define ENUM_METHOD_NAME(EnumName)

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

CConstRef< CSeq_literal > GetGapSeq_literal(void) const

returns gap Seq-data object ref returns null if it's not a gap or an unspecified gap

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

CSeqMap::ESegmentType GetType(void) const

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

TSeqPos GetPosition(void) const

return position of current segment in sequence

CConstRef< CSeq_literal > GetRefGapLiteral(void) const

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

const CSeqMap_CI & GetCurrentSeqMap_CI() const

bool IsInGap(void) const

true if current position of CSeqVector_CI is inside of sequence gap

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

static TThisType GetWhole(void)

#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 const string BoolToString(bool value)

Convert bool to string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

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

Case-insensitive equality of a substring with another 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.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

Tdata & Set(void)

Assign a value to data member.

bool IsRsite(void) const

Check if variant Rsite is selected.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

bool IsMap(void) const

Check if variant Map is selected.

const TUser & GetUser(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TMap & GetMap(void) const

Get the variant data.

list< CRef< CSeq_feat > > Tdata

const TExt & GetExt(void) const

Get the Ext member data.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

@ e_User

user defined object

unsigned int

A callback function used to compare two keys in a database.

static const TModelUnit kGapBarHeight

static const string kColorGapsKey

static const int kBarHeight

static const string kDefProfile

static const string kShowLabelKey

static const int kSeqTooltipLength

CSequenceTrack.

static const string kBaseKey

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