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NCBI C++ ToolKit: src/gui/packages/pkg_sequence/feature_search_tool.cpp Source File

name(

);

sl_ctx !=

;

;

;

& pattern,

m_PatternType(pt_type),

m_CaseSensitive(case_sensitive),

m_FeatTypesSet(feat_types)

strText =

;

lbl = ft_it->GetDescription();

strText += strText.empty()?

:

;

(strText.empty()) {

strText =

;

list<string> strList;

list<string> strList;

strList.push_back(ft_it->GetDescription());

wxFlexGridSizer * sz =

wxFlexGridSizer(0, 4, 0, 0);

sz->AddGrowableCol(3);

wxStaticText* stat1 =

wxStaticText(parent, wxID_STATIC,

(

));

->Add(stat1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

0, (

wxString*)

);

wxStaticText* stat2 =

wxStaticText( parent, wxID_STATIC,

(

));

->Add(stat2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

0, (

wxString*)

);

->Add(

wxStaticText( parent, wxID_STATIC,

(

),

wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

(

),

(

),

wxDefaultPosition, wxDefaultSize,

wxStaticText* stat3 =

wxStaticText( parent, wxID_STATIC,

(

));

->Add(stat3, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

wxTE_PROCESS_ENTER );

->Add(

,1, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

->GetSelection() !=

(

+ 1) ) {

sc_locs.push_back(sl);

sep(

);

( ! s_locs.empty()) {

s_locs.resize(s_locs.size() - sep.size());

s_pat =

->GetPattern();

=

+ s_pat +

+ s_locs;

(

->GetScopedLocs().empty()) {

(

->GetPattern().empty()) {

(!loc.

()) {

( ! feat_types.empty()) {

& scope = *sc_loc.m_Scope;

& annot_names = sc_loc.m_AnnotNames;

feat_iter(scope, seq_loc, sel);

(

> 0 &&

% 100) {

& loc_label,

,

cnt_found,

& ctx_name)

strand =

;

(locplustrand.find_last_of(

) == (locplustrand.length() - 1)) {

& loc_name,

& strand,

& acc_name,

& ctx_name)

kUpdateIncrement = 200;

(

>= kUpdateIncrement) {

re_snp(

);

(

& res_it : SNPSearchResultList) {

(

& var_it : res_it.second) {

(placements.size() == 1);

(placements.size() != 1)

& pl = placements.front();

(

& it : annot_names) {

sel.AddNamedAnnots(it);

sel.IncludeNamedAnnotAccession(it);

feat_it(scope, pl->GetLoc(), sel);

(gene_ref.IsSetLocus() &&

(gene_ref.GetLocus())) {

(gene_ref.IsSetAllele() &&

(gene_ref.GetAllele())) {

(gene_ref.IsSetDesc() &&

(gene_ref.GetDesc())) {

(gene_ref.IsSetMaploc() &&

(gene_ref.GetMaploc())) {

(gene_ref.IsSetLocus_tag() &&

(gene_ref.GetLocus_tag())) {

(gene_ref.IsSetSyn()) {

User-defined methods of the data storage class.

size_t GetSize(void) const

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CObjectList * GetObjectList()

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

string GetDescription() const

CConfigurableItems - a static list of items that can be configured.

CSeqLocToolQuery::TFeatTypeItemSet TFeatTypeItemSet

virtual void x_DoSearch()

performs searching, assuming that params are correct; Implement in derived classes

CFeatureSearchJob(CSeqLocToolQuery &query)

virtual bool x_ValidateParams()

returns true if Job params are correct, implement in derived classes

CSeqLocToolQuery::SScopedLoc TScopedLoc

bool x_Match(const string &text)

CSeqLocToolQuery::TFeatTypeItem TFeatTypeItem

CRef< CSeqLocToolQuery > m_Query

CSeqLocToolQuery::TScopedLocs TScopedLocs

void x_SearchFeatures(TScopedLocs &scoped_locs, const TFeatTypeItemSet &feat_types)

void x_AddToResults(CObject &obj, objects::CScope &scope, const string &loc_name, const string &ctx_name)

CObjectList Data structure representing a list of CObjects with associated Scopes and other optional ...

int AddRow(CObject *obj, objects::CScope *scope)

void SetString(int col, int row, const string &val)

void Append(const CObjectList &list)

adds rows from the given list, the lists must have identical sets of columns

int AddColumn(EColumnType type, const string &name, int col=-1)

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

string GetString(const string &key, const string &default_val=kEmptyStr) const

void GetStringList(const string &key, list< string > &val) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

void UpdateContextCombo(wxChoice *combo)

TFeatTypeItemSet m_FeatTypesSet

CRef< CDMSearchResult > m_TempResult

holds temporary results, guarded by Mutex

string m_Descr

human-readable description of the Job

CMutex m_Mutex

synchronizes access to the Job members

CRef< CAppJobError > m_Error

CObjectList m_AccList

accumulates found objects before they are transferred to m_ResultList

vector< SScopedLoc > TScopedLocs

static const CFeatList * GetFeatList()

namespace ncbi::objects::

IDMSearchQuery - abstract data mining query.

