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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/uncul__tax__tool_8cpp_source.html below:

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

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

: m_TopSeqEntry(seh), m_Workbench(workbench)

(parent,

, caption, pos,

, style);

( wxWindow* parent, wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxFrame::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

Centre(wxBOTH|wxCENTRE_ON_SCREEN);

wxBoxSizer* itemBoxSizer1 =

wxBoxSizer(wxVERTICAL);

SetSizer(itemBoxSizer1);

wxPanel* itemDialog1 =

wxPanel( itemFrame1,

, wxDefaultPosition, wxDefaultSize, wxTAB_TRAVERSAL );

itemBoxSizer1->Add(itemDialog1, 1, wxGROW, 0);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxArrayString itemChoiceStrings, itemChoiceStringsWritable;

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

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

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 2);

->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+2 <

->GetNumberCols())

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

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

itemBoxSizer4->Add(itemStringConstraintPanel, 0, wxALIGN_CENTER_VERTICAL|wxALL|

, 0);

itemBoxSizer2->Add(itemAecrPanel, 0, wxALIGN_CENTER_HORIZONTAL|wxALL|

, 1);

wxBoxSizer* itemBoxSizer15 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer15, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 2);

wxButton* itemButton13 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer15->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton15 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer15->Add(itemButton15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton11 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer15->Add(itemButton11, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer15->Add(itemButton12, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton16 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer15->Add(itemButton16, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton14 =

wxButton( itemDialog1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer15->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

expand_col->

().SetTitle(

);

expand_col->

().SetField_name(

);

expand_col->

().SetString();

current_col->

().SetTitle(

);

current_col->

().SetField_name(

);

current_col->

().SetString();

suggested_col->

().SetTitle(

);

suggested_col->

().SetField_name(

);

suggested_col->

().SetString();

bogus_col->

().SetField_name(

);

bogus_col->

().SetString();

->SetColumns().push_back(id_col);

->SetColumns().push_back(expand_col);

->SetColumns().push_back(current_col);

->SetColumns().push_back(suggested_col);

->SetColumns().push_back(bogus_col);

vector<string> suggestions;

vector<bool> verified;

taxname =

[

].second->GetSource().GetTaxname();

suggested = suggestions[

];

(taxname == suggested && verified[

])

id_col->

().SetId().push_back(

);

expand_col->

().SetString().push_back(

);

current_col->

().SetString().push_back(taxname);

suggested_col->

().SetString().push_back(suggested);

bogus_col->

().SetString().push_back(

);

select_all =

;

(wxMessageBox(

(

),

(

), wxOK | wxCANCEL,

) == wxOK)

(

= 0;

< values_table->

(

).GetData().GetString().

();

++)

(!current.empty() && !suggested.empty() && current != suggested && (

->IsInSelection(

,0) || select_all))

current_to_suggested[current] = suggested;

taxname =

[

].second->GetSource().GetTaxname();

(current_to_suggested.

(taxname) != current_to_suggested.

())

edited_biosource.

().SetTaxname(current_to_suggested[taxname]);

orig_obj->

(biosource);

(old != taxname)

uncultured =

;

sp =

;

spdot =

;

taxname = taxname.substr(uncultured.length());

taxname = taxname.substr(0,taxname.length()-sp.length());

taxname = taxname.substr(0,taxname.length()-spdot.length());

,

,

,

,

,

,

,

(CBioSource::TSubtype::const_iterator subtype = biosource.

().begin(); subtype != biosource.

().end(); ++subtype)

name = (*subtype)->GetName();

CBioSource::TSubtype::iterator subtype = biosource.

().begin();

( subtype != biosource.

().end())

erased =

;

name = (*subtype)->GetName();

(new_note.empty())

subtype = biosource.

().erase(subtype);

(*subtype)->SetName(new_note);

vector<CRef<COrg_ref> > rq_list;

rq_list.push_back(org);

(reply->IsSetReply() && !reply->GetReply().empty())

t3reply = reply->GetReply().front();

((*status)->IsSetProperty() && (*status)->GetProperty() ==

&& (*status)->IsSetValue() && (*status)->GetValue().IsStr())

rank = (*status)->GetValue().GetStr();

(reply && reply->

())

+taxname+suffix;

rank2 =

(reply2);

(rank2 ==

)

(rank ==

)

( is_species_specific )

( is_species_specific)

(rank ==

)

& bsrc =

[

].second->GetSource();

submit.

(bsrc.GetTaxname());

(standard_taxname.empty())

submit.

(standard_taxname);

standard_taxname = name2;

submit.

(standard_taxname);

vector<CRef<COrg_ref> > rq_list;

rq_list.push_back(org);

(reply->IsSetReply())

(CTaxon3_reply::TReply::const_iterator reply_it = reply->GetReply().begin(); reply_it != reply->GetReply().end(); ++reply_it)

(reply_orig && reply_orig->

()) {

(standard_taxname.empty())

suggestions[

] =

(reply,

,standard_taxname);

(

= 0;

< values_table->

(

).GetData().GetString().

();

++)

(suggested.empty())

no_fix =

;

values_table->

()[3]->SetData().SetString()[

] = suggested.substr(0,pos);

(glyph_col >= 0 && glyph_col+2 <

->GetNumberCols())

taxon_present =

;

taxon_present =

;

(!taxon_present || !begins_with_uncultured)

((*it)->IsSource()) {

(

=0;

<

->GetNumberCols();

++)

(

->GetColLabelValue(

) ==

(

))

(

=0;

<

->GetNumberRows();

++)

(

=0;

<

->GetNumberRows();

++)

sel_srv->GetActiveObjects(

);

->SetTable(gridAdapter,

);

->AutoSizeColumns();

(glyph_col >= 0 && glyph_col+2 <

->GetNumberCols())

const string & GetTaxname(void) const

bool IsSetTaxname(void) const

void AddCommand(IEditCommand &command)

CUndoManager & GetUndoManager()

CProjectService - a service providing API for operations with Workspaces and Projects.

void MakeColumnReadOnly(int pos, bool val=true)

void InitColumnCollapse(int col)

void SetValuesTable(CRef< objects::CSeq_table > table)

CRef< objects::CSeq_table > GetValuesTable()

const CSeqTable_column & GetColumn(CTempString column_name) const

virtual CRef< CTaxon3_reply > SendOrgRefList(const vector< CRef< COrg_ref > > &list, COrg_ref::fOrgref_parts result_parts=COrg_ref::eOrgref_default, fT3reply_parts t3result_parts=eT3reply_default)

Undo/Redo interface for editing operations.

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

IWorkbench is the central interface in the application framework.

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

const char * kSequenceIdColLabel

static void cleanup(void)

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

#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 NCBI_THROW(exception_class, err_code, message)

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

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

void CleanupForTaxnameChange(CObjectInfo oi)

objects::CSeq_entry_Handle GetTopSeqEntryFromScopedObject(SConstScopedObject &obj)

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another 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.

@ eNocase

Case insensitive compare.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

bool IsSetOrg(void) const

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

bool IsSetSubtype(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

const TLineage & GetLineage(void) const

Get the Lineage member data.

bool IsSetLineage(void) const

lineage with semicolon separators Check if a value has been assigned to Lineage data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

bool IsSetOrgname(void) const

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

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

const TColumns & GetColumns(void) const

Get the Columns member data.

void SetHeader(THeader &value)

Assign a value to Header data member.

vector< CRef< CSeqTable_column > > TColumns

void SetData(TData &value)

Assign a value to Data data member.

TNum_rows GetNum_rows(void) const

Get the Num_rows member data.

const TString & GetString(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

TColumns & SetColumns(void)

Assign a value to Columns data member.

@ eField_id_location_id

location Seq-id

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

const TSource & GetSource(void) const

Get the variant data.

TSource & SetSource(void)

Select the variant.

bool IsData(void) const

Check if variant Data is selected.

const TData & GetData(void) const

Get the variant data.

bool IsSetStatus(void) const

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

const TStatus & GetStatus(void) const

Get the Status member data.

bool IsSetOrg(void) const

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

bool IsError(void) const

Check if variant Error is selected.

const TError & GetError(void) const

Get the variant data.

const TOrg & GetOrg(void) const

Get the Org member data.

const TMessage & GetMessage(void) const

Get the Message member data.

bool IsSetMessage(void) const

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

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

void GetViewObjects(IWorkbench *workbench, TConstScopedObjects &objects)

void ReportUsage(const wxString &dialog_name)

Report opening & accepting events in the editing package.

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

const GenericPointer< typename T::ValueType > T2 value

#define FOR_EACH_DBXREF_ON_ORGREF(Itr, Var)

FOR_EACH_DBXREF_ON_ORGREF EDIT_EACH_DBXREF_ON_ORGREF.

#define FOR_EACH_SEQENTRY_ON_SEQSET(Itr, Var)

FOR_EACH_SEQENTRY_ON_SEQSET EDIT_EACH_SEQENTRY_ON_SEQSET.

#define FOR_EACH_SEQDESC_ON_SEQENTRY(Itr, Var)

FOR_EACH_SEQDESC_ON_SEQENTRY EDIT_EACH_SEQDESC_ON_SEQENTRY.

#define row(bind, expected)

CRef< CCmdComposite > CleanupCommand(objects::CSeq_entry_Handle orig_seh, bool extended, bool do_tax)

wxString ToWxString(const string &s)

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