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NCBI C++ ToolKit: src/gui/packages/pkg_snp/track/snp_track.cpp Source File

=

;

);

(iter->second == layout) {

, m_eLayout(eLayout_Adaptive)

, m_IconLayout(eIcon_Layout,

,

,

)

, m_PreferredTitle(sTitle)

(!sLayout.empty()) {

(!sFilter.empty())

bShowLabels =

;

bIsLayoutOnlyChange =

;

wxMenuItemList& item_list = menu.GetMenuItems();

(wxMenuItemList, iter, item_list) {

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

!=

) {

bIsLayoutOnlyChange =

;

bIsLayoutOnlyChange =

;

bIsLayoutOnlyChange =

;

(bIsLayoutOnlyChange) {

( !preset_style.empty() ) {

settings[

] = preset_style;

(preset_style.empty()) {

<< iter->first <<

<< iter->second);

}

(std::exception&) {

<< iter->first <<

<< iter->second);

=

;

( ; feature_iter; ++feature_iter) {

( ; graph_iter; ++graph_iter) {

graph.push_back(pGraph);

seq_entry.SetAnnot().push_back(pAnnot);

s_MaxFeatures(30 * 1000 * 1000);

(nFeats > s_MaxFeatures) {

;

(

);

+=

;

+=

;

}

(

(*first_glyph) ==

(

)) {

( !src_annots.

() ) {

sAnnot(iter->second);

track_settings.count(

) ? track_settings[

] :

));

feat_track->SetAnnot(sAnnot);

(

&

: src_annots) {

.first,

.second->m_Title));

config_set->

().push_back(

(settings, track_proxy, is_clinvar_track));

->SetLegend_text(

);

(is_clinvar_track) {

->SetLegend_text(

);

->SetSubkey(

);

show_only_pathogenic{

};

}

(std::exception&) {

);

choice->SetValues().push_back(

,

,

));

choice->SetValues().push_back(

,

,

));

choice->SetValues().push_back(

,

));

choice->SetValues().push_back(

,

,

));

->SetChoice_list().push_back(choice);

->SetCheck_boxes().push_back(

,

,

,

, show_only_pathogenic,

));

isInsertion(

);

vector<string> Ngbrs;

(Ngbrs.size() == 4 &&

NStr::StringToNumeric<int>(Ngbrs[3]) - NStr::StringToNumeric<int>(Ngbrs[2]) == 1) {

(std::exception&) {

(

,

);

sColorKey(

);

(VariationClass)

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

iParamsCache->second;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

CAppJobNotification Notification send by CAppJobEventTranslator.

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.

void SetConfig(CConstRef< CFeatureParams > conf)

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

CFeatureParams: the data structure holding feature rendering parameters.

CGlTextureFont m_LabelFont

ELabelPosition m_LabelPos

EBoxStyle

how the box of the feature is drawn

@ eBox_Insertion

additional decoration for the box

@ eBox_Deletion

add an inverted triangle to mark a deletion

@ ePos_Side

always on 5' side

void Add(CSeqGlyph *obj)

Append a layout object to the end.

CRef< CInlineLayout > m_Inline

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

void SetConfig(const CSeqGraphicConfig &config)

void x_DeregisterIcon(TIconID id)

deregister an icon if already registered.

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

@ eIcon_Layout

icon id for setting layout style

ILayoutTrackHost * m_LTHost

Top level host owning the tracks.

string m_Msg

special message need to show on title bar

string GetTitle() const

get the track title.

void x_OnLayoutChanged()

update the layout.

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.

const string & GetProfile() const

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.

void x_RegisterIcon(const SIconInfo &icon)

register track icons.

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

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

const TSeqRange & GetVisSeqRange() const

const TModelUnit & GetScale() const

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

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

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)

void LoadData(const TSeqRange &range, CSnpJob::SParams &p, SSnpFilter *filter)

static void GetAnnotNames(SConstScopedObject &object, map< string, string > &annots, const TSeqRange &range, const ILayoutTrackFactory::SExtraParams &params)

static CRgbaColor GetSNPColor(const objects::CSeq_feat &feat, const CRegistryReadView &ColorView)

CRef< CFeatureParams > SetParamsTemplate()

CRef< CFeatureParams > m_ParamsTemplate

CConstRef< CFeatureParams > GetFeatureParams(const objects::CSeq_feat &feat, const CRegistryReadView &ColorView) const

static CRef< CSNPFeatureParams > CreateSNPFeatureParams()

TParamsCache m_ParamsCache

void Reset(CConstRef< CFeatureParams > OrigParams)

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

CRenderingContext * m_Context

the rendering context

const CRenderingContext * GetRenderingContext() const

Get the rendering context.

list< CRef< CSeqGlyph > > TObjects

int GetObjectSpace() const

namespace ncbi::objects::

CSnpBitfield is a facade for representing any version of the SNP bitfield.

