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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/view__graphic_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence/view_graphic.cpp Source File

"The Graphical View provides an overview of annotations "

"on sequence, with extensive drill-down capabilities.",

: m_GraphicPanel(

)

=

[0].object.GetPointer();

scope =

[0].scope.GetPointer();

(seq_entry && seq_entry->

())

seq = &seq_entry->

();

wxString strInitializing =

(

);

(

);

(!ws)

;

settings = doc->GetViewSettings(view_type, view_ins_id);

(

<<

<< settings);

(

!= params) {

(!param_settings.empty()) {

(

<<

<< param_settings);

settings = param_settings;

vector<string>

;

(tokens.size() == 2) {

);

wxMessageBox(

(

),

(

),

wxOK | wxICON_EXCLAMATION);

<< id_desc);

(setting_map.count(

) != 0) {

(setting_map.count(

) != 0) {

(loc && !loc->

()) {

}

(setting_map.count(

) != 0) {

( !tokens.empty() ) {

(tokens.size() > 1) {

((*itr)->GetName() ==

) {

* seq_id =

*

(&itLoc->GetObject());

(seqIds.

(handle) == seqIds.

()) {

(

(

) ==

(*it_obj)) {

*

(it_obj->GetPointer()) ) {

( ; id_iter; ++id_iter) {

}

(

* id_loc =

*

(it_obj->GetPointer()) ) {

}

(

*

(it_obj->GetPointer()) !=

) {

(vrange.

(bsh, this_range)) {

}

( std::exception& e ){

<<

* iview = *iter;

(view_p && view_p->

() !=

()) {

list<TSeqRange> vis_ranges;

( !vis_ranges.empty() ) {

tmp_objs.push_back(vref);

}

( std::exception& e ){

<<

* iview = *iter;

(view_u && view_p && view_p->

() == view_u->

()) {

siblings.erase(iter);

dm_srv->AttachContext(*

);

dm_srv->DetachContext(*

);

->GetAnnotNames();

sid(

);

slabel(

);

type_info&

=

(object);

seq_entry.

();

type_info&

=

(object);

seq_entry.

();

found_good =

;

found_bad =

;

(

= 0;

<

.size();

++) {

(found_bad) {

(

= 0;

<

.size(); ++

) {

* loc =

*

(iter->object.GetPointer());

* scope =

*

(iter->scope.GetPointer());

ranges[idh] += range;

(ranges.size() == 1) {

TRanges::iterator iter = ranges.begin();

loc->

().SetFrom(iter->second.GetFrom());

loc->

().SetTo (iter->second.GetTo());

loc->

(*iter->first.GetSeqId());

(!widget || !widget->

())

settings =

;

(!markers.empty()) {

settings +=

+ markers;

project.SaveViewSettings(view_type, view_ins_id, settings);

project.SetDirty(

);

(

.IsStr() &&

.GetStr() ==

) {

& field_id = (*it)->GetLabel();

(!field_id.

())

((

==

) &&

.IsStr())

.GetStr();

(!prj_folder.IsSetItems())

vector< CIRef<INonAsnTrackDataFactory> > data_factories;

(data_factories.empty())

(

& prj_item : prj_folder.GetItems()) {

(!prj_item->GetItem().IsOther())

(

&factory : data_factories) {

(track_data.

()) {

(

& prj_folder : prj_folder.GetFolders()) {

vector< TRangeWithFuzz > TRanges

User-defined methods of the data storage class.

std::invoke_result< _Fty, ICanceled & >::type GUI_AsyncExec(_Fty &&_Fnarg, const wxString &msg=wxT("Accessing network..."))

const CSeq_id * GetFirstId() const

CEvent - generic event implementation TODO TODO - Attachments.

string GetDefaultAssembly() const

wxString GetWorkDir() const

CUndoManager & GetUndoManager()

CSeqGraphicWidget * GetWidget()

vector< TRelation > TRelationVector

static void FindRelations(objects::CScope &scope, const CObject &obj, const string &to_type_in, TRelationVector &relations)

SConstScopedObject & GetObject()

const objects::CUser_object * GetParams() const

CProjectService - a service providing API for operations with Workspaces and Projects.

virtual void x_ReportInvalidInputData(TConstScopedObjects &objects)

use this function to report incompatible data in InitView()

virtual void OnProjectChanged()

virtual void x_UpdateContentLabel()

CRef< objects::CScope > m_Scope

virtual string GetClientLabel(IWMClient::ELabel ltype=IWMClient::eDefault) const

returns the client label (name) to be displayed in UI

virtual objects::CScope * x_GetScope() const

virtual void x_AttachToProject(CGBDocument &doc)

TId GetId() const

retrieve a unique ID for this view

virtual void RefreshViewWindow()

virtual bool x_HasProject() const

objects::CGBProjectHandle::TId GetProjectId()

EEventSubtype GetSubtype() const

CProjectViewTypeDescriptor - holds description of a project view type.

virtual void SetWorkbench(IWorkbench *workbench)

IView implementation.

void GetReflectionInfo(const objects::CSeq_id &id, list< TSeqRange > &visible_ranges, CRgbaColor &color, string &label) const

Retrieve all information relevant to showing view reflection - that is, displaying the location of si...

vector< SObject > TObjects

@ fConvert_NoExpensive

do not perform any expensive tests (such as fetching from the network)

class CRgbaColor provides a simple abstraction for managing colors.

CSelectionEvent CSelectionEvent is used for broadcasting selection between views.

static bool MatchIdWithId(const objects::CSeq_id &id1, objects::CScope &scope1, const objects::CSeq_id &id2, objects::CScope &scope2)

bool HasRangeSelection() const

Range Selection - represents a collection of selected segments.

void GetAllObjects(TConstObjects &objs) const

void AddRangeSelection(const objects::CSeq_id &id, const TRangeColl &segs)

objects::CScope & GetScope()

const objects::CHandleRangeMap & GetRangeSelection() const

bool AddObjectSelection(const CObject &obj)

list< CRef< CSeqGlyph > > TObjects

Base class for all serializable objects.

Template class for iteration on objects of class C (non-medifiable version)

CUICommandRegistry is a centralized registry where all application commands should be registered.

@ eOpenGraphicalViewEvent

@ eWidgetDataChanged

notification from child to parent that the underlying data has changed

CViewTypeDescriptor - holds description of a view type.

bool Clamp(const objects::CBioseq_Handle &handle, TSeqRange &range) const

Alter the supplied range according to the rules provided in the policy and the supplied new location.

bool Match(const objects::CSeq_id &id) const

See if we can match the supplied range.

void AddLocation(const objects::CSeq_loc &loc)

Interface for testing cancellation request in a long lasting operation.

virtual const CViewTypeDescriptor & GetViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

IView - represents a standard visual part of Workbench UI.

IVisibleRangeClient - represents an object that wants notifications about visible range changes.

CFingerprint identifies an instance of IWMClient and is used for labeling layout positions.

IWorkbench is the central interface in the application framework.

iterator_bool insert(const value_type &val)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

virtual void RegisterFileAlias(const wxArtID &anId, const wxArtClient &aClient, const wxSize &aSize, const wxString &aName, long aType=wxBITMAP_TYPE_ANY, int anIndex=-1)

static const struct name_t names[]

static const char * str(char *buf, int n)

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.

virtual const CObject * x_GetOrigObject() const

virtual void GetCompatibleToolBars(vector< string > &names)

returns the names of toolbars compatible with this class (toolbars that are relevant and useful in th...

virtual void x_OnSetSelection(CSelectionEvent &evt)

override in derived classes in order to handle selection broadcast

#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)

void Info(CExceptionArgs_Base &args)

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

vector< CIRef< IView > > TViews

virtual void GetViews(TViews &views)=0

get all registered views

virtual IViewManagerService * GetViewManagerService()=0

static CRef< objects::CSeq_loc > CreateSeq_loc(const objects::CSeq_id &id, const CRangeCollection< TSeqPos > &ranges)

#define EXT_POINT__NONASN_TRACK_DATA_FACTORY

virtual string GetExtensionIdentifier() const

CViewGraphicFactory.

