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

=

;

(iter != sm_LevelMap.end()) {

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

(iter->second == level) {

(iter != sm_LabelPosMap.end()) {

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

(iter->second == pos) {

);

, m_ResolveSequences(

)

, m_UseCutoff(

)

(preset_style.empty()) {

level_str = view.

(

);

level_str = iter->second;

(level_str.length() == 1) {

(

<<

<< iter->first <<

<< iter->second);

( !preset_style.empty() ) {

settings[

] = preset_style;

(

<<

);

num_finished = 0;

drop_label =

;

+= (

!= 1 ?

:

);

(

, 0);

(range.

()) {

->SetHelp() =

;

->SetLegend_text(

);

<< iter->first <<

<< iter->second);

->SetHidden_settings().push_back(

( !is_chromosome ) {

is_chromosome = seg_level > 1;

is_chromosome;

CAppJobNotification Notification send by CAppJobEventTranslator.

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

void SetObjects(const CLayoutGroup::TObjectList &objs)

const THighlights & GetHighlights() const

CLayoutGroup & SetGroup()

const CLayoutGroup::TObjectList & GetChildren() const

CLayoutGroup::TObjectList & SetChildren()

CRef< CLayeredLayout > m_Layered

void SetLayoutPolicy(ILayoutPolicy *policy)

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

static CGuiRegistry & GetInstance()

access the application-wide singleton

CJobResultBase – the basic job result class holding a token.

string GetTitle() const

get the track title.

void x_OnLayoutChanged()

update the layout.

TTrackAttrFlags m_Attrs

various track attributes

@ fNavigable

Track has navigation controls.

const string & GetProfile() const

void x_SetStatus(const string &msg, int progress)

void SetMsg(const string &msg)

void SetProfile(const string &preset_style)

CLayoutTrack inline method implmentation.

CRef< CSeqGraphicConfig > m_gConfig

global configuration.

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

string GetString(const string &key, const string &default_val=kEmptyStr) 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...

CRef< CSGSequenceDS > GetSeqDS() const

const TSeqRange & GetVisSeqRange() const

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

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 GetLabelPosRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

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)

objects::CScope & GetScope(void) const

Get the scope from the handle.

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.

CSGJobResult – the data structure holding the seqgraphic job results.

void LoadSegmentMap(const TSeqRange &range, int cutoff, TJobToken token)

void SetSegmentLevel(ESegmentLevel level)

Set which segment level to show.

int GetSegmentMapLevels(const TSeqRange &range) const

Get total number of segment map levels.

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

Query if there is segment maps for given level.

void SetChromosome(bool flag)

ESegmentLevel

It is not technically correct to name a specific segment level as config/scaffold and component becau...

@ eAdaptive

show either contigs or components based on range

void LoadSegmentMapSeqIDs(CSeqGlyph::TObjects &objs, TJobToken token)

TSeqPos GetSequenceLength() const

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

ELabelPosition m_LabelPos

CGlTextureFont m_LabelFont

@ ePos_Inside

inside the rendered bar

@ ePos_Above

above the rendered bar

@ ePos_Side

always on 5' side

CSegmentConfig::TSegMapQuality GetSeqQuality() const

void SetConfig(CRef< CSegmentConfig > config)

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

virtual void SetHideLabel(bool b)

Force to hide label.

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...

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

bool x_IsChromosome(CSGSegmentMapDS &ds) const

CSegmentMapTrack(CSGSegmentMapDS *ds, CRenderingContext *r_cntx)

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

load the track settings.

CRef< CSegmentConfig > m_Config

virtual ~CSegmentMapTrack()

static const string & LevelValueToStr(TSegmentLevel level)

static const string & LabelPosValueToStr(CSegmentConfig::ELabelPosition pos)

virtual void x_SaveSettings(const string &preset_style)

save part of settings to a profile string.

void x_SaveConfiguration(const string &preset_style) const

bool x_NeedHighlight(const CSegmentGlyph *seg) const

static CSegmentConfig::ELabelPosition LabelPosStrToValue(const string &pos)

virtual void x_UpdateData()

update track content.

void x_AddSegmentMapLayout(const CSGJobResult &result)

virtual const CTrackTypeInfo & GetTypeInfo() const

virtual string GetFullTitle() const

get a more meaningful title.

virtual void x_OnJobCompleted(CAppJobNotification &notify)

static CTrackTypeInfo m_TypeInfo

static TSegmentLevel LevelStrToValue(const string &level)

CRef< CSGSegmentMapDS > m_DS

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

void SetHighlightsColor(const CRgbaColor &hl_color)

CRenderingContext * m_Context

the rendering context

unique_ptr< CRgbaColor > m_HighlightsColor

Highlight color.

void SetHighlighted(bool flag)

list< CRef< CSeqGlyph > > TObjects

const string & GetLabelPos() const

const string & GetSizeLevel() const

int GetObjectSpace() const

const string & GetColorTheme() const

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

TBase::const_iterator const_iterator

static CRef< objects::CHiddenSetting > CreateHiddenSetting(const string &name, const string &value)

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

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.

#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 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)

void SetFontFace(EFontFace face, bool use_bitmap_overrides=true)

void SetFontSize(unsigned int size)

Set/get font size in points.

void Set(float r, float g, float b)

set the color from an Fl_Color

CRef< CObject > GetResult() const

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

TThisType & Set(position_type from, position_type to)

#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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int 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.

static string & ToLower(string &str)

Convert string to lower case – string& version.

static const char label[]

Tdata & Set(void)

Assign a value to data member.

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

const int kSegmentLoadLimit

CStaticArrayMap< string, CSegmentConfig::ELabelPosition > TLabelPosMap

static const TLabelPosStr s_LabelPosStrs[]

SStaticPair< const char *, CSegmentConfig::ELabelPosition > TLabelPosStr

static const size_t kMaxSegmentMapRows

CSegmentMapTrack.

static const string kDefProfile

SStaticPair< const char *, CSegmentMapTrack::TSegmentLevel > TLevelStr

DEFINE_STATIC_ARRAY_MAP(TLevelMap, sm_LevelMap, s_LevelStrs)

static const int kSegmentCutoff

static string kDefTrackTitle

static const size_t kCompactThreshold

static const TLevelStr s_LevelStrs[]

static const string kBaseKey

CStaticArrayMap< string, CSegmentMapTrack::TSegmentLevel > TLevelMap

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

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

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