Classes
class	CLBLASTUIDataSource
	CLBLASTUIDataSource. More...

class	CLBLASTUIDataSourceType
	CLBLASTUIDataSourceType. More...

class	CLBLASTUILoadManager
	CLBLASTUILoadManager. More...

class	CBamUIDataSource
	CBamUIDataSource. More...

class	CBamUIDataSourceType
	CBamUIDataSourceType. More...

class	CBamUILoadManager

class	CBamLoadOptionPanel
	CBamLoadOptionPanel. More...

class	CBamLoadOptionPanel::CDropTarget

Typedefs
typedef set< string >	CBamLoadOptionPanel::TBamFiles

typedef vector< pair< string, string > >	CBamLoadOptionPanel::TBamWithIndexFiles

Enumerations
enum	ELBLASTCommands { eCmdLoadDB = 12351 }
	commands introduced by BAM data source More...

enum	CLBLASTUILoadManager::EState { CLBLASTUILoadManager::eInvalid = -1 , CLBLASTUILoadManager::eSelectDir , CLBLASTUILoadManager::eSelectProject , CLBLASTUILoadManager::eCompleted }

enum	EBamCommands { eCmdLoadBamFile = 12350 }
	commands introduced by BAM data source More...

enum	CBamUILoadManager::EState { CBamUILoadManager::eInvalid = -1 , CBamUILoadManager::eSelectBam , CBamUILoadManager::eBamIndex , CBamUILoadManager::eCoverageGraph , CBamUILoadManager::eRefSequences , CBamUILoadManager::eSelectProject , CBamUILoadManager::eCompleted }

enum	{ CBamLoadOptionPanel::ID_CBAMLOADOPTIONPANEL = 10070 , CBamLoadOptionPanel::ID_BAM_INPUT = 10071 , CBamLoadOptionPanel::ID_BUTTON = 10072 }
	Control identifiers. More...

enum	{ CBamLoadOptionPanel::ID_PARSING_TEXT = 10100 , CBamLoadOptionPanel::ID_PARSING_PROGRESS }

enum	CBamLoadOptionPanel::EParseState { CBamLoadOptionPanel::eParseComplete , CBamLoadOptionPanel::eParseRunning , CBamLoadOptionPanel::eParseCanceling }

Functions
	CLBLASTUIDataSource::CLBLASTUIDataSource (CLBLASTUIDataSourceType &type)

	CLBLASTUIDataSource::~CLBLASTUIDataSource ()

	CLBLASTUIDataSourceType::CLBLASTUIDataSourceType ()
	CLBLASTUIDataSourceType. More...

	CLBLASTUILoadManager::CLBLASTUILoadManager ()
	CLBLASTUILoadManager. More...

	CBamUIDataSource::CBamUIDataSource (CBamUIDataSourceType &type)

	CBamUIDataSource::~CBamUIDataSource ()

bool	CBamUIDataSource::x_GetBamInputs (const objects::CUser_object &obj, string &path, string &files, string &idx, string &target_assm) const

bool	CBamUIDataSource::x_GetSrzAccession (const objects::CUser_object &obj, string &srz) const

bool	CBamUIDataSource::x_GetCSraInputs (const objects::CUser_object &obj, string &file) const

bool	CBamUIDataSource::x_GetSraAccession (const objects::CUser_object &obj, string &sra) const

	CBamUIDataSourceType::CBamUIDataSourceType ()
	CBamUIDataSourceType. More...

	CBamUILoadManager::CBamUILoadManager ()
	CBamUILoadManager. More...

void	CBamUILoadManager::x_GetBamRefSeqs (const CBamLoadOptionPanel::TBamWithIndexFiles &files, const string &mappedAcc)

void	CBamUILoadManager::x_GetCSraRefSeqs (const CBamLoadOptionPanel::TBamFiles &accessions)

void	CBamUILoadManager::x_GetSrzRefSeqs (const CBamLoadOptionPanel::TBamFiles &accessions)

	CBamLoadOptionPanel::CBamLoadOptionPanel ()

	CBamLoadOptionPanel::CBamLoadOptionPanel (wxWindow *parent, wxWindowID id=ID_CBAMLOADOPTIONPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxTAB_TRAVERSAL)

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

	CBamLoadOptionPanel::~CBamLoadOptionPanel ()

void	CBamLoadOptionPanel::Init ()

void	CBamLoadOptionPanel::CreateControls ()

void	CBamLoadOptionPanel::OnBamInputTextUpdated (wxCommandEvent &event)
	wxEVT_COMMAND_TEXT_UPDATED event handler for ID_BAM_INPUT More...

void	CBamLoadOptionPanel::OnButtonClick (wxCommandEvent &event)
	wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON More...

wxBitmap	CBamLoadOptionPanel::GetBitmapResource (const wxString &name)
	Retrieves bitmap resources. More...

wxIcon	CBamLoadOptionPanel::GetIconResource (const wxString &name)
	Retrieves icon resources. More...

static bool	CBamLoadOptionPanel::ShowToolTips ()

void	CBamLoadOptionPanel::OnTimer (wxTimerEvent &event)

string	CBamLoadOptionPanel::GetInput () const

void	CBamLoadOptionPanel::SetInput (const string &input)

bool	CBamLoadOptionPanel::IsInputValid ()

bool	CBamLoadOptionPanel::HasBamFile () const

bool	CBamLoadOptionPanel::SetIndexFiles ()

string	CBamLoadOptionPanel::GetBamFilePath () const

const TBamWithIndexFiles &	CBamLoadOptionPanel::GetBamFiles () const

const TBamFiles &	CBamLoadOptionPanel::GetCSraFiles () const

const TBamFiles &	CBamLoadOptionPanel::GetSrzAccs () const

const TBamFiles &	CBamLoadOptionPanel::GetSraAccs () const

void	CBamLoadOptionPanel::SetFilenames (const wxArrayString &filenames)

void	CBamLoadOptionPanel::AddFilenames (const wxArrayString &filenames)

void	CBamLoadOptionPanel::x_ValidateInput ()

	CBamLoadOptionPanel::CDropTarget::CDropTarget (CBamLoadOptionPanel &panel)

virtual wxDragResult	CBamLoadOptionPanel::CDropTarget::OnData (wxCoord x, wxCoord y, wxDragResult def)

Variables
CRef< CLBLASTUIDataSourceType >	CLBLASTUIDataSource::m_Type

CUIObject	CLBLASTUIDataSource::m_Descr

IServiceLocator *	CLBLASTUIDataSource::m_SrvLocator

bool	CLBLASTUIDataSource::m_Open

CUIObject	CLBLASTUIDataSourceType::m_Descr

IServiceLocator *	CLBLASTUILoadManager::m_SrvLocator

wxWindow *	CLBLASTUILoadManager::m_ParentWindow

CUIObject	CLBLASTUILoadManager::m_Descriptor

EState	CLBLASTUILoadManager::m_State

string	CLBLASTUILoadManager::m_RegPath

string	CLBLASTUILoadManager::m_SavedInput

string	CLBLASTUILoadManager::m_AssmAcc

vector< CRef< objects::CSeq_id > >	CLBLASTUILoadManager::m_RefSeqIds

CLBLASTParamsPanel *	CLBLASTUILoadManager::m_ParamsPanel

CProjectSelectorPanel *	CLBLASTUILoadManager::m_ProjectSelPanel

SProjectSelectorParams	CLBLASTUILoadManager::m_ProjectParams

CLBLASTLoadParams	CLBLASTUILoadManager::m_LBLASTParams

CRef< CBamUIDataSourceType >	CBamUIDataSource::m_Type

CUIObject	CBamUIDataSource::m_Descr

IServiceLocator *	CBamUIDataSource::m_SrvLocator

bool	CBamUIDataSource::m_Open

CUIObject	CBamUIDataSourceType::m_Descr

IServiceLocator *	CBamUILoadManager::m_SrvLocator

wxWindow *	CBamUILoadManager::m_ParentWindow

CUIObject	CBamUILoadManager::m_Descriptor

EState	CBamUILoadManager::m_State

string	CBamUILoadManager::m_RegPath

string	CBamUILoadManager::m_SavedInput

string	CBamUILoadManager::m_SamtoolsPath

string	CBamUILoadManager::m_AssmAcc

vector< CConstRef< objects::CSeq_id > >	CBamUILoadManager::m_RefSeqIds

CBamLoadOptionPanel *	CBamUILoadManager::m_OptionPanel

CBamIndexingPanel *	CBamUILoadManager::m_IndexingPanel

CBamRefSequencesPanel *	CBamUILoadManager::m_RefSequencesPanel

CBamCoverageGraphPanel *	CBamUILoadManager::m_GraphPanel

CProjectSelectorPanel *	CBamUILoadManager::m_ProjectSelPanel

SProjectSelectorParams	CBamUILoadManager::m_ProjectParams

wxBoxSizer *	CBamLoadOptionPanel::m_MainSizer

CRichTextCtrl *	CBamLoadOptionPanel::m_BamInput

wxBoxSizer *	CBamLoadOptionPanel::m_ParseProgressSizer

CBamLoadOptionPanel &	CBamLoadOptionPanel::CDropTarget::m_Panel

bool	CBamLoadOptionPanel::m_UpdatingStyle = false

EParseState	CBamLoadOptionPanel::m_State = eParseComplete

bool	CBamLoadOptionPanel::m_TextChanged = false

wxTextAttr	CBamLoadOptionPanel::m_DefStyle

wxTextAttr	CBamLoadOptionPanel::m_ErrStyle

size_t	CBamLoadOptionPanel::m_InputNum
	total number of valid inputs More...

size_t	CBamLoadOptionPanel::m_ErrNum
	number of token with errors More...

TBamWithIndexFiles	CBamLoadOptionPanel::m_BamFiles

TBamFiles	CBamLoadOptionPanel::m_CSraFiles

TBamFiles	CBamLoadOptionPanel::m_SrzAccs

TBamFiles	CBamLoadOptionPanel::m_SraAccs

wxTimer	CBamLoadOptionPanel::m_Timer

std::unique_ptr< async_job >	CBamLoadOptionPanel::m_ValidateJob

IExtension interface implementation
virtual string	CLBLASTUIDataSource::GetExtensionIdentifier () const
	returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this" More...

virtual string	CLBLASTUIDataSource::GetExtensionLabel () const
	returns a displayable label for this extension ( please capitalize the key words - "My Extension" ) More...

IServiceLocatorConsumer implementation
virtual void	CLBLASTUIDataSource::SetServiceLocator (IServiceLocator *locator)

IUIDataSource interface implementation
virtual IUIDataSourceType &	CLBLASTUIDataSource::GetType () const

virtual const IUIObject &	CLBLASTUIDataSource::GetDescr ()
	returns UI description of the object (label, icon etc.) More...

virtual bool	CLBLASTUIDataSource::IsOpen ()
	a Data source needs to be open before use and closed after. More...

virtual bool	CLBLASTUIDataSource::Open ()
	Prepares Data Source for use, any initialization that can be potentially time-consuming or may require error handling shall be done in this function, not in a constructor. More...

virtual bool	CLBLASTUIDataSource::Close ()

virtual void	CLBLASTUIDataSource::EditProperties ()

virtual IUIToolManager *	CLBLASTUIDataSource::GetLoadManager ()

virtual int	CLBLASTUIDataSