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

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

SetSize(wxSize(280, 750));

(vector<const CFeatListItem *>, ft_it, feat_list) {

feat_type = item.

();

[pair<int,int>(feat_type,feat_subtype)] = desc;

(existing.

(desc) == existing.

())

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

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

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

->InsertColumn(0,

,wxLIST_FORMAT_LEFT,237);

wxBoxSizer* itemBoxSizer5 =

wxBoxSizer(wxHORIZONTAL);

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

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxVERTICAL);

itemBoxSizer5->Add(itemBoxSizer6, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticBox* itemStaticBoxSizer7Static =

wxStaticBox(itemDialog1,

,

(

));

wxStaticBoxSizer* itemStaticBoxSizer7 =

wxStaticBoxSizer(itemStaticBoxSizer7Static, wxVERTICAL);

itemBoxSizer6->Add(itemStaticBoxSizer7, 0, wxALIGN_LEFT|wxALL, 5);

itemStaticBoxSizer7->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

itemRadioButton9->SetValue(

);

itemStaticBoxSizer7->Add(itemRadioButton9, 0, wxALIGN_LEFT|wxALL, 5);

itemStaticBoxSizer7->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

itemStaticBoxSizer7->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

wxStaticBox* itemStaticBoxSizer15Static =

wxStaticBox(itemDialog1,

,

(

));

wxStaticBoxSizer* itemStaticBoxSizer15 =

wxStaticBoxSizer(itemStaticBoxSizer15Static, wxVERTICAL);

itemBoxSizer6->Add(itemStaticBoxSizer15, 0, wxALIGN_LEFT|wxALL, 5);

itemRadioButton16->SetValue(

);

itemStaticBoxSizer15->Add(itemRadioButton16, 0, wxALIGN_LEFT|wxALL, 5);

itemStaticBoxSizer15->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

itemStaticBoxSizer15->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

wxStaticBox* itemStaticBoxSizer17Static =

wxStaticBox(itemDialog1,

,

(

));

wxStaticBoxSizer* itemStaticBoxSizer17 =

wxStaticBoxSizer(itemStaticBoxSizer17Static, wxVERTICAL);

itemBoxSizer6->Add(itemStaticBoxSizer17, 0, wxALIGN_LEFT|wxALL, 5);

wxArrayString strands,

;

strands.Add(

(

));

strands.Add(

(

));

strands.Add(

(

));

.Add(

(

));

.Add(

(

));

.Add(

(

));

itemStaticBoxSizer17->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

itemStaticBoxSizer17->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

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

modified =

;

item =

->GetNextItem(item, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

( item == -1 )

;

list<string> non_refseq;

refseq.push_back(*it);

non_refseq.push_back(*it);

(non_refseq.size()) {

( !accs.empty() ) {

( !accs.empty() ) {

( !lines.empty() ) {

(list<string>, iter, lines) {

(iter != lines.begin()) {

ostream <<

<< *iter << endl;

ostream << *iter << endl;

list< CConstRef<CUser_object> > objs;

objs.push_back(sub_o);

ostream <<

;

method =

->GetData().GetStr();

ostream <<

;

(method ==

|| method ==

) {

( !core.empty() ) {

( !core.empty() ) {

s =

;

ostream << s << endl;

stringstream& ostream,

objects::CSeq_feat& feat, objects::CScope& scope)

ostream <<

<< endl;

range = feat.GetLocation().GetTotalRange();

ostream <<

;

ostream <<

ostream <<

(feat.IsSetProduct()) {

ostream <<

feat_it(scope, feat.GetLocation(), sel);

(; feat_it ; ++feat_it) {

string::size_type pos = s.find_first_not_of(

);

( pos != string::npos ){

string::size_type lpos = string::npos;

lpos = s.find_first_of(

, pos );

( lpos == string::npos ){

= s.substr( pos );

= s.substr( pos, lpos - pos );

ostream <<

<< endl;

}

( lpos != string::npos );

(

feat (tse); feat; ++feat)

filter =

;

(subtypeAnyFlag)

= feat->GetOriginalFeature().GetData().Which();

desc =

[pair<int,int>(

,subtype)];

(feat->GetOriginalFeature().CanGetData())

= feat->GetOriginalFeature().GetData().Which();

subtype = feat->GetOriginalFeature().GetData().GetSubtype();

desc =

[pair<int,int>(

,subtype)];

&scope = tse.GetScope();

pattern =

->GetLineText(0).ToStdString();

(

);

pattern =

->GetLineText(0).ToStdString();

(CBioseq_Handle::TId::const_iterator idh = bsh.

().begin(); idh != bsh.

().end(); ++idh)

}

(

&) {}

(

exception&) {}

(strand ==

(

) && feat->GetOriginalFeature().IsSetLocation() && feat->GetOriginalFeature().GetLocation().GetStrand() ==

) go =

;

(strand ==

(

) && feat->GetOriginalFeature().IsSetLocation() && feat->GetOriginalFeature().GetLocation().GetStrand() ==

) go =

;

(

==

(

) && feat->GetOriginalFeature().IsSetLocation())

(

==

(

) && feat->GetOriginalFeature().IsSetLocation())

new_feat->

(feat->GetOriginalFeature());

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()

void AddCommand(IEditCommand &command)

~CCorrectIntervalOrder()

Destructor.

wxCheckBox * m_CheckBox_id

vector< string > m_Descriptions

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

vector< bool > m_SubtypeAnyFlag

void ApplyToCSeq_entry(objects::CSeq_entry_Handle tse, CRef< CCmdComposite > composite, const string &name, bool subtypeAnyFlag, bool &modified)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

static bool ShowToolTips()

Should we show tooltips?

wxChoice * m_ChoiceStrand

void CreateControls()

Creates the controls and sizers.

map< pair< int, int >, string > m_Types

virtual CRef< CCmdComposite > GetCommand()

wxTextCtrl * m_TextCtrl_id

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

Creation.

wxRadioButton * m_RadioButton

void Init()

Initialises member variables.

wxRadioButton * m_RadioButton_id

CCorrectIntervalOrder()

Constructors.

CFeatListItem - basic configuration data for one "feature" type.

string GetDescription() const

CFlatFileConfig & SetNeverTranslateCDS(bool val=true)

static string GetSeqFeatText(const CMappedFeat &feat, CScope &scope, const CFlatFileConfig &cfg, CRef< feature::CFeatTree > ftree=null)

namespace ncbi::objects::

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

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

static void s_Render_SeqFeat(stringstream &ostream, const objects::CSeq_feat &feat, objects::CScope &scope)

static void s_RenderAccList(stringstream &ostream, const CUser_field::TData::TStrs &item_data, const string &title)

static void s_Render_Feat_Evidence(stringstream &ostream, const CSeq_feat &feat, CScope &)

#define ID_CORRECT_INTERVAL_ORDER_TEXTCTRL

#define ID_CORRECT_INTERVAL_ORDER_CHECKBOX1

#define ID_CORRECT_INTERVAL_ORDER_CHECKBOX

#define ID_CORRECT_INTERVAL_ORDER_RADIOBUTTON3

#define ID_LISTCTRL_CORRECT_INTERVAL_ORDER

#define ID_CORRECT_INTERVAL_ORDER_RADIOBUTTON1

#define ID_CORRECT_INTERVAL_ORDER_TEXTCTRL1

#define ID_CORRECT_INTERVAL_ORDER_CHOICE2

#define ID_CORRECT_INTERVAL_ORDER_RADIOBUTTON2

#define ID_CORRECT_INTERVAL_ORDER_RADIOBUTTON

#define ID_CORRECT_INTERVAL_ORDER_CHOICE1

#define ID_CORRECT_INTERVAL_ORDER_OKCANCEL

static const char * str(char *buf, int n)

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

vector< const objects::CFeatListItem * > GetSortedFeatList(objects::CSeq_entry_Handle seh, size_t max=numeric_limits< size_t >::max())

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

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

Set object to copy of another one.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

EAccessionInfo

For IdentifyAccession (below)

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const TId & GetId(void) const

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

position_type GetLength(void) const

#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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

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

Join strings using the specified delimiter.

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 void Wrap(const string &str, SIZE_TYPE width, IWrapDest &dest, TWrapFlags flags, const string *prefix, const string *prefix1)

@ fWithCommas

Use commas as thousands separator.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

const TData & GetData(void) const

Get the Data member data.

vector< CRef< CUser_field > > TFields

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TObject & GetObject(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

vector< CStringUTF8 > TStrs

vector< CRef< CUser_field > > TData

const TExts & GetExts(void) const

Get the Exts member data.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsSetExts(void) const

set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.

const TExt & GetExt(void) const

Get the Ext member data.

@ e_Other

for historical reasons, 'other' = 'refseq'

bool CorrectIntervalOrder(CSeq_loc &loc)

Correct the order of consecutive intervals with the same Seq-id on the same strand.

static void text(MDB_val *v)

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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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