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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/update__multi__seq__dlg_8cpp_source.html below:

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

: m_UpdMultiSeqInput(0), m_Updated(0), m_Skipped(0)

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style)

: m_UpdMultiSeqInput(&updmultiseq_in), m_UpdateCmd(

), m_Updated(0), m_Skipped(0)

(parent,

, caption, pos,

, style);

identNum =

.GetIdenticalUpdates().size();

nonIdentNum =

.GetNonIdenticalUpdates().size();

oss <<

<< identNum + nonIdentNum <<

;

(identNum > 1) {

oss << identNum <<

;

oss << identNum + nonIdentNum <<

;

(

&& it :

.GetIdenticalUpdates()) {

wxPoint& pos,

wxSize&

,

style )

SetExtraStyle(wxWS_EX_BLOCK_EVENTS | wxWS_EX_VALIDATE_RECURSIVELY);

CDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 1, wxEXPAND | wxALL, 5);

=

wxNotebook( itemDialog1,

, wxDefaultPosition, wxDefaultSize, wxBK_TOP );

wxPanel* itemPanel5 =

wxPanel(

,

, wxDefaultPosition, wxDefaultSize, wxTAB_TRAVERSAL );

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxVERTICAL);

itemPanel5->SetSizer(itemBoxSizer6);

wxStaticText* itemStaticText7 =

wxStaticText( itemPanel5, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(itemStaticText7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString m_NonIdenticalListStrings;

wxStaticText* itemStaticText9 =

wxStaticText( itemPanel5, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer6->Add(itemStaticText9, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString m_IdenticalListStrings;

wxPanel* itemPanel12 =

wxPanel(

,

, wxDefaultPosition, wxDefaultSize, wxTAB_TRAVERSAL );

wxBoxSizer* itemBoxSizer13 =

wxBoxSizer(wxVERTICAL);

itemPanel12->SetSizer(itemBoxSizer13);

wxStaticText* itemStaticText14 =

wxStaticText( itemPanel12, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemStaticText14, 0, wxALIGN_CENTER_HORIZONTAL | wxALL, 5);

wxArrayString m_NoUpdateListStrings;

wxStaticText* itemStaticText16 =

wxStaticText( itemPanel12, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemStaticText16, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString m_UnmatchedListStrings;

wxBoxSizer* itemBoxSizer18 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer13->Add(itemBoxSizer18, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

itemBoxSizer18->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer18->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer3->Add(

, 0, wxGROW|wxALL, 2);

wxBoxSizer* itemBoxSizer22 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer22, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton23 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer22->Add(itemButton23, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton24 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer22->Add(itemButton24, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton25 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer22->Add(itemButton25, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton26 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer22->Add(itemButton26, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton27 =

wxButton( itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer22->Add(itemButton27, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemButton23->Disable();

itemButton24->Disable();

itemButton25->Disable();

(

&& it : updates) {

(

&& it : identicals) {

(

&& it : noUpdates) {

(

&& it : noUpdates) {

tuple<objects::CSeq_id_Handle, CConstRef<objects::CSeq_align> >

(

accept_atleast_one = (

.GetBioseqLength() <

.GetBioseqLength());

(align_vector.size() > 1)

(

<<

);

(align_vector.empty())

(

<<

);

best_align = 0;

(

= 0;

< align_vector.size(); ++

) {

(

j =

+ 1; j < align_vector.size(); ++j) {

(best_align < align_vector.size());

std::get<1>(

) = align_vector[best_align];

}

(

);

(it->IsComplete()) {

& res = (*it)();

upd_input->

(std::get<1>(res).GetPointerOrNull());

(!seq_name.empty()) {

(idh_it !=

.

() && idh_it->second == idH)

(

&& it : ident_updates) {

(annot && annot->

()) {

(

& it : updates) {

[idH = it.first,

= it.second->GetOldBioseq(),

= it.second->GetUpdateBioseq()](

& canceled)

return s_CreateAlign(idH, subject, query, canceled);

},

));

(

&& it : update_pairs) {

(annot && annot->

()) {

return s_CreateAlign(idH, subject, query, canceled);

},

));

selected = wxNOT_FOUND;

(selected != wxNOT_FOUND) {

(seq_name.empty()) {

(selected != wxNOT_FOUND) {

(seq_name.empty())

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

(upd_input.

()) {

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

.Enable(

);

.Enable(

);

.Enable(

);

(selected != wxNOT_FOUND) {

(selected != wxNOT_FOUND) {

(

&& it : identicals) {

wxString ext =

(

);

wxFileDialog open_dlg(

,

(

), wxEmptyString, wxEmptyString, ext, wxFD_OPEN | wxFD_FILE_MUST_EXIST);

(open_dlg.ShowModal() == wxID_CANCEL) {

wxString filename = open_dlg.GetPath();

(line_reader.

()) {

pos = s.first.

(

);

(string::npos != pos)

unmatchedOldSeqs.emplace(s.first.substr(0, pos), s.second);

vector<string> ignored_lines;

(!line_reader->

()) {

(

&& it : ids) {

(ids.size() != 2) {

ignored_lines.push_back(line);

oldidh_it = unmatchedOldSeqs.find(ids[0]);

(oldidh_it == unmatchedOldSeqs.end()) {

oldidh_it = unmatchedOldSeqs.find(ids[1]);

ignored_lines.push_back(line);

(oldidh_it == unmatchedOldSeqs.end()) {

(

+ ids[1] +

);

ignored_lines.push_back(line);

update_pairs.emplace(oldidh_it->second, updidh_it->second);

(

&& it : update_pairs) {

(nonident_updates.

(old_idh) != nonident_updates.

()) {

.emplace(old_id_label, old_idh);

(identicals.

(old_idh) != identicals.

()) {

.emplace(old_id_label, old_idh);

(!ignored_lines.empty()) {

=

;

(

&& it : ignored_lines) {

.push_back(

);

.push_back(

);

(noupdate_sel == wxNOT_FOUND || unmatched_sel == wxNOT_FOUND) {

(

);

pair.emplace(oldidh_it->second, updidh_it->second);

(nonident_updates.

(old_idh) != nonident_updates.

()) {

(identicals.

(old_idh) != identicals.

()) {

(selectNonIdent == wxNOT_FOUND && selectIdent == wxNOT_FOUND) {

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

(selectNonIdent != wxNOT_FOUND) {

(selectIdent != wxNOT_FOUND) {

(seq_name.empty())

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

(selectNonIdent == wxNOT_FOUND && selectIdent == wxNOT_FOUND) {

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

(selectNonIdent != wxNOT_FOUND) {

(selectIdent != wxNOT_FOUND) {

seq_name =

(sel_list.GetString(selected));

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

sel_list.Delete(selected);

( ! sel_list.IsEmpty()) {

(selected > sel_list.GetCount() - 1) {

selected = sel_list.GetCount() - 1;

sel_list.SetSelection(selected);

seq_name =

(sel_list.GetString(selected));

(other_list && !other_list->IsEmpty()) {

other_list->SetSelection(0);

seq_name =

(other_list->GetString(selected));

(

selected = 0; selected <

->GetCount(); ++selected) {

(

selected = 0; selected <

->GetCount(); ++selected) {

oss <<

<<

<<

;

(!

.empty()) {

wxMessageBox(

(

),

(

), wxOK | wxICON_INFORMATION);

retcode = (

> 0) ? wxOK : wxCLOSE;

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

void AddCommand(IEditCommand &command)

virtual void EndModal(int retCode)

virtual void SetRegistryPath(const string &path)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

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

CRegistryReadView GetReadView(const string &section) const

CRegistryWriteView GetWriteView(const string &section)

Sequence update exception class.

Class responsible for executing the sequence update for one old-update sequence pair.

bool IsReverseComplemented() const

void GetNotImportedFeatsReport(CNcbiOstream &out) const

CRef< CCmdComposite > Update(bool create_general_only)

Main function responsible to update the old sequence with the update sequence.

TNameToIDHandleMap m_UnmatchedUpdSeqs

wxButton * m_MapSelection

wxListBox * m_UnmatchedList

void OnIdle(wxIdleEvent &event)

virtual void x_SaveSettings(CRegistryWriteView view) const

void x_CreatePairwiseAlignments()

void x_FillNoUpdateList()

void x_LaunchJobs(const CUpdateMultipleSeq_Input::TIDToUpdInputMap &updates)

CRef< CCmdComposite > x_UpdateSelected(const string &seq_name, bool create_general_only)

CUpdateMultipleSeq_Input * m_UpdMultiSeqInput

void OnUpdateAllSequenceClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_OKALL

wxListBox * m_NoUpdateList

virtual void x_LoadSettings(const CRegistryReadView &view)

override these functions in derived classes

void x_SkipSelected(wxListBox &sel_list, unsigned int selected, wxListBox *other_list)

void x_CreateAlignmentForIdenticalUpdates()

void OnStopUpdatingClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_STOP

TNameToIDHandleMap m_SeqList

void x_FillNonIdenticalList()

string x_GetCurrentSelection()

static bool ShowToolTips()

Should we show tooltips?

static void s_ReportIdenticalPairs(const CUpdateMultipleSeq_Input &input)

void x_FillIdenticalList()

void OnUpdateThisSequenceClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_OKTHIS

void OnMapSelectionUpdate(wxUpdateUIEvent &event)

void Init()

Initialises member variables.

void OnSkipThisSequenceClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_SKIP

@ ID_UPDMULTSEQ_PNL2_LISTBOX1

@ ID_UPDMULTSEQ_PNL1_LISTBOX2

@ ID_UPDMULTSEQ_PNL2_BTN1

@ ID_UPDMULTSEQ_PNL2_LISTBOX2

@ ID_UPDMULTSEQ_PNL1_LISTBOX1

@ ID_UPDMULTSEQ_PNL2_BTN2

void x_GenerateAlignments(const CUpdateMultipleSeq_Input::TOldToUpdateMap &update_pairs)

void x_FillUnmatchedList()

