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

objects::SAnnotSelector& sel,

& range,

window,

calc_min,

fixed_scale)

<

Type>

left == 0 ? right : (left < right ? left : right);

( !col_val_min.

(annot, 0, min_val) ||

!col_val_step.

(annot, 0, val_step) ||

!col_val.

(annot, 0, values)) {

TDataType g_max = (TDataType)(255 * val_step + min_val);

de_quant[0] = (float)min_val;

(

= 1;

< 256; ++

) {

de_quant[

] = de_quant[

- 1] + (float)val_step;

r_end =

(rows - 1);

= (r_start + r_end) / 2;

}

((

)pos != from && r_start < r_end - 1);

(

= (r_start + r_end) / 2; (size_t)

< rows; ++

) {

( col_pos.

(annot,

, pos) ) {

((

)pos > to)

;

de_quant[(

char)values[

]]);

de_quant[(

char)values[

]]);

->m_ObjectList.push_back(fref);

}

(std::exception& ex) {

vector<string>& annots_allowed)

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos) {

, sel, range, scale, calc_min, fixed_scale) );

&

=

&

(

.object.GetObject());

sid(

);

slabel(

);

);

, m_FixedScale(

)

(

<<

);

= objs.size();

wxMenuItem* item_min = menu.AppendCheckItem(id_base,

(

));

wxMenuItem* item_scale = menu.AppendCheckItem(id_base + 1,

(

));

(

!= item_min->IsChecked()) {

( !src_annots.

() ) {

ds_pointer->

(iter->first);

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

track->SetTitle(iter->second);

const TAnnotNames & GetAnnotNames(void) const

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CAppJobNotification Notification send by CAppJobEventTranslator.

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

CEpigenomicsDSType - Epigenomics data source type.

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

create an instance of the layout track type using default settings.

virtual string GetExtensionLabel() const

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

virtual bool IsSharable() const

check if the data source can be shared.

virtual string GetExtensionIdentifier() const

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

CEpigenomicsDS - Epigenomics data source.

void GetAnnotNames(const TSeqRange &range, TAnnotNameTitleMap &annots, const vector< string > &annots_allowed)

void LoadData(const TSeqRange &range, TModelUnit scale, bool calc_min=false, bool fixed_scale=false)

CEpigenomicsDS(objects::CScope &scope, const objects::CSeq_id &id)

CEpigenomicsDS.

void SetAnnot(const string &annot)

CEpigenomicsDS inline methods.

CEpigenomicsJob(const string &desc, objects::CBioseq_Handle handle, const objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, bool calc_min, bool fixed_scale)

bool m_FixedScale

use global scale or dynamic scale

virtual EJobState x_Execute()

method truly doing the job.

bool m_CalcMin

add min graph

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

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.

CEpigenomicsTrack – A special track for showing epigenomics map.

virtual void x_OnJobCompleted(CAppJobNotification &notify)

CRef< CEpigenomicsDS > m_DS

CEpigenomicsTrack(CEpigenomicsDS *ds, CRenderingContext *r_cntx)

string m_AnnotDesc

detailed track title

bool m_CalcMin

Superinpose min graph on top of max graph?.

virtual string GetFullTitle() const

get a more meaningful title.

virtual ~CEpigenomicsTrack()

virtual const CTrackTypeInfo & GetTypeInfo() const

virtual void x_UpdateData()

update track content.

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

load the track settings.

void x_OnSettingsIconClicked()

virtual void x_SaveSettings(const string &preset_style)

save part of settings to a profile string.

static CTrackTypeInfo m_TypeInfo

CEpigenomicsTrack.

bool m_FixedScale

Dynamic or fixed graph scale.

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

void x_AddGraphs(const CSGJobResult &result)

void SetObjects(const CLayoutGroup::TObjectList &objs)

CLayoutGroup & SetGroup()

CLayoutGroup::TObjectList & SetChildren()

CRef< CSimpleLayout > m_Simple

void SetLayoutPolicy(ILayoutPolicy *policy)

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

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 > GetHistParams(TFeatSubtype subtype) const

Get histogram settings using feature subtype.

const string & GetAnnotName() const

void SetDialogHost(IGlyphDialogHost *host)

void SetAxisMaxFixed(TDataType max)

const string & GetTitle() const

void SetConfig(const CSeqGraphicConfig &config)

@ eIcon_Settings

icon id for track settings

ILayoutTrackHost * m_LTHost

Top level host owning the tracks.

string GetTitle() const

get the track title.

virtual void x_OnIconClicked(TIconID id)

Mouse left-click event handler on an icon.

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.

void x_RegisterIcon(const SIconInfo &icon)

register track icons.

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

const TSeqRange & GetVisSeqRange() const

const TModelUnit & GetScale() const

class CRgbaColor provides a simple abstraction for managing colors.

objects::SAnnotSelector m_Sel

our annotation selector

TSeqRange m_Range

target range

objects::CBioseq_Handle m_Handle

target sequence

static string ComposeProfileString(const TKeyValuePairs &settings)

TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")

Launch either a background or foreground job.

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.

objects::CBioseq_Handle m_Handle

void SetAdaptive(bool flag)

CSGJobResult – the data structure holding the seqgraphic job results.

CRenderingContext * m_Context

the rendering context

list< CRef< CSeqGlyph > > TObjects

CRef< CHistParamsManager > GetHistParamsManager() const

Get histogram config manager.

CRef< CAppJobError > m_Error

bool TryGet(const CFeat_CI &feat_ci, Value &v) 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 string kTrackTitle

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 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.

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

static string GetAnnotName(const objects::CSeq_annot_Handle &annot_handle)

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static void SetAnnot(objects::SAnnotSelector &sel, const string &annot)

help function for setting up an annotation.

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

help function for setting selector resolve depth.

CRef< CObject > GetResult() const

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

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

EJobState

Job states (describe FSM)

size_t GetSeq_tableNumRows(void) const

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

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

Case-insensitive equality of a substring with another string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

@ eField_id_location_from

interval from

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

#define row(bind, expected)

A help struct for storing information about a icon.

TEMPLATE binary functor base struct.

TEMPLATE STRUCT non_zero_min.

virtual binary_functor< Type > * clone() const

Type operator()(const Type &left, const Type &right) const

void UseDefaultMarginWidth(wxMenu &menu)

Using default menu item margin width.

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