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

s_name(

);

;

;

;

wxFlexGridSizer * sz =

wxFlexGridSizer(1, 1, 0, 0);

sz->AddGrowableCol(0);

wxDefaultPosition, wxDefaultSize,

wxTE_PROCESS_ENTER );

->Add(

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

total_uids = 0;

* pSearchResultAsObject(iSNPSearchResult->GetPointer());

NewRow(obj_list->

(pSearchResultAsObject, scope.

()));

((*iSNPSearchResult)->CanGetPlacements(),

);

(Placements.size(),

);

obj_list->

(1, NewRow, (*iSNPSearchResult)->GetId().GetTag().GetStr());

((*iSNPSearchResult)->CanGetExt()) {

(pSNPSearchResult) {

(Placements.size(),

);

(pId,

);

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

CObjectList * GetObjectList()

CRef< CObjectList > m_ObjectList

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

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

void AddObjectLabel(const string &name, CLabel::ELabelType type)

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

CObject * GetObject(int row)

access to values (row, column)

void SetInteger(int col, int row, int val)

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

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

CSNPTableModel()

CSNPTableModel.

virtual wxVariant GetExtraValueAt(int row, int col) const

IDMSearchFormController * m_Controller

virtual void UpdateContexts()

updates m_ContextCombo

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

virtual void OnSearchEnabled(bool)

IDMSearchQuery - abstract data mining query.

IDataMiningContext IDataMiningContext represents an abstract context for a Search.

#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_ASSERT(expr, mess)

virtual bool x_ValidateParams()

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

virtual void x_LoadSettings(const CRegistryReadView &view)

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

virtual string GetExtensionLabel() const

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

virtual string GetExtensionIdentifier() const

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

virtual CObjectListTableModel * x_GetNewOLTModel() const

factory method creating new column handler for CObjectListWidget

CSNPSearchTool()

IDMSearchTool.

virtual CIRef< IDMSearchForm > CreateSearchForm()

factory method for creating a form representing the tool

CSNPSearchJob(CSNPSearchQuery &query)

CSNPSearchJob.

virtual wxSizer * GetWidget(wxWindow *parent)

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

CRef< CSNPSearchQuery > m_Query

virtual string GetDescription() const

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

virtual IUITool * Clone() const

virtual CRef< CSearchJobBase > x_CreateJob(IDMSearchQuery &query)

implementing CSearchToolBase pure virtual function

virtual string GetName() const

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

virtual void UpdateContexts()

updates m_ContextCombo

CSNPSearchQuery(const string &terms)

CSNPSearchTool.

virtual void x_SaveSettings(CRegistryWriteView view) const

virtual void x_SetupColumns(CObjectList &obj_list)

add custom columns if needed

virtual CIRef< IDMSearchQuery > ConstructQuery()

list< TSNPSearchCompoundResult > TSNPSearchCompoundResultList

results of a search for one or several ids

list< CRef< CVariation > > TSNPSearchResultList

various placements of a variation

virtual bool IsCanceled() const override

static const string c_SNPVarExt_GeneSymbol

EJobState

Job states (describe FSM)

static const string c_SNPVarExt_QueryId

static const string c_SNPVarExt_Comment

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

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

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

TSeqPos GetStop(ESeqLocExtremes ext) const

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TStr & GetStr(void) const

Get the variant data.

const TTag & GetTag(void) const

Get the Tag member data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

list< CRef< CVariantPlacement > > TPlacements

bool CanGetPlacements(void) const

Check if it is safe to call GetPlacements method.

const TPlacements & GetPlacements(void) const

Get the Placements member data.

list< CRef< CUser_object > > TExt

bool CanGetAssembly(void) const

Check if it is safe to call GetAssembly method.

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

const TLoc & GetLoc(void) const

Get the Loc member data.

CRef< objects::CObjectManager > om

#define row(bind, expected)

static CS_CONTEXT * context

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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