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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/apply__rna__its__dlg_8cpp_source.html below:

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

(; iter != sm_ITSMap.end(); ++iter){

(iter->second == field_type){

(iter != sm_ITSMap.end()){

(; iter != sm_IGSMap.end(); ++iter){

(iter->second == field_type){

(iter != sm_IGSMap.end()){

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemCBulkCmdDlg1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 3);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 2);

itemBoxSizer3->Add(5, 5, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxBoxSizer* itemBoxSizer7 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString m_ITSRadioboxStrings;

m_ITSRadioboxStrings.Add(

(

));

m_ITSRadioboxStrings.Add(

(

));

=

wxRadioBox( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, m_ITSRadioboxStrings, 1, wxRA_SPECIFY_ROWS );

itemBoxSizer7->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxArrayString itemChoiceStrings;

wxFlexGridSizer* itemFlexGridSizer10 =

wxFlexGridSizer(5, 3, -1, -1);

itemBoxSizer2->Add(itemFlexGridSizer10, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

first_choice.

=

wxChoice( itemCBulkCmdDlg1,

, wxDefaultPosition, wxDefaultSize, itemChoiceStrings, 0 );

itemFlexGridSizer10->Add(first_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

first_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(first_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

first_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(first_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

second_choice.

=

wxChoice( itemCBulkCmdDlg1,

, wxDefaultPosition, wxDefaultSize, itemChoiceStrings, 0 );

itemFlexGridSizer10->Add(second_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

second_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(second_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

second_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(second_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

third_choice.

=

wxChoice( itemCBulkCmdDlg1,

, wxDefaultPosition, wxDefaultSize, itemChoiceStrings, 0 );

itemFlexGridSizer10->Add(third_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

third_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(third_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

third_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(third_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

fourth_choice.

=

wxChoice( itemCBulkCmdDlg1,

, wxDefaultPosition, wxDefaultSize, itemChoiceStrings, 0 );

itemFlexGridSizer10->Add(fourth_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

fourth_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(fourth_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

fourth_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(fourth_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

fifth_choice.

=

wxChoice( itemCBulkCmdDlg1,

, wxDefaultPosition, wxDefaultSize, itemChoiceStrings, 0 );

itemFlexGridSizer10->Add(fifth_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

fifth_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(fifth_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

fifth_choice.

=

wxTextCtrl( itemCBulkCmdDlg1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer10->Add(fifth_choice.

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 2);

wxBoxSizer* itemBoxSizer28 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer28, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

=

wxButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer28->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxButton( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer28->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer28->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxWindow::InitDialog();

(; iter != sm_IGSMap.end(); ++iter){

TVecSeqFeat::iterator feat_it = featlist.begin();

(*feat_it)->SetPartial(

);

feat_it = featlist.end() - 1;

(*feat_it)->SetPartial(

);

wxWindow::TransferDataFromWindow();

event_id = 1;

(event.GetId()) {

event_id = event_id + 2;

event_id = event_id + 3;

row_sel = 0;

[row_sel].from->ChangeValue(wxEmptyString);

}

(

[row_sel].from->GetLineLength(0) > 0){

(from_value.find_first_not_of(

) !=

){

(from > 1 && row_sel >= 1){

row_sel = 0;

((from_value.find_first_not_of(

) !=

) || (to_value.find_first_not_of(

) !=

)){

wxArrayString labels;

align_present =

;

align_present =

;

sel_scope = it->scope;

}

(sel_scope != it->scope) {

=

;

modified =

;

(seqentry || (seqsubmit && seqsubmit->

())) {

(seqentry || (seqsubmit && seqsubmit->

())) {

* ptr = it->object.GetPointer();

(seqloc && seqloc->

()) {

}

(bsh.

()){

(bioseq->

()) {

}

(bioseq->

()){

}

(bioseq_set) {

( ! featlist.empty()) {

TVecConstSeqFeat::iterator feat_it = featlist.begin();

( ; feat_it != featlist.end(); ++feat_it) {

( ! bsh )

;

=

;

}

(align_nr == 1) {

answer = wxMessageBox (

(

),

(

),

wxYES_NO | wxCANCEL | wxICON_QUESTION);

( !entry || entry.

() )

;

( ; b_iter; ++b_iter) {

(*b_iter, featlist, composite, modified);

answer = wxMessageBox (

(

),

(

), wxYES_NO | wxCANCEL | wxICON_QUESTION);

( ; b_iter; ++b_iter) {

(*b_iter, featlist, composite, modified);

(*b_iter, featlist, composite, modified);

( ! featlist.empty()) {

(alignments.size() == 1) {

& tgseq_id = (*target_id).GetObject();

,

,

,

, create_general_only, &listener);

(listener.