virtual string GetExtensionLabel() const

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

virtual void CreateViewWindow(wxWindow *parent)

create Window corresponding to the view

CConstRef< objects::CSeq_id > m_SeqId

virtual void GetVisibleRanges(CVisibleRange &vrange) const

populate a visible range event for broadcasting

virtual void RegisterCommands(CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)

called by the framework to give Factory a chance to register commands used by view

void OnWidgetDataChanged(CEvent *evt)

virtual IView * CreateInstanceByFingerprint(const TFingerprint &fingerprint) const

if fingerprint is recognized - creates and returns a new instance

virtual void SetWorkbench(IWorkbench *workbench)

IView implementation.

virtual const CViewTypeDescriptor & GetTypeDescriptor() const

return an object providing meta information about thei view type

virtual const wxMenu * GetMenu()

returns a menu (must be deleted by the caller) menu injections should follow a separator named "Contr...

virtual CRef< objects::CScope > GetSearchScope()

virtual CRef< objects::CSeq_loc > GetSearchLoc()

virtual void DestroyViewWindow()

destroy Window corresponding to the view

string x_GetViewSettingsFromParams(const objects::CUser_object *params)

void x_SetNonAsnInput(const objects::CProjectFolder &prj_folder)

void x_UpdateVisRangeLayout(const IViewManagerService::TViews &views)

virtual string GetDMContextName()

returns Name of the context to be used in UI

void OnOpenGraphicalView(CEvent *evt)

virtual void RegisterIconAliases(wxFileArtProvider &provider)

called by the framework to give Factory a chance to register images used by view

virtual bool IsCompatibleWith(const CObject &object, objects::CScope &scope)

CGraphicPanel * m_GraphicPanel

virtual bool InitView(TConstScopedObjects &objects, const objects::CUser_object *params)

initialize view with data, inside this function the view must call CProjectService::AttachView to con...

virtual set< string > GetAnnotNames() const

virtual const CProjectViewTypeDescriptor & GetProjectViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

virtual void OnViewReleased(IView &)

virtual void OnWidgetRangeChanged()

virtual IView * CreateInstance() const

creates a view instance

virtual void OnViewAttached(IView &)

void SaveSettingsAtProject(objects::CGBProjectHandle &project) const

virtual void SetOrigObject(SConstScopedObject &obj)

virtual void OnVisibleRangeChanged(const CVisibleRange &vrange, IVisibleRangeClient *source)

void GetSelection(CSelectionEvent &evt) const

get selection for broadcasting

bool x_NeedsConversion(const CObject &object, objects::CScope &scope)

CIRef< INonAsnTrackData > m_NonAsnTrackData

virtual int TestInputObjects(TConstScopedObjects &objects)

tests input objects (not using object conversion) and returns a combination of ETestResult flags bett...

virtual wxWindow * GetWindow()

returns a pointer to the wxWindow representing the client

virtual bool x_MergeObjects(TConstScopedObjects &objects)

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

CRef< objects::CScope > scope

void GetExtensionAsInterface(const string &ext_point_id, vector< CIRef< I > > &interfaces)

GetExtensionAsInterface() is a helper function that extracts all extensions implementing the specifie...

vector< CConstRef< CObject > > TConstObjects

virtual const string & GetIconAlias() const

virtual const string & GetHelpId() const

#define ON_EVENT(type, id, handler)

#define END_EVENT_MAP()

Ends definition of Command Map.

CConstRef< CObject > object

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

virtual void AddListener(CEventHandler *listener, int pool_name=ePool_Default)

Add a listener.

vector< SConstScopedObject > TConstScopedObjects

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TRange GetTotalRange(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const CSeq_id_Handle & GetSeq_id_Handle(void) const

Get handle of id used to obtain this bioseq handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

vector< CRef< CUser_field > > TData

bool IsWhole(void) const

Check if variant Whole is selected.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

@ eSimilarObjectsAccepted

CProjectViewTypeDescriptor s_ViewGraphicTypeDescr("Graphical Sequence View", "graphical_view", "Graphical View", "The Graphical View provides an overview of annotations " "on sequence, with extensive drill-down capabilities.", "GRAPHICAL_VIEW", "Sequence", false, "Seq-loc", eSimilarObjectsAccepted)

CViewGraphic.

void ReportIDError(const string &id_label, bool is_local, const string &title="Error message")

wxString ToWxString(const string &s)

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