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

,

,

,

m_MenuBarMenu.reset(cmd_reg.

(kViewMenu));

obj =

[0].object.GetPointer();

scope =

[0].scope.GetPointer();

(!ws)

;

}

;

&&

->GetData().GetAlign().front()->CanGetSegs()

->GetData().GetAlign().front()->GetSegs().IsSparse()

||

->GetData().GetAlign().front()->GetSegs().IsSpliced()

unique_ptr<IAlnSegmentIterator> p_it(

->CreateSegmentIterator(

, total_r,

));

->GetSeqFromAln(master_row, aln_coll, seq_coll);

vector<TNumrow> rows;

objs.reserve(rows.size());

(vector<TNumrow>, it, rows) {

->GetAlnFromSeq(master_row, coll, aln_coll);

vector<CAlnVec::TNumrow> sel_rows;

sel_rows.push_back(row_handle->

());

(pos == id_loc->m_Range.GetFrom()) {

= (pos == id_loc->m_Range.GetTo());

sel_rows.push_back(

);

vector<TNumrow> rows;

(vector<TNumrow>, it, rows) {

(evt->

()) {

sid(

);

slabel(

);

type_info&

=

(object);

annot && annot->

();

type_info&

=

(object);

(

->IsSetAnnot() && !

->GetAnnot().empty() &&

->GetAnnot().front()->IsAlign()) {

found_good =

;

found_bad =

;

*

= oitr->object;

* scope = oitr->scope;

(found_bad) {

(

= 0;

<

.size(); ++

) {

( scope ==

){

* const_obj = it->object;

aligns.push_back( align );

( action ==

){

* const_id =

*

( it->object.GetPointer() );

( !const_id )

;

list< CRef< CSeq_align > > aligns;

( annot && annot->

() ){

aligns =

list< CRef< CSeq_align >

&>( annot->

().

() );

( num_seqs <= 0 ){

(

q = 0; q < num_seqs; q++ ){

(seq_id.

(*const_id)) {

chosen_aligns.push_back(*aix);

( idh == chosen_idh ){

chosen_aligns.push_back( *aix );

list< CRef< CSeq_align > > aligns;

( annot && annot->

() ){

aligns =

list< CRef< CSeq_align >

&>( annot->

().

() );

( num_seqs <= 0 ){

(

q = 0; q < num_seqs; q++ ){

( all_idh_set.

( idh ).second ){

list< CRef< CSeq_align > > aligns;

( annot && annot->

() ){

aligns =

list< CRef< CSeq_align >

&>( annot->

().

() );

( num_seqs <= 0 ){

(

q = 0; q < num_seqs; q++ ){

( common_idh_set.

() ){

common_idh_set = idh_set;

( idh_set.

( *hix ) != idh_set.

() ){

intersection.

( *hix );

( intersection.

() ){

common_idh_set = intersection;

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemPanel1->SetSizer(itemBoxSizer2);

wxStaticText* v_StatusText =

wxStaticText(

), wxDefaultPosition, wxSize(-1, 50), 0

itemBoxSizer2->Add(v_StatusText, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

itemBoxSizer2->Add(

, 1, wxGROW|wxALL, 5 );

( !

->TransferDataFromWindow() ){

( !

.empty());

TransferDataToWindow();

User-defined methods of the data storage class.

CRangeCollection< TSeqPos > TRangeColl

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

initial data set from which an alignment will be build

CRef< IAlnMultiDataSource > CreateDataSource()

virtual void SetListener(CDataChangeNotifier::IListener *pListener)

Subscribe a new listener for data source.

void PreCreateDataSource(bool sparse)

void SetMergeFlags(TMergeFlags flags, bool set)

Set/clear merge flags.

@ fAllowTranslocation

Allow translocations on the same row.

@ fSkipSortByScore

In greedy algos, skip sorting input alignments by score thus allowing for user-defined sort order.

CUpdate - notification send by CUIDataSource to the listener.

CEvent - generic event implementation TODO TODO - Attachments.

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

void SetManager(CMAViewManager *aManager)

virtual void LoadSettings()

virtual bool GetSelection(TConstScopedObjects &buf)

Return the selected item.

