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

name(

);

sl_ctx !=

;

;

;

wxFlexGridSizer * sz =

wxFlexGridSizer(1, 4, 0, 0);

sz->AddGrowableCol(3);

->Add(

wxStaticText( parent, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

0, (

wxString*)

);

->Add(

wxStaticText( parent, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

->Add(

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

sc_locs.push_back(sl);

sep(

);

it->m_Scope.GetPointer());

( !s_locs.empty() ) {

list<CSeq_id_Handle> idhs;

(list<string>, iter, toks) {

& s = *iter;

<<

<< e.

());

(

level = 0;

level < 5 && !

() && idhs.size(); ++level) {

( ; idhs.size() && map_it && !

(); ++map_it) {

list<CSeq_id_Handle>::iterator id_it = idhs.begin();

( ; id_it != idhs.end(); ) {

(

% 20 == 0) {

+

(

<<

<<

.

() <<

<< found);

& loc_name,

& ctx_name)

kUpdateIncrement = 20;

(

>= kUpdateIncrement) {

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

CObjectList * GetObjectList()

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)

virtual void UpdateContexts()

updates m_ContextCombo

void UpdateContextCombo(wxChoice *combo)

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

TScopedLocs & GetScopedLocs()

vector< SScopedLoc > TScopedLocs

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

#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 Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

static bool Match(const objects::CSeq_id &id1, const objects::CSeq_id &id2, objects::CScope *scope=NULL)

check to see if two seq-ids are identical.

virtual CIRef< IDMSearchQuery > ConstructQuery()

CComponentSearchTool()

IDMSearchTool.

virtual string GetExtensionLabel() const

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

CRef< CComponentSearchTool > m_Tool

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

virtual string GetExtensionIdentifier() const

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

virtual wxSizer * GetWidget(wxWindow *parent)

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

virtual bool x_ValidateParams()

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

virtual CRef< CSearchJobBase > x_CreateJob(IDMSearchQuery &query)

implementing CSearchToolBase pure virtual function

virtual IUITool * Clone() const

virtual void x_CreateWidgets()

virtual EJobState x_DoSearch()

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

virtual bool IsCompatible(IDataMiningContext *context)

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

CComponentSearchQuery(TScopedLocs &locs, const string &ids)

CComponentSearchQuery.

CRef< CComponentSearchQuery > m_Query

CComponentSearchQuery::TScopedLocs TScopedLocs

CComponentSearchJob(CComponentSearchQuery &query)

CComponentSearchJob.

virtual void x_SetupColumns(CObjectList &obj_list)

add custom columns if needed

virtual void UpdateContexts()

updates m_ContextCombo

virtual CIRef< IDMSearchForm > CreateSearchForm()

factory method for creating a form representing the tool

CComponentSearchForm(CComponentSearchTool &tool)

CComponentSearchForm.

virtual string GetName() const

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

virtual IDMSearchTool * x_GetTool()

CComponentSearchQuery::TScopedLocs TScopedLocs

virtual string GetDescription() const

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

vector< ISeqLocSearchContext * > m_SeqLocContexts

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

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TRange GetTotalRange(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

@ eGetId_ForceGi

return only a gi-based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

const CSeqMap & GetSeqMap(void) const

Get sequence map.

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

CSeqMap::ESegmentType GetType(void) const

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

TSeqPos GetPosition(void) const

return position of current segment in sequence

CSeqMap_CI ResolvedRangeIterator(CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const

Iterate segments in the range with specified strand coordinates.

@ eSeqRef

reference to Bioseq

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().

position_type GetLength(void) const

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

Convert int to string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fWithCommas

Use commas as thousands separator.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

void SetFrom(TFrom value)

Assign a value to From data member.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsSetVersion(void) const

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

Defines: CTimeFormat - storage class for time format.

#define row(bind, expected)

CRef< objects::CScope > m_Scope

CRef< objects::CSeq_loc > m_Loc

static CS_CONTEXT * context

string ToStdString(const wxString &s)

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