IDataMiningContext IDataMiningContext represents an abstract context for a Search.

virtual string GetDMContextName()=0

returns Name of the context to be used in UI

virtual CRef< objects::CScope > GetSearchScope()=0

virtual set< string > GetAnnotNames() const

virtual CRef< objects::CSeq_loc > GetSearchLoc()=0

iterator_bool insert(const value_type &val)

std::ofstream out("events_result.xml")

main entry point for tests

static const char location[]

#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 LOG_POST(message)

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

void Info(CExceptionArgs_Base &args)

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

request an annotation selector for a given type

bool m_CaseSensitive

regular expression to apply

objects::CSeq_feat_Handle x_SearchForSNP(const objects::CSeq_loc &seq_loc, objects::CScope &scope, const set< string > &annot_names)

virtual void x_LoadSettings(const CRegistryReadView &view)

CFeatureSearchForm(CFeatureSearchTool &tool)

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

CRef< CFeatureSearchTool > m_Tool

virtual string ToString() const

Prepare a string representation of a query (for logging and debugging)

virtual CRef< CSearchJobBase > x_CreateJob(IDMSearchQuery &query)

implementing CSearchToolBase pure virtual function

virtual void x_SaveSettings(CRegistryWriteView view) const

wxHyperlinkCtrl * m_HyperLink

CRegexp * m_Pattern

search patteern for "Exact Match" and "Wildcard" modes

CFeatureSearchQuery::TScopedLocs TScopedLocs

TPatternType m_PatternType

CFeatureSearchQuery(TScopedLocs &locs, const string &pattern, bool case_sensitive, TPatternType pt_type, const TFeatTypeItemSet &feat_types)

CFeatureSearchQuery.

CFeatureSearchTool()

CFeatureSearchTool.

virtual IDMSearchTool * x_GetTool()

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

virtual CIRef< IDMSearchQuery > ConstructQuery()

virtual CIRef< IDMSearchForm > CreateSearchForm()

factory method for creating a form representing the tool

virtual wxSizer * GetWidget(wxWindow *parent)

return a widget associated with the form; the form controls the lifetime of the widget (do not delete...

string SeqLocToString(const objects::CSeq_loc &loc)

virtual void x_CreateWidgets()

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual bool IsCompatible(IDataMiningContext *context)

retuns true if the tool is compatible with the provided Search Context

virtual void x_SetupColumns(CObjectList &obj_list)

add custom columns if needed

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

vector< ISeqLocSearchContext * > m_SeqLocContexts

list< string > m_FeatureTypes

void x_AddFeatToResults(const objects::CSeq_feat &feat, objects::CScope &scope, const string &loc_label, const int cnt, const int cnt_found, const string &ctx_name)

TPatternType m_PatternType

virtual IUITool * Clone() const

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

list< TSNPSearchCompoundResult > TSNPSearchCompoundResultList

results of a search for one or several ids

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

static void Search(const std::string &sTerms, const std::string &sAssemblyAccession, TSNPSearchCompoundResultList &ResultList)

search for given SNP ID(s) and get a list of results

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

bool IsSetComment(void) const

const CSeqFeatData & GetData(void) const

bool IsSetExcept_text(void) const

const string & GetComment(void) const

const string & GetExcept_text(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(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.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

TObjectType & GetObject(void) const

Get object.

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

CTempString GetMatch(CTempString str, size_t offset=0, size_t idx=0, TMatch flags=fMatch_default, bool noreturn=false)

Get matching pattern and subpatterns.

ECompile

Flags for compile regular expressions.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool MatchesMask(CTempString str, CTempString mask, ECase use_case=eCase)

Match "str" against the "mask".

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

Truncate whitespace in a string (in-place)

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.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

ECase

Which type of string comparison.

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.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

const TGene & GetGene(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CVariantPlacement > > TPlacements

static void text(MDB_val *v)

#define row(bind, expected)

CRef< objects::CScope > m_Scope

CRef< objects::CSeq_loc > m_Loc

set< string > m_AnnotNames

static CS_CONTEXT * context

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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