() > 0) {

(

= 0;

< listener.

();

++) {

wxOK | wxICON_ERROR,

);

vector<CConstRef<CSeq_align> > alignments;

( ; align_it; ++align_it) {

((*align_id)->Match(**bseq_id)) {

alignments.size();

found =

;

(CBioseq::TId::const_iterator bseq_id = bseqIDs.begin(); bseq_id != bseqIDs.end() && !found; ++bseq_id) {

((*align_id)->Match(**bseq_id)) {

& prop_id = (*iter).GetObject();

((*bseq_id)->Match(prop_id)) {

const_featlist;

aln_from = 0, seq_from =

;

aln_to = 0, seq_to =

;

const_featlist;

aln_from = aln_from - 1;

(seq_from <

) { seq_from =

; }

(seq_from >

) {

const_featlist;

(

<<

<< e.

());

const_featlist;

aln_to = aln_to - 1;

(seq_to >

) { seq_to =

; }

const_featlist;

(seq_from == seq_to) {

featlist.push_back(new_feat);

featlist.push_back(new_feat);

const_featlist;

const_featlist;

(from <

) { from =

; }

const_featlist;

const_featlist;

(to >

) { to =

; }

const_featlist;

featlist.push_back(new_feat);

featlist.push_back(new_feat);

const_featlist;

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

CStaticArrayMap< string, CApplyRNAITSDlg::ERNA_IGSType > TIGSMap

DEFINE_STATIC_ARRAY_MAP(TITSMap, sm_ITSMap, s_Rna_ITSStrings)

SStaticPair< const char *, CApplyRNAITSDlg::ERNA_ITSType > TITSLabelPair

static const TITSLabelPair s_Rna_ITSStrings[]

USING_SCOPE(ncbi::objects)

static const char * kApplyChoice

SStaticPair< const char *, CApplyRNAITSDlg::ERNA_IGSType > TIGSLabelPair

static const TIGSLabelPair s_Rna_IGSStrings[]

CStaticArrayMap< string, CApplyRNAITSDlg::ERNA_ITSType > TITSMap

#define ID_TEXTCTRL_SFROM

#define ID_LEAVE_DIALOG_UP

#define ID_TEXTCTRL_FOFROM

#define ID_RADIOBOX_ITS_IGS

#define ID_TEXTCTRL_FFROM

#define ID_TEXTCTRL_TFROM

#define ID_TEXTCTRL_FIFROM

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

const CSeq_id & GetSeqId(TNumrow row) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TDim GetNumRows(void) const

TVecConstSeqId m_PropSeqids

void AddFeatures(const CBioseq_Handle &bsh, TVecConstSeqFeat &featlist, CRef< CCmdComposite > composite, bool &modified)

ERNA_ITSType GetNextRNA_ITSChoice(ERNA_ITSType field_type)

IAlnExplorer::TNumrow x_GetRow(const CBioseq &bioseq)

void Apply_RNAITS_ToTSE(CRef< CCmdComposite > composite, bool &modified)

bool x_WasPropagatedTo(const CBioseq_Handle &bsh)

returns true if features were already propagated to the sequence

void OnAnyOtherChoiceSelected(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=10307, const wxString &caption=_("Apply rRNA_ITS"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

static ERNA_ITSType GetRNA_ITSTypeFromName(const string &label)

~CApplyRNAITSDlg()

Destructor.

void OnGoClick(wxCommandEvent &event)

vector< CRef< CSeq_feat > > TVecSeqFeat

void x_Set_ITSArray(wxArrayString &Its_tags)

TVecConstSeqFeat GetRNAITSList_AlignCoordFromDlg(const CBioseq_Handle &bsh)

void OnCancelClick(wxCommandEvent &event)

bool x_IsThereAlignment(void)

TVecConstSeqId x_SeqIdsAlignedWith(const CBioseq_Handle &bsh, const CSeq_align &align)

obtains a vector of seqIds aligned with bsh through the given alignment - used for feature propagatio...

