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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bulk__cds__edit_8cpp_source.html below:

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

IMPLEMENT_DYNAMIC_CLASS(

, wxDialog )

BEGIN_EVENT_TABLE(

, wxDialog )

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

: m_FeatHandles(feat_handles)

(parent,

, caption, pos,

, style);

( wxWindow* parent, wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

SetLayoutAdaptationMode(wxDIALOG_ADAPTATION_MODE_ENABLED);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxArrayString itemChoiceStrings, itemChoiceStringsWritable;

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

(values_table->GetNum_rows() < 1)

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

itemBoxSizer3->Add(

, 0, wxALIGN_TOP|wxALL, 5);

->SetTable(gridAdapter,

);

->AutoSizeColumns();

l_height =

->GetColLabelSize();

->SetColLabelSize( 2 * l_height );

((*it)->IsSetHeader() && (*it)->GetHeader().IsSetTitle() )

title = (*it)->GetHeader().GetTitle();

itemChoiceStrings.Add(wxString(title));

itemChoiceStringsWritable.Add(wxString(title));

(glyph_col >= 0 && glyph_col+1 <

->GetNumberCols())

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer5 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer13 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton14 =

wxButton( itemDialog1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton15 =

wxButton( itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemButton15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

id_col->SetHeader().SetField_id(objects::CSeqTable_column_info::eField_id_location_id);

expand_col->SetHeader().SetTitle(

);

expand_col->SetHeader().SetField_name(

);

expand_col->SetData().SetString();

name_col->SetHeader().SetTitle(

);

name_col->SetHeader().SetField_name(

);

name_col->SetData().SetString();

desc_col->SetHeader().SetTitle(

);

desc_col->SetHeader().SetField_name(

);

desc_col->SetData().SetString();

loc_col->SetHeader().SetTitle(

);

loc_col->SetHeader().SetField_name(

);

loc_col->SetData().SetString();

comment_col->SetHeader().SetTitle(

);

comment_col->SetHeader().SetField_name(

);

comment_col->SetData().SetString();

ec_number_col->SetHeader().SetTitle(

);

ec_number_col->SetHeader().SetField_name(

);

ec_number_col->SetData().SetString();

activity_col->SetHeader().SetTitle(

);

activity_col->SetHeader().SetField_name(

);

activity_col->SetData().SetString();

bogus_col->SetHeader().SetTitle(

);

bogus_col->SetHeader().SetField_name(

);

bogus_col->SetData().SetString();

->SetColumns().push_back(id_col);

->SetColumns().push_back(expand_col);

->SetColumns().push_back(name_col);

->SetColumns().push_back(desc_col);

->SetColumns().push_back(loc_col);

->SetColumns().push_back(comment_col);

->SetColumns().push_back(ec_number_col);

->SetColumns().push_back(activity_col);

->SetColumns().push_back(bogus_col);

(!fi->IsSetProduct())

;

(!prot_bsh || !prot_bsh.

())

;

name,desc,loc,comment;

prot_feat_ci(prot_bsh, sel);

(

.IsSetName())

name =

.GetName().front();

(

.IsSetDesc())

desc =

.GetDesc();

( fi->GetOriginalSeq_feat()->IsSetLocation() )

fi->GetOriginalSeq_feat()->GetLocation().GetLabel(&loc);

(fi->GetOriginalSeq_feat()->IsSetComment())

comment = fi->GetOriginalSeq_feat()->GetComment();

ec_feat_action->

(*fi);

vector<string>& ec_values = ec_feat_action->

();

ec_number =

(ec_values,

);

act_feat_action->

(*fi);

vector<string>& act_values = act_feat_action->

();

activity =

(act_values,

);

id_col->SetData().SetId().push_back(

);

expand_col->SetData().SetString().push_back(

);

name_col->SetData().SetString().push_back(name);

desc_col->SetData().SetString().push_back(desc);

loc_col->SetData().SetString().push_back(loc);

comment_col->SetData().SetString().push_back(comment);

ec_number_col->SetData().SetString().push_back(ec_number);

activity_col->SetData().SetString().push_back(activity);

bogus_col->SetData().SetString().push_back(

);

not_asked =

;

(!fi->IsSetProduct())

;

(!prot_bsh || !prot_bsh.

())

;

new_cds->

(*fi->GetOriginalSeq_feat());

name,desc,loc;

save_old_name;

prot_feat_ci(prot_bsh, sel);

modified =

;

(

.IsSetName())

name =

.GetName().front();

(

.IsSetDesc())

desc =

.GetDesc();

(row < values_table->GetColumn(

).GetData().GetString().

())

(new_name != name)

(new_name.empty())

new_feat->

().SetProt().ResetName();

(new_feat->

().SetProt().SetName().empty())

new_feat->

().SetProt().SetName().push_back(new_name);

new_feat->

().SetProt().SetName().front() = new_name;

save_old_name = name;

(row < values_table->GetColumn(

).GetData().GetString().

())

(new_desc != desc)

(new_desc.empty())

new_feat->

().SetProt().ResetDesc();

new_feat->

().SetProt().SetDesc() = new_desc;

ec_feat_action->

(*fi);

vector<string>& ec_values = ec_feat_action->

();

old_ec_number =

(ec_values,

);

new_ec_number;

(row < values_table->GetColumn(

).GetData().GetString().