EVariationClass GetVariationClass() const

static string s_AdjustAnnotName(const string &sAnnotName)

! this is a temporary function for an interim period when SNP filters are taken from !...

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

CSnpTrackFactory.

virtual const CTrackTypeInfo & GetThisTypeInfo() const

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

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

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

static CTrackTypeInfo m_TypeInfo

virtual void x_UpdateData()

update track content.

void SetAnnot(const string &name)

virtual const CTrackTypeInfo & GetTypeInfo() const

virtual string GetFullTitle() const

get a more meaningful title.

virtual bool CheckRange(TSeqRange range, string &sMsg, size_t &nFeats)

objects::CFeat_CI x_GetFeat_CI(const TSeqRange &range)

virtual void x_SaveSettings(const string &preset_style)

save the track settings to a profile string.

CRef< CSNPFeatureParams > m_Params

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

load the track settings.

CSnpTrack(CSGSnpDS *ds, CRenderingContext *r_cntx, const string &sFilter, const string &sTitle, const string &sLayout="")

bool x_IsOverviewMode() const

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

objects::CGraph_CI x_GetGraph_CI(const TSeqRange &range)

virtual void x_OnJobCompleted(CAppJobNotification &notify)

void x_ProcessJobResult()

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

@ eLayout_Features

Show features whenever possible.

@ eLayout_Labels

Show labels and cascade features (CLayeredLayoutPolicy)

@ eLayout_Density

Always show density.

@ eLayout_Adaptive

All SNPs drawn in one line.

CRef< SSnpFilter > m_Filter

void x_AddSnpsLayout(const SSnpJobResult &result)

CRef< SSnpJobResult > m_JobResult

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

TBase::const_iterator const_iterator

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

CTrackTypeInfo - holds description of a layout track type.

const string & GetDescr() const

const string & GetId() const

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_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.

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

#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 NCBI_ASSERT(expr, mess)

#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...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

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

check if a given annotation is an extended NAA (named accession[.version][number],...

void SetFontFace(EFontFace face, bool use_bitmap_overrides=true)

void SetFontSize(unsigned int size)

Set/get font size in points.

CGlPoint< TModelUnit > TModelPoint

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

static size_t EstimateSNPCount(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

static CGraph_CI GetGraph_CI(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

static CFeat_CI GetFeat_CI(const TSeqRange &range, const string &sAnnotName, CBioseq_Handle &Handle)

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

Set object to copy of another one.

const CSeq_graph & GetMappedGraph(void) const

Graph mapped to the master sequence.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

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 list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

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.

const TData & GetData(void) const

Get the Data member data.

Tdata & Set(void)

Assign a value to data member.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

const TExt & GetExt(void) const

Get the Ext member data.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_graph > > TGraph

list< CRef< CSeq_feat > > TFtable

unsigned int

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

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

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

static const TLayoutStr s_LayoutStrs[]

CStaticArrayMap< string, CSnpTrack::ELayout > TLayoutMap

const string & s_LayoutValueToStr(CSnpTrack::ELayout layout)

static CFeatureParams::EBoxStyle s_GetBoxStyle(const CSeq_feat &feat)

static const string kDefProfile

static CSnpBitfield::EVariationClass s_GetVariationClass(const CSeq_feat &feat)

DEFINE_STATIC_ARRAY_MAP(TLayoutMap, sm_LayoutMap, s_LayoutStrs)

static CSnpTrack::ELayout s_LayoutStrToValue(const string &layout)

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

CSnpTrack.

static const string kBaseKey

TIconID m_Id

must be unique within the context

bool bPreferFeat

Return feat glyphs instead of histogram glyphs.

bool bAdaptive

Only return feat glyphs when not overview.

CRenderingContext * r_cntx

CSeqGlyph::TObjects listObjs

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

void UseDefaultMarginWidth(wxMenu &menu)

Using default menu item margin width.

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