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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__tool__manager_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/blast_tool_manager.cpp Source File

: m_Descriptor(

,

,

,

,

),

m_ParentWindow(

),

m_UseNucForMixInput(

),

m_OptionsPanel(

),

;

action ==

;

action ==

;

}

;

task->Init_SubmitSearch(

);

task->SetLoadingOptions(options);

handle->SetOptions().Validate();

;

(scope != it2->scope) {

;

vector<CProjectService::TProjectId> projects;

(projects.empty()){

* seqLoc =

*

(o.object.GetPointer());

* seqId =

*

(o.object.GetPointer());

* bioSeq =

*

(o.object.GetPointer());

original.push_back(o);

(h && seqSet.

(h).second) {

(h && seqSet.

(h).second) {

(h && seqSet.

(h).second) {

(bioSeqSet) {

(; iter; ++iter) {

(h && seqSet.

(h).second) {

(it != seqLocs.

()) {

other.

(other.end(), it->second.

(), it->second.

());

(!original.empty())

(

&

: seqLocs) {

(

& j :

.second) {

* seq_loc =

*

(j.object.GetPointer());

(!seq_loc || !seq_loc->

())

target[

.first].push_back(j);

field->

().SetObject(*param_obj);

(wxOK != wxMessageBox(

,

, wxOK | wxCANCEL))

void AsyncConvertObjects(const CTypeInfo *typeInfo, const TConstScopedObjects &inputObjects, map< string, TConstScopedObjects > &results)

CDataLoadingAppTask - a task that executes CDataLoadingAppJob.

static string MakeKey(const string &section, const string &key, const string &delim=CGuiRegistry::kDecimalDot)

create a key from a section and a subkey

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

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

CProjectService - a service providing API for operations with Workspaces and Projects.

void GetObjProjects(TConstScopedObjects &objects, vector< TProjectId > &ids)

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

bool GetBool(const string &key, bool default_val=false) const

bool HasField(const string &key) const

Does a field with this section and key exist in this view?

CConstRef< objects::CUser_field > GetField(const string &key) const

provide raw field access

CRef< objects::CUser_field > SetField(const string &key)

provide raw field access

void Set(const string &key, int val)

access a named key at this level, with no recursion

CProjectSelectOptions - describes how new Project Items shall be added to a workspace.

Template class for iteration on objects of class C (non-medifiable version)

IServiceLocator - an abstract mechanism for locating services.

IUIObject - object that provides basic properties often required in a UI object.

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static TDSRET convert(TDSSOCKET *tds, TDSICONV *conv, TDS_ICONV_DIRECTION direction, const char *from, size_t from_len, char *dest, size_t *dest_len)

#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 ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

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

const string & GetMsg(void) const

Get message string.

void Trace(CExceptionArgs_Base &args)

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

virtual string GetExtensionIdentifier() const

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

CRef< blast::CBlastOptionsHandle > ToBlastOptions(bool local=false) const

virtual void LoadSettings()

virtual string GetExtensionLabel() const

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

bool TransferDataFromWindow()

bool TransferDataToWindow()

virtual const IUIObject & GetDescriptor() const

Returns the object describing this tool (UI meta data).

vector< TConstScopedObjects > m_InputObjects

void Setup(CNetBLASTUIDataSource &ds, const string &tool_name)

bool x_ValidateParams()

validate parameters after Params page

virtual void InitUI()

Initializes the Manager before using it in UI.

TConstScopedObjects & GetSeqLocs()

virtual wxPanel * GetMaxPanel()

Return the panel that occupies max size on display, to calculate dialog window size.

CBLASTSearchParamsPanel * m_ParamsPanel

IServiceLocator * m_SrvLocator

virtual bool CanDo(EAction action)

Indicates whether given transition is possible in the current state.

virtual void x_CreateOptionsPanelIfNeeded()

virtual bool DoTransition(EAction action)

Performs transition if possible and returns true, otherwise the function shall warn the user about th...

wxWindow * m_ParentWindow

SProjectSelectorParams m_ProjectParams

virtual IAppTask * QuickLaunch()

virtual wxPanel * GetCurrentPanel()

Return the panel corresponding to the current state of Tool Manager.

virtual IAppTask * GetTask()

Once parameters are gathered and validated this function is called to produce the final Task object t...

CBLASTToolManager()

CBLASTToolManager.

map< string, TConstScopedObjects > m_ProtObjects

void FromUserObject(const objects::CUser_object &user_obj)

CUIObject m_Descriptor

describes the Manager's UI properties

string m_LocalWinMaskDirPath

virtual void SetRegistryPath(const string &path)

virtual void SetServiceLocator(IServiceLocator *srv_locator)

Sets / unsets Service Locator.

virtual bool CanQuickLaunch() const

bool TransferDataToWindow()

virtual bool x_IsNucInput() const

defines whether Nucleotide or Protein options shall be selected by default

virtual void SaveSettings() const

virtual bool IsCompletedState()

Manager goes into "Complete" state when "Finish" button is pressed and all input data is gatherred an...

CBLASTSearchOptionsPanel * m_OptionsPanel

void SetParams(CBLASTParams *params)

void x_InitProjectParams()

virtual void x_SelectCompatibleInputObjects()

virtual void RestoreDefaults()

Restores the default options for the current panel.

virtual string SetInputObjects(const vector< TConstScopedObjects > &input)

sets input objects that can be used as arguments for the tool.

bool Create(wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(), long style=wxTAB_TRAVERSAL)

virtual void CleanUI()

CleanUI() is called after the host finished using the manager.

virtual void SetParentWindow(wxWindow *parent)

void SetParams(CBLASTParams *params, map< string, TConstScopedObjects > *nuc_objects, map< string, TConstScopedObjects > *prot_objects)

void PrintParams(const string &log_title) const

LOG_POST params for forensic purposes.

CRef< CNetBLASTUIDataSource > GetBLASTDataSource()

bool TransferDataFromWindow()

virtual bool IsFinalState()

True if Tool Manager has reached its final state, i.e.

virtual void SaveSettings() const

override in derived classes

virtual bool x_CreateParamsPanelIfNeeded()

virtual string GetCategory()

returns the name for the ToolCategory to which the tool belongs.

virtual void LoadSettings()

ESubjectType GetSubjectType() const

map< string, TConstScopedObjects > m_NucObjects

objects::CUser_object * ToUserObject() const

void NcbiErrorBox(const string &message, const string &title="Error")

specialized Message Box function for reporting critical errors

virtual void SetLogEvent(const string &log_event)

virtual const string & GetLabel() const

vector< SConstScopedObject > TConstScopedObjects

const CSeq_id * GetId(void) const

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

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

TObjectType & GetObject(void) const

Get object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetData(TData &value)

Assign a value to Data data member.

const struct ncbi::grid::netcache::search::fields::KEY key

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

SProjectSelectorParams - holds data for CProjectSelectorPanel.

void SelectProjectByObjects(TConstScopedObjects &objects, CProjectService *srv)

is all objects belong to the same project - selects the project

TProjectId m_SelectedProjectId

bool m_CreateFolder

package in a single item

void ToLoadingOptions(CSelectProjectOptions &options)

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