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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/kalign__tool_8cpp_source.html below:

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

39 #include <wx/msgdlg.h> 49 "Create an alignment using Kalign"

50 "Fast multiple sequence alignment tool, concentrating on local regions. Suitable for large alignments."

51 "https://www.ncbi.nlm.nih.gov/tools/gbench/manual5/#MSATools"

52 "Multiple Sequence Aligners"

59 return "kalign_tool"

;

65 return "Kalign Tool"

;

136

wxMessageBox(

wxT

(

"No objects that can be proccessed were selected."

137 wxT

(

"Kalign Tool Error"

), wxOK | wxICON_ERROR);

149 if

( gui_seq_info ) {

150 if

(gui_seq_info->IsProtein()) {

151

proteins.push_back(*it2);

154

genomic.push_back(*it2);

159 objects

= (proteins.size() > genomic.size()) ? proteins : genomic;

163

wxMessageBox(

wxT

(

"You have to select at least 2 either genomic or protein locations to run Kalign tool."

164 wxT

(

"Kalign Tool Error"

), wxOK | wxICON_ERROR);

175

vector<CSelectProjectOptions::TProjectId> projects;

179 if

(projects.empty())

CDataLoadingAppJob - a base class for Jobs loading data into projects.

CDataLoadingAppTask - a task that executes CDataLoadingAppJob.

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

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

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

void Set_CreateNewProject(const string &folder=kEmptyStr)

void Set_AddToExistingProject(TProjectId &project_id, const string &folder=kEmptyStr)

IRegSettings An interface for objects that save / restore settings using CGuiRegistry.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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...

virtual IAppTask * QuickLaunch()

CKalignToolParams m_Params

virtual CAlgoToolManagerParamsPanel * x_GetParamsPanel()

returns a pointer to the parameters panel, override in derived classes

CKalignTool()

CKalignTool.

virtual bool x_ValidateParams()

validates user input in Parameters panel, report errors if any

virtual bool x_CreateParamsPanelIfNeeded()

returns / creates Parameters panel, override in derived classes see cpp file for example

virtual void CleanUI()

override this function in a derived class and clean extra members

virtual string GetExtensionLabel() const

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

virtual IRegSettings * x_GetParamsAsRegSetting()

return a pointer to Parameters object as IRegSettings interface

CKalignToolPanel * m_Panel

virtual CDataLoadingAppJob * x_CreateLoadingJob()

factory method for creating the job that executes the tool algorithm override in derived classes

virtual wxPanel * GetMaxPanel()

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

TConstScopedObjects & SetObjects()

virtual void x_SelectCompatibleInputObjects()

virtual void InitUI()

override this function in a derived class and initialize extra members

vector< SConstScopedObject > TConstScopedObjects

TObjectType * Release(void)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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