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

,

,

,

initialized =

;

( ! initialized ){

wxMenu* view_menu =

wxMenu();

view_menu->Append( wxID_SEPARATOR,

(

) );

wxMenu* bar_menu =

wxMenu();

bar_menu->Append(

,

(

), view_menu );

=

wxPanel( parent );

wxBoxSizer* main_sizer =

wxBoxSizer( wxVERTICAL );

->SetSizer( main_sizer );

->PopEventHandler(

);

TIdExtract id_extract;

TAlnIdMap aln_id_map( id_extract, container.size() );

ITERATE( CAlnContainer, aln_it, container ){

aln_id_map.push_back( **aln_it );

} catch( CAlnException e ){

LOG_POST( Error << "Skipping this alignment: " << e.what() );

TAlnStats aln_stats( aln_id_map );

if ( !aln_stats.CanBeAnchored() ) {

LOG_POST( Error << "Input alignments cannot be anchored because they don't share at least one common sequence." );

CAlnUserOptions aln_user_options;

TAnchoredAlnVec anchored_aln_vec;

CreateAnchoredAlnVec( aln_stats, anchored_aln_vec, aln_user_options );

BuildAln( anchored_aln_vec, m_AnchoredAln, aln_user_options );

if( m_AnchoredAln.GetDim() == 1 ){

m_AnchoredAln = CAnchoredAln();

aln_user_options.m_MergeAlgo = CAlnUserOptions::ePreserveRows;

BuildAln( anchored_aln_vec, m_AnchoredAln, aln_user_options );

CRef<CSparseAln> sparse_aln;

sparse_aln.Reset( new CSparseAln( m_AnchoredAln, *GetScope() ) );

m_Model.reset( new CAlnSpanVertModel( *sparse_aln ) );

->SetMarkIndels( aln_type );

->SetThreshold( 1000000 );

*

= cso_it->object.GetPointer();

ref.

( align );

((*iter)->IsEmpty()) {

(ranges.find(idh) == ranges.end()) {

range = (*iter)->GetTotalRange();

ranges[idh] += range;

(TRangeMap, iter, ranges) {

loc->

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

loc->

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

loc->

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

range = (*iter)->GetTotalRange();

ranges[idh] += range;

(TRangeMap, iter, ranges) {

total_rows =

->GetNumRows();

( total_rows != 1 ){

( rows_shown != total_rows ){

status_msg +=

;

( rows_selected > 0 ){

status_msg +=

;

sid(

);

slabel(

);

found_good =

;

found_bad =

;

(

= 0;

<

.size();

++ ){

type_info&

=

(*obj);

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

initial data set from which an alignment will be build

void SetSyncCreate(bool sync)

CRef< IAlnMultiDataSource > CreateDataSource()

void PreCreateDataSource(bool sparse)

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.

virtual void OnProjectChanged()

virtual void x_UpdateContentLabel()

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

unique_ptr< const wxMenu > m_MenuBarMenu

virtual bool x_HasProject() const

EEventSubtype GetSubtype() const

CProjectViewTypeDescriptor - holds description of a project view type.

virtual void OnWidgetSelChanged()

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

CSelectionEvent CSelectionEvent is used for broadcasting selection between views.

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

bool HasObjectSelection()

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

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

EEventType GetType() const

CViewTypeDescriptor - holds description of a view type.

void AddLocation(const objects::CSeq_loc &loc)

IwxTableModel * GetModel() const

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

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

int GetNumRowsVisible() const

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.

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)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CAlnSpanWidget * m_AlnWidget

virtual int TestInputObjects(TConstScopedObjects &objects)

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

CRef< IAlnMultiDataSource > m_DataSource

virtual wxWindow * GetWindow()

returns a pointer to the wxWindow representing the client

virtual void RegisterIconAliases(wxFileArtProvider &provider)

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

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

virtual string GetExtensionIdentifier() const

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

vector< CConstRef< CSeq_align > > m_InputAligns

virtual void SetRegistryPath(const string &reg_path)

virtual void GetSelection(CSelectionEvent &evt) const

get selection for broadcasting

virtual IView * CreateInstanceByFingerprint(const TFingerprint &fingerprint) const

if fingerprint is recognized - creates and returns a new instance

virtual IView * CreateInstance() const

creates a view instance

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 void LoadSettings()

virtual const CObject * x_GetOrigObject() const

CConstRef< CSeq_annot > m_OrigAnnot

original data object passed to the view

virtual void OnWidgetSelChanged()

virtual void x_CreateMenuBarMenu()

initializes m_MenuBarMenu; override in derived classes

virtual void CreateViewWindow(wxWindow *parent)

create Window corresponding to the view

CConstRef< CBioseq > m_OrigBioseq

virtual const CProjectViewTypeDescriptor & GetProjectViewTypeDescriptor() const

returns a Descriptor for the View Type supported by the Factory

virtual void SaveSettings() const

virtual void x_UpdateStatusMessage()

CConstRef< CSeq_align > m_OrigAlign

void x_InitMenuResources()

virtual const CViewTypeDescriptor & GetTypeDescriptor() const

return an object providing meta information about thei view type

virtual void OnWidgetRangeChanged()

virtual string GetExtensionLabel() const

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

static CProjectViewTypeDescriptor m_TypeDescr

wxStatusBar * m_StatusBar

unique_ptr< CAlnSpanVertModel > m_Model

virtual void x_PostAttachToProject()

virtual void GetVisibleRanges(CVisibleRange &vrange) const

populate a visible range event for broadcasting

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

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

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool NotNull(void) const THROWS_NONE

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

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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

@ eSimilarObjectsAccepted

wxString ToWxString(const string &s)

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