@ ID_CCONVERSIONRESULTPANEL

virtual bool Create(wxWindow *parent, wxWindowID id=SYM_CONVRESPANEL_IDNAME, const wxPoint &pos=SYM_CONVRESPANEL_POSITION, const wxSize &size=SYM_CONVRESPANEL_SIZE, long style=SYM_CONVRESPANEL_STYLE)

virtual void CreateControls()

virtual void EnforceOneViewPerObject()

Force OneViewPerObject true, and lock it.

CObjectListWidget * m_ObLiWgt

CMAViewManager * m_Manager

virtual void SetObjects(CObjectList &objs)

add your methods here

CMAPanel()

CMAPanel implementation.

virtual void SetRegistryPath(const string &path)

virtual void SaveSettings() const

virtual void FinalizeParams()

virtual wxPanel * GetCurrentPanel()

return the panel corresponding to the current state the function may create a new panel or return a p...

CMAViewManager(IProjectViewFactory &factory)

virtual CMAPanel * CreateAnchorPanel()

virtual void FinalizeAnchor()

virtual bool NeedAnchorPanel(TConstScopedObjects &objects)

virtual bool DoTransition(EAction action)

CMAViewManager implementation.

virtual bool CanDo(EAction action)

indicates whether a transition (action) is possible

void Clear(objects::CScope *scope)

void Add(ISelObjectHandle *obj_handle, CObject &obj)

void GetMatches(const CObject &object, objects::CScope &scope, TResults &results) const

CObjectList Data structure representing a list of CObjects with associated Scopes and other optional ...

int AddRow(CObject *obj, objects::CScope *scope)

SConstScopedObject & GetObject()

const objects::CUser_object * GetParams() const

virtual bool CanDo(EAction action)

indicates whether a transition (action) is possible

virtual wxPanel * GetCurrentPanel()

return the panel corresponding to the current state the function may create a new panel or return a p...

virtual bool DoTransition(EAction action)

perform transition if possible and returns true, otherwise the function shall warn the user about the...

wxWindow * m_ParentWindow

TConstScopedObjects m_OutputObjects

The output objects after view-specific object conversion and possible object aggregation.

virtual void LoadSettings()

virtual void SaveSettings() const

virtual void SetRegistryPath(const string &path)

virtual bool Create(wxWindow *parent, wxWindowID id=ID_CPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxNO_BORDER|wxTAB_TRAVERSAL)

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 x_UpdateContentLabel()

virtual objects::CScope * x_GetScope() const

virtual void x_AttachToProject(CGBDocument &doc)

ISelectionService * m_SelectionService

virtual bool x_HasProject() const

EEventSubtype GetSubtype() const

CProjectViewTypeDescriptor - holds description of a project view type.

TThisType & CombineWith(const TRange &r)

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

CRowDisplayStyle is a base class representing a display style for IAlignRow.

void SetDefaultStyle(CRowDisplayStyle *style)

assumes ownership

void SetWidgetStyle(const CWidgetDisplayStyle *style)

CSelectionEvent CSelectionEvent is used for broadcasting selection between views.

vector< CConstRef< objects::CSeq_id > > TIds

const TIdLocs & GetIdLocs() const

bool HasRangeSelection() const

Range Selection - represents a collection of selected segments.

static bool sm_MatchAlnLocs

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

void GetRangeSelectionAsLocs(TConstObjects &objs) const

vector< CConstRef< CIdLoc > > TIdLocs

objects::CScope & GetScope()

const objects::CHandleRangeMap & GetRangeSelection() const

const TIds & GetIds() const

bool HasObjectSelection()

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

bool AddObjectSelection(const CObject &obj)

TDim CheckNumRows(void) const

Validatiors.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

bool IsEntrys(void) const

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

wxMenu * CreateMenu(const SwxMenuItemRec *items)

create a menu from a static definition (see WX_*_MENU macros)

CViewTypeDescriptor - holds description of a view type.

void LoadTableSettings(const CRegistryReadView &view, bool byName=false)

void SaveTableSettings(CRegistryWriteView &view, bool saveSorting=true) const

IAlnExplorer::TNumrow TNumrow

Alignment segment iterator interface.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

virtual const CViewTypeDescriptor & GetViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

virtual void OnSelectionChanged(ISelectionClient *source)=0

notifies Service and its observers about changes in selection

IView - represents a standard visual part of Workbench UI.

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

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)

void WidgetsData_RegisterCommands(CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)

Register standard commands defined in this file and wxWidgets headers.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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.