CUpdateMultiSeq_Dlg()

Constructors.

static string s_GetSeqIDLabel(const objects::CSeq_id_Handle &idh)

void OnIdentSeqSelected(wxCommandEvent &event)

wxEVT_COMMAND_LISTBOX_SELECTED event handler for ID_UPDMULTSEQ_PNL1_LISTBOX2

set< objects::CSeq_id_Handle > m_Running

void OnLoadMapClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_PNL2_BTN1

list< job_future< TAlignResult > > m_Futures

~CUpdateMultiSeq_Dlg()

Destructor.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void OnCloseWindow(wxCloseEvent &event)

wxEVT_CLOSE_WINDOW event handler for ID_CUPDATEMULTISEQ_DLG

wxListBox * m_IdenticalList

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void OnMapSelectionClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_PNL2_BTN2

void OnCancelClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for wxID_CANCEL

wxButton * m_IdenticalUpdBtn

void x_UpdateAlignmentPanel(const string &seq_name)

wxListBox * m_NonIdenticalList

void OnNonIdentSeqSelected(wxCommandEvent &event)

wxEVT_COMMAND_LISTBOX_SELECTED event handler for ID_UPDMULTSEQ_PNL1_LISTBOX1

void OnRemoveIdenticalsClick(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_UPDMULTSEQ_PNL1_BTN

CUpdateSeqPanel * m_UpdSeqPanel

void OnRemoveIdenticalUpdate(wxUpdateUIEvent &event)

TNameToIDHandleMap m_UnmatchedOldSeqs

CRef< CCmdComposite > m_UpdateCmd

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

Creation.

void CreateControls()

Creates the controls and sizers.

void x_UpdateNotebookAfterMapping(void)

const TSeqIDHVector & GetSeqsWithoutUpdates() const

const TIDToUpdInputMap & GetNonIdenticalUpdates() const

vector< objects::CSeq_id_Handle > TSeqIDHVector

bool HaveIdenticalResidues(const objects::CSeq_id_Handle &idh1, const objects::CSeq_id_Handle &idh2)

CRef< CUpdateSeq_Input > GetUpdateInput(const objects::CSeq_id_Handle &idh) const

const TSeqIDHVector & GetUnmatchedUpdateSeqs() const

const TIDToUpdInputMap & GetIdenticalUpdates() const

void PrepareMultipleSequenceInputs()

bool AppendOld_UpdateSeqPairs(const TOldToUpdateMap &update_pairs)

objects::CSeq_entry_Handle GetOldEntry()

SUpdateSeqParams GetData()

void LoadSettings(const CRegistryReadView &view)

void SaveSettings(CRegistryWriteView view) const

void UpdatePanel(bool running, const CUpdateSeq_Input *updseq_in=nullptr)

Function updates the panel with new (old, update) sequence pair.

void SetData(const SUpdateSeqParams &params)

void SetAlignment(const objects::CSeq_align *align)

static CRef< objects::CSeq_annot > s_Align2IdenticalSeq(const objects::CBioseq_Handle &subject, const objects::CBioseq_Handle &query)

const objects::CBioseq_Handle & GetUpdateBioseq(void) const

const objects::CBioseq_Handle & GetOldBioseq(void) const

Interface for testing cancellation request in a long lasting operation.

Stores parameters regarding the type of sequence update, on how to handle existing features and on ho...

@ eSeqUpdateReplace

do not change the old sequence

const_iterator end() const

const_iterator find(const key_type &key) const

static bool CompareAlignments(const objects::CSeq_align &align_first, const objects::CSeq_align &align_sec)

Returns true if the first alignment is 'better' than the second one Compares the Blast scores and in ...

static vector< CConstRef< objects::CSeq_align > > RunBlast2Seq(const objects::CBioseq_Handle &subject, const objects::CBioseq_Handle &query, bool accept_atleast_one, ICanceled *canceled=nullptr)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

EDialogReturnValue NcbiInfoBox(const string &message, const string &title="Info")

specialized Message Box function for reporting general information messages

EDialogReturnValue NcbiMessageBox(const string &message, TDialogType type=eDialog_Ok, EDialogIcon icon=eIcon_Exclamation, const string &title="Error", EDialogTextMode text_mode=eRaw)

CTempString GetCurrentLine(void) const

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

CConstRef< CSeq_id > GetSeqId(void) const

@ eContent

Untagged human-readable accession or the like.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool IsNull(void) const THROWS_NONE

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

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.

virtual bool IsCanceled(void) const =0

bool IsOssEmpty(CNcbiOstrstream &oss)

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

static const char label[]

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

job_function_traits< _Fty >::future job_async(const _Fty &_Fnarg, const string &descr)

Lightweight interface for getting lines of data with minimal memory copying.

void ReportUsage(const wxString &dialog_name)

Report opening & accepting events in the editing package.

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

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

static tuple< objects::CSeq_id_Handle, CConstRef< objects::CSeq_align > > s_CreateAlign(CSeq_id_Handle idH, CBioseq_Handle subject, CBioseq_Handle query, ICanceled &canceled)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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