())

(new_ec_number != old_ec_number)

new_feat->

().SetProt().ResetEc();

vector<string> new_values;

(

&

: new_values)

new_feat->

().SetProt().SetEc().push_back(

);

act_feat_action->

(*fi);

vector<string>& act_values = act_feat_action->

();

old_activity =

(act_values,

);

(row < values_table->GetColumn(

).GetData().GetString().

())

(new_activity != old_activity)

new_feat->

().SetProt().ResetActivity();

vector<string> new_values;

(

&

: new_values)

new_feat->

().SetProt().SetActivity().push_back(

);

( fi->GetOriginalSeq_feat()->IsSetLocation() )

fi->GetOriginalSeq_feat()->GetLocation().GetLabel(&loc);

changed_feat =

;

(row < values_table->GetColumn(

).GetData().GetString().

())

(!save_old_name.empty())

(new_comment.empty())

new_comment = save_old_name;

=

;

answer = wxMessageBox(

(

),

(

), wxYES_NO | wxCANCEL | wxICON_QUESTION,

);

(answer == wxCANCEL)

(answer == wxYES)

(dlg.ShowModal() == wxID_OK) {

(new_comment != comment)

(new_comment.empty())

changed_feat =

;

partial_start_val = partial_start_feat_col->

(*fi->GetOriginalSeq_feat());

new_partial_start_val;

(row < values_table->GetColumn(

).GetData().GetString().

())

(new_partial_start_val != partial_start_val)

(new_partial_start_val.empty())

changed_feat =

;

partial_stop_val = partial_stop_feat_col->

(*fi->GetOriginalSeq_feat());

new_partial_stop_val;

(row < values_table->GetColumn(

).GetData().GetString().

())

(new_partial_stop_val != partial_stop_val)

(new_partial_stop_val.empty())

changed_feat =

;

new_mrna->

(*orig_mrna);

new_mrna->

().SetRna().SetRnaProductName(prot_name, remainder);

;

wxMessageDialog dlg(

,

(

),

(

),wxOK|wxCANCEL|wxCENTRE);

(dlg.ShowModal() == wxID_OK)

USING_SCOPE(ncbi::objects)

vector< CSeq_feat_Handle > m_FeatHandles

static bool ShowToolTips()

Should we show tooltips?

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

Creation.

void CreateControls()

Creates the controls and sizers.

CRef< CCmdComposite > GetCommandFromValuesTable(CRef< objects::CSeq_table >)

void OnClickCancel(wxCommandEvent &event)

CSeqTableGridPanel * m_GridPanel

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void GetUpdateMRNAProductNameCmd(CRef< CSeq_feat > cds, CScope &scope, const string &prot_name, CRef< CCmdComposite > composite)

void Init()

Initialises member variables.

wxCheckBox * m_CopyProtNameToComment

virtual const CObject * RowToScopedObjects(int row, TConstScopedObjects &objects, CBioseq_Handle &bsh)

CRef< objects::CSeq_table > GetChoices(CRef< objects::CSeq_table > values_table)

CRef< CCmdComposite > GetCommand()

CApplyEditconvertPanel * m_AecrPanel

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CRef< objects::CSeq_table > GetValuesTableFromSeqEntry()

CStringConstraintSelect * m_StringConstraintPanel

void OnClickOk(wxCommandEvent &event)

bool IsReadOnlyColumn(string column_name)

void AddCommand(IEditCommand &command)

objects::edit::EExistingText GetExistingTextHandler()

void AllowAdditionalQual(bool val)

static CRef< CFeatureSeqTableColumnBase > Create(const string &sTitle, objects::CSeqFeatData::ESubtype subtype=objects::CSeqFeatData::eSubtype_any)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

CConstRef< objects::CSeq_submit > m_SeqSubmit

Seq-loc and seq-align mapper exceptions.

void MakeColumnReadOnly(int pos, bool val=true)

void InitColumnCollapse(int col)

CRef< objects::CSeq_table > GetValuesTable()

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name; do nothing if no such qualifier exists.

void SetProtXref(CProt_ref &value)

const CSeqTable_column & GetColumn(CTempString column_name) const

virtual void SetFeat(CSeq_feat_Handle fh)

void SetTopSeqEntry(CSeq_entry_Handle seh)

const vector< string > & GetValues(void)

IWorkbench is the central interface in the application framework.

CIRef< IEditingAction > CreateAction(CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class=kEmptyStr, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >(NULL))

const string kPartialStart

const string kPartialStop

const char * kSequenceIdColLabel

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

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)

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

bool IsProtein(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

void SetHeader(THeader &value)

Assign a value to Header data member.

vector< CRef< CSeqTable_column > > TColumns

const TString & GetString(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetComment(void) const

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

void SetComment(const TComment &value)

Assign a value to Comment data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

void ResetComment(void)

Reset Comment data member.

const TComment & GetComment(void) const

Get the Comment member data.

const TProt & GetProt(void) const

Get the variant data.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

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

CRef< CSeqTable_column > AddStringColumnToTable(CRef< CSeq_table > table, string label)

void AddValueToColumn(CRef< CSeqTable_column > column, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)

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

#define row(bind, expected)

@ eExistingText_replace_old

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

wxString ToWxString(const string &s)

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