CIRef< T > GetServiceByType()

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

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

CAlnMultiDSBuilder m_Builder

virtual const SwxMenuItemRec * GetMenuDef() const

simpler way to provide a static menu using macros defined earlier in this file

virtual void OnProjectChanged()

void GetSelection(CSelectionEvent &evt) const

get selection for broadcasting

virtual bool x_GetSeqRangeSelection(CAlnMultiWidget::TRangeColl &seq_coll) const

virtual void x_RebuildObjectIndex()

virtual void x_GetRowSeqLoc(CAlnVec::TNumrow row, CSelectionEvent::TRangeColl &loc) const

virtual bool x_MergeObjects(TConstScopedObjects &objects)

CConstRef< objects::CSeq_annot > m_OrigAnnot

original data object passed to the view

CRef< COpenViewManager > m_ViewManager

virtual void DestroyViewWindow()

destroy Window corresponding to the view

void OnAlnWidgetSelChanged(CEvent *evt)

virtual void x_OnSetSelection(CSelectionEvent &evt)

override in derived classes in order to handle selection broadcast

IAlnExplorer::TNumrow GetNumrow() const

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

virtual void CreateViewWindow(wxWindow *parent)

create Window corresponding to the view

void OnOpenGraphicalView(CEvent *evt)

virtual IView * CreateInstanceByFingerprint(const TFingerprint &fingerprint) const

if fingerprint is recognized - creates and returns a new instance

virtual void SaveSettings() const

CRowStyleCatalog m_StyleCatalog

virtual string GetExtensionLabel() const

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

virtual void OnDSChanged(CDataChangeNotifier::CUpdate &update)

virtual void LoadSettings()

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

virtual wxWindow * GetWindow()

returns a pointer to the wxWindow representing the client

virtual const CObject * x_GetOrigObject() const

virtual IView * CreateInstance() const

creates a view instance

virtual const CViewTypeDescriptor & GetTypeDescriptor() const

return an object providing meta information about thei view type

virtual void RegisterIconAliases(wxFileArtProvider &provider)

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

virtual string GetExtensionIdentifier() const

CMultiAlignViewFactory.

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

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

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 bool x_GetValidInputData(const CObject *obj)

virtual int TestInputObjects(TConstScopedObjects &objects)

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

CIRef< IAlnMultiDataSource > m_DataSource

CConstRef< objects::CSeq_align > m_OrigAlign

virtual void SetRegistryPath(const string &reg_path)

CAlnMultiWidget * m_AlnWidget

virtual const CProjectViewTypeDescriptor & GetProjectViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

const TEventID GetID(void) const

Inline Implementation.

vector< CConstRef< CObject > > TConstObjects

virtual const string & GetIconAlias() const

#define END_EVENT_MAP()

Ends definition of Command Map.

#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

@ eCmdZoomSeq

Zoom to Selection.

CConstRef< CSeq_id > GetSeqId(void) const

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

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,...

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_align > > TAlign

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

ON_EVENT(CAlnMultiPane::CEvent, CAlnMultiPane::eLinearSelChanged, &CMultiAlignView::OnAlnWidgetSelChanged) ON_EVENT(CAlnMultiPane

vector< CConstRef< CSeq_id > > TRSeqIdVector

CProjectViewTypeDescriptor s_MultiAlignViewTypeDescr("Multiple Sequence Alignment View", "multi_align_view", "Multiple Sequence Alignment View hint", "View for the multiple alignments with each column and residue colored according to its degree of mismatch", "MULTI_ALIGN_VIEW", "Alignment", false, "Seq-align", eAnyObjectsAccepted)

CMultiAlignView.

static const char * kDMGroupList

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

#define SYM_CONVRESPANEL_POSITION

#define SYM_CONVRESPANEL_IDNAME

#define SYM_CONVRESPANEL_STYLE

CConversionResultPanel.

#define SYM_CONVRESPANEL_SIZE

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

#define row(bind, expected)

#define WX_DEFINE_MENU(name)

New macros for defining menus for use with CUICommandRegistry.

#define WX_SUBMENU(label)

#define WX_MENU_SEPARATOR_L(label)

#define WX_MENU_ITEM(cmd)

#define WX_MENU_SEPARATOR()

wxString ToWxString(const string &s)

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