Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/remove__gene__xrefs_8cpp_source.html below:

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

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

(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);

itemStaticBoxSizer7->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

wxStaticBox* itemStaticBoxSizer17Static =

wxStaticBox(itemDialog1,

, wxEmptyString);

wxStaticBoxSizer* itemStaticBoxSizer17 =

wxStaticBoxSizer(itemStaticBoxSizer17Static, wxHORIZONTAL);

itemBoxSizer2->Add(itemStaticBoxSizer17, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText4 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemStaticBoxSizer17->Add(itemStaticText4, 0, wxALIGN_TOP|wxALL, 5);

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

(!

.IsSetXref()) {

any_removed =

;

CSeq_feat::TXref::iterator xit =

.SetXref().begin();

(xit !=

.SetXref().end()) {

((*xit)->IsSetData() && (*xit)->GetData().IsGene() &&

(*xit)->GetData().GetGene().IsSuppressed()) {

xit =

.SetXref().erase(xit);

(

.IsSetXref() &&

.GetXref().empty()) {

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 );

item =

->GetNextItem(item, wxLIST_NEXT_ALL, wxLIST_STATE_SELECTED);

( item == -1 )

;

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)];

go = constraint->DoesTextMatch(

.str());

modified =

;

(

feat_ci(seh); feat_ci; ++feat_ci)

modified =

;

((*xref)->IsSetData() && (*xref)->GetData().IsGene())

(

feat_ci(seh); feat_ci; ++feat_ci)

(

feat_ci(seh); feat_ci; ++feat_ci)

(

feat_ci(seh); feat_ci; ++feat_ci)

(parent.

())

(

feat_ci(seh); feat_ci; ++feat_ci)

(parent.

())

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()

static bool RemoveOrphanLocus_tagGeneXrefs(CSeq_feat &f, CBioseq_Handle bsh)

Removes orphaned locus_tag Gene-xrefs.

static bool RemoveOrphanLocusGeneXrefs(CSeq_feat &f, CBioseq_Handle bsh)

Removes orphaned locus Gene-xrefs.

static bool RemoveUnnecessaryGeneXrefs(CSeq_feat &f, CScope &scope)

Removes unnecessary Gene-xrefs.

static bool RemoveNonsuppressingGeneXrefs(CSeq_feat &f)

Removes non-suppressing Gene-xrefs.

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)

wxCheckBox * m_Suppressing

CRemoveGeneXrefs()

Constructors.

static CRef< CCmdComposite > RemoveNonsuppressing(CSeq_entry_Handle seh)

wxCheckBox * m_Nonsuppressing

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

~CRemoveGeneXrefs()

Destructor.

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

static bool ShowToolTips()

Should we show tooltips?

vector< bool > m_SubtypeAnyFlag

CStringConstraintPanel * m_StringConstraintPanel

static CRef< CCmdComposite > RemoveOrphanLocus_tag(CSeq_entry_Handle seh)

static CRef< CCmdComposite > RemoveAll(CSeq_entry_Handle seh)

void Init()

Initialises member variables.

static CRef< CCmdComposite > RemoveUnnecessary(CSeq_entry_Handle seh)

virtual CRef< CCmdComposite > GetCommand()

bool Create(wxWindow *parent, wxWindowID id=14000, const wxString &caption=_("Remove Gene Xrefs"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

static CRef< CCmdComposite > RemoveOrphanLocus(CSeq_entry_Handle seh)

wxCheckBox * m_Unnecessary

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void CreateControls()

Creates the controls and sizers.

bool RemoveSuppressingGeneXrefs(CSeq_feat &f)

vector< string > m_Descriptions

namespace ncbi::objects::

void SetStringSelection(const wxString &str)

CRef< edit::CStringConstraint > GetStringConstraint()

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

#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...

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...

TSeqPos GetBioseqLength(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

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

Convert int to 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.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref 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 TXref & GetXref(void) const

Get the Xref member data.

void ResetXref(void)

Reset Xref data member.

const TExt & GetExt(void) const

Get the Ext member data.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ eMol_na

just a nucleic acid

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

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

USING_SCOPE(ncbi::objects)

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_SUPPRESSING_CHECKBOX

#define ID_UNNECESSARY_CHECKBOX

#define ID_REMOVE_GENE_XREFS_LISTCTRL

#define ID_REMOVE_GENE_XREFS_OKCANCEL

#define ID_NONSUPPRESSING_CHECKBOX

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define ERASE_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

ERASE_SEQFEATXREF_ON_SEQFEAT.

#define EDIT_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4