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NCBI C++ ToolKit: src/gui/packages/pkg_alignment/dot_matrix_view.cpp Source File

,

wxMenu* view_menu =

wxMenu();

wxMenu* dm_menu =

wxMenu();

view_menu->Append(

,

(

), dm_menu);

wxMenu* bar_menu =

wxMenu();

bar_menu->Append(

,

(

), view_menu );

*

= it->object.GetPointer();

( aligns.size() > 0 ){

[0].scope.GetPointer();

(! s_coll.

()) {

(! q_coll.

()) {

vector<const CSeq_align*> sel_aligns;

(THits, it_hit, hits) {

& hit = **it_hit;

(evt.

(align, *scope, **it_obj, evt.

())) {

sel_aligns.push_back(&align);

(

<<

);

sid(

);

slabel(

);

found_good =

;

found_bad =

;

(

= 0;

<

.size();

++ ){

type_info&

=

(*obj);

vector< CConstRef<objects::CSeq_align> > aligns;

(aligns.size() > 0)

num_objects =

.size();

(num_objects == 0)

vector<int>();

vector<int>(num_objects, 0);

CRangeCollection< TSeqPos > TRangeColl

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

CIRef< IHitMatrixDataSource > CreateDataSource()

void Init(objects::CScope &scope, const objects::CSeq_align &align)

initial data set from which an alignment will be build

virtual void OnProjectChanged()

virtual void x_UpdateContentLabel()

virtual CRef< objects::CScope > GetScope() const

unique_ptr< const wxMenu > m_MenuBarMenu

virtual objects::CScope * x_GetScope() const

virtual bool x_HasProject() const

EEventSubtype GetSubtype() const

CProjectViewTypeDescriptor - holds description of a project view type.

CSelectionEvent CSelectionEvent is used for broadcasting selection between views.

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)

static bool Match(const CObject &obj1, objects::CScope &scope1, const CObject &obj2, objects::CScope &scope2)

objects::CScope & GetScope()

const objects::CHandleRangeMap & GetRangeSelection() const

bool HasObjectSelection()

Object Selection - represents select Objects (such as features, alignments, etc)

bool AddObjectSelection(const CObject &obj)

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

wxMenuItem * AppendMenuItem(wxMenu &menu, TCmdID cmd_id) const

EEventType GetType() const

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.

vector< IHit * > THitAdapterCont

virtual const objects::CSeq_align * GetSeqAlign() const =0

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.

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

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.

void Error(CExceptionArgs_Base &args)

virtual CUICommandRegistry & GetUICommandRegistry()=0

returns an instance of Command Registry associated with the Workbench

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

TModelRect & GetVisibleRect(void)

virtual wxWindow * GetWindow()

returns a pointer to the wxWindow representing the client

virtual const CViewTypeDescriptor & GetTypeDescriptor() const

return an object providing meta information about thei view type

virtual IView * CreateInstanceByFingerprint(const TFingerprint &fingerprint) const

if fingerprint is recognized - creates and returns a new instance

CIRef< IHitMatrixDataSource > m_DataSource

virtual const CObject * x_GetOrigObject() const

virtual IView * CreateInstance() const

creates a view instance

CDotMatrixViewFactory()

CDotMatrixViewFactory.

void GetSelection(CSelectionEvent &evt) const

get selection for broadcasting

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

virtual vector< int > CombineInputObjects(const TConstScopedObjects &objects)

CHitMatrixWidget * m_AlnWidget

virtual void x_OnSetSelection(CSelectionEvent &evt)

override in derived classes in order to handle selection broadcast

virtual void DestroyViewWindow()

destroy Window corresponding to the view

virtual string GetExtensionIdentifier() const

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

virtual const CProjectViewTypeDescriptor & GetProjectViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

virtual int TestInputObjects(TConstScopedObjects &objects)

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

virtual objects::CScope * x_PreAttachToProject(TConstScopedObjects &objects)

virtual string GetExtensionLabel() const

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

vector< CConstRef< objects::CSeq_align > > TAlignVector

virtual void CreateViewWindow(wxWindow *parent)

create Window corresponding to the view

virtual void RegisterIconAliases(wxFileArtProvider &provider)

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

virtual void x_PostAttachToProject()

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

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

virtual void x_CreateMenuBarMenu()

initializes m_MenuBarMenu; override in derived classes

virtual void GetVisibleRanges(CVisibleRange &vrange) const

populate a visible range event for broadcasting

static CProjectViewTypeDescriptor m_TypeDescr

vector< CConstRef< CObject > > TConstObjects

virtual const string & GetIconAlias() const

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

Add a listener.

vector< SConstScopedObject > TConstScopedObjects

void SetId(CSeq_id &id)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetTo(TTo value)

Assign a value to To data member.

const CharType(& source)[N]

@ eSimilarObjectsAccepted

void ExtractSeqAligns(const T &obj, vector< CConstRef< objects::CSeq_align > > &aligns)

This is the place where elements of the new Alignment Library will be collected.

wxString ToWxString(const string &s)

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