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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/fuse_features.cpp Source File

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

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

modified =

;

(field_name.empty())

vector<CSeq_feat_Handle> entry_handles;

(constraint && !constraint_field.empty())

*feat =

*

( (*obj_it)->GetOriginalObject() );

entry_handles.push_back(fh);

& cds = feat->GetOriginalFeature();

entry_handles.push_back(feat->GetSeq_feat_Handle());

(

= 0;

< entry_handles.size();

++)

(deleted_feats.

(feat1) == deleted_feats.

())

changed =

;

(

j =

+ 1; j < entry_handles.size(); j++)

( deleted_feats.

(feat2) == deleted_feats.

() &&

(!new_product_id) {

deleted_feats.

(feat2);

new_feat->

(partial_start || partial_stop);

new_feat->

().SetWhole().Assign(*new_product_id);

->AddCommand(*retranslate_cmd);

wxSizerItemList& slist = sizer->GetChildren();

(wxSizerItemList::iterator iter = slist.begin(); iter != slist.end(); ++iter, ++

) {

((*iter)->IsSizer()) {

}

((*iter)->IsWindow()) {

wxWindow* child = (*iter)->GetWindow();

wxSizer* subsizer = child->GetSizer();

modified =

;

(

feat_it(seh); feat_it; ++feat_it)

(feat_it->GetOriginalFeature().IsSetData())

new_feat->

(feat_it->GetOriginalFeature());

CSeq_loc& feat_loc = feat_it->GetLocation();

new_loc->

(feat_loc);

vector<pair<int,int> > ranges;

ranges.push_back(pair<int, int>(feat_start, feat_stop));

(

j = 1; j < ranges.size(); j++)

(ranges[j].

== ranges[

].second + 1)

ranges[

].second = ranges[j].second;

ranges[j].first = -1;

ranges[j].second = -1;

new_start = ranges[

].first;

new_stop = ranges[

].second;

(new_start < 0 || new_stop < 0)

(feat_start != new_start)

(feat_stop != new_stop)

loc_it.

(new_stop);

@ eExtreme_Positional

numerical value

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

objects::CSeq_entry_Handle m_TopSeqEntry

bool Create(wxWindow *parent, wxWindowID id, const wxString &title, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxDEFAULT_FRAME_STYLE, const wxString &name=wxFrameNameStr)

void AddCommand(IEditCommand &command)

void PopulateFeatureListbox(void)

virtual string GetFieldName(const bool subfield=false)

Returns the name of the field as selected in the panel.

virtual string GetFieldName(const bool subfield=false)

Returns the name of the field as selected in the panel.

void ListPresentFeaturesFirst(const objects::CSeq_entry_Handle &entry, vector< const objects::CFeatListItem * > *featlist=nullptr)

void UpdateChildrenFeaturePanels(wxSizer *sizer)

void CreateControls()

Creates the controls and sizers.

~CFuseFeaturesDlg()

Destructor.

CFeatureTypePanel * m_FeatureType

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

virtual CRef< CCmdComposite > GetCommand()

CFeatureFieldNamePanel * m_FeatureConstraint

CStringConstraintPanel * m_StringConstraintPanel

void Init()

Initialises member variables.

void ProcessUpdateFeatEvent(wxCommandEvent &event)

static bool ShowToolTips()

Should we show tooltips?

bool Create(wxWindow *parent, wxWindowID id=11000, const wxString &caption=_("Fuse Features"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

CFuseFeaturesDlg()

Constructors.

static CRef< CCmdComposite > apply(CSeq_entry_Handle seh)

vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(objects::CBioseq_Handle bsh)

static const CFeatList * GetFeatList()

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

CRef< edit::CStringConstraint > GetStringConstraint()

IWorkbench is the central interface in the application framework.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

const string kPartialStart

#define EVT_UPDATE_FEATURE_LIST(id, fn)

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

#define ID_FUSE_FEATURES_OKCANCEL

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void SetFrom(TSeqPos from)

Set the range from position.

void SetTo(TSeqPos to)

Set the range to position.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

void Delete(void)

Delete current element, and make iterator to point to the next element.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

bool HasChanges(void) const

return true of any part was changed since initialization

bool IsEmpty(void) const

True if the current location is empty.

TRange GetRange(void) const

Get the range.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

constexpr bool empty(list< Ts... >) noexcept

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

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

CRef< CCmdComposite > GetRetranslateCDSCommand(objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)

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