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void OnITSRadioBoxSelected(wxCommandEvent &event)

vector< CConstRef< CSeq_id > > TVecConstSeqId

TVecConstSeqFeat x_UpdatePartials(TVecSeqFeat &featlist)

if required, sets the first and last features incomplete

CApplyRNAITSDlg()

Constructors.

void Propagate_RNAITSList(const CBioseq_Handle &bsh, TVecConstSeqFeat &featlist, CRef< CCmdComposite > composite, bool &modified, bool create_general_only)

virtual void SetRegistryPath(const string &reg_path)

virtual string GetErrorMessage()

void OnFirstChoiceSelected(wxCommandEvent &event)

ERNA_IGSType GetNextRNA_IGSChoice(ERNA_IGSType field_type)

static const string & GetRNA_IGSName(ERNA_IGSType field_type)

void x_Set_IGSArray(wxArrayString &Igs_tags)

static ERNA_IGSType GetRNA_IGSTypeFromName(const string &label)

wxCheckBox * m_AlignCoords

vector< CConstRef< CSeq_feat > > TVecConstSeqFeat

void Apply_RNAITS_ToBioseqSet(CSeq_entry_Handle entry, CRef< CCmdComposite > composite, bool &modified)

virtual void SaveSettings() const

static const string & GetRNA_ITSName(ERNA_ITSType field_type)

void x_SaveAndDestroyFrame()

static bool ShowToolTips()

Should we show tooltips?

wxRadioBox * m_ITSRadiobox

vector< CConstRef< CSeq_align > > x_GetAlignments(const CBioseq_Handle &bsh)

obtains all dense-seg type alignments where this bioseq is present, in this seq-entry

TVecConstSeqFeat ObtainRNAITSList(const CBioseq_Handle &bsh)

void CreateControls()

Creates the controls and sizers.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

virtual CRef< CCmdComposite > GetCommand()

CBulkCmdDlg pure virtual functions.

void OnCtrlToKillFocus(wxFocusEvent &event)

virtual void LoadSettings()

TVecConstSeqFeat GetRNAITSList_SeqCoordFromDlg(const CBioseq_Handle &bsh)

void Init()

Initialises member variables.

vector< SRNAITSChoice > m_ChoiceList

void OnCloseWindow(wxCloseEvent &event)

void Apply_RNAITS_ToBioseq(const CBioseq_Handle &bsh, CRef< CCmdComposite > composite, bool &modified, bool create_general_only)

void OnCtrlFromKillFocus(wxFocusEvent &event)

SIZE_TYPE x_BioseqInAlignments(const CBioseq_Handle &bsh)

returns the number of dense-seg type alignment which the bioseq belongs to

TConstScopedObjects GetSelectedObjects()

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)

bool GetTopLevelSeqEntryAndProcessor()

ICommandProccessor * m_CmdProccessor

void AddCommand(IEditCommand &command)

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.

Default implementation of IMessageListener: collects all messages posted.

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

int GetInt(const string &key, int default_val=0) const

access a named key at this level, with no recursion

void Set(const string &key, int val)

access a named key at this level, with no recursion

bool IsEntrys(void) const

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

@ eBackwards

Towards lower seq coord (to the left if plus strand, right if minus)

@ eForward

Towards higher seq coord (to the right if plus strand, left if minus)

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

IWorkbench is the central interface in the application framework.

void PropagateToTarget(CRef< CCmdComposite > composite, const vector< CConstRef< objects::CSeq_feat >> &feat_list, objects::CBioseq_Handle src, objects::CBioseq_Handle target, const objects::CSeq_align &align, bool stop_at_stop, bool cleanup_partials, bool merge_abutting, bool extend_over_gaps, bool create_general_only, CMessageListener_Basic *listener, objects::CObject_id::TId *feat_id=nullptr)

CRef< objects::CSeq_feat > AddRibosomalRNA(const objects::CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)

CRef< objects::CSeq_feat > AddMiscRNA(const objects::CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)

#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 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.

vector< SConstScopedObject > TConstScopedObjects

virtual size_t Count(void) const

Get total number of collected messages.

virtual string GetText(void) const =0

Get text message.

virtual const IMessage & GetMessage(size_t index) const

Get a previously collected message.

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

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

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

const CSeq_align & GetOriginalSeq_align(void) const

Get original alignment.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

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

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 & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static const char label[]

const TDenseg & GetDenseg(void) const

Get the variant data.

bool IsSetSegs(void) const

Check if a value has been assigned to Segs data member.

vector< CRef< CSeq_id > > TIds

const TIds & GetIds(void) const

Get the Ids member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

bool IsSetIds(void) const

sequences in order Check if a value has been assigned to Ids data member.

const TWhole & GetWhole(void) const

Get the variant data.

bool IsWhole(void) const

Check if variant Whole is selected.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

@ eMol_na

just a nucleic acid

bool FocusedOnNucleotides(TConstScopedObjects &objects, const objects::CSeq_entry_Handle &tse)

void ReportUsage(const wxString &dialog_name)

Report opening & accepting events in the editing package.

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

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

const GenericPointer< typename T::ValueType > T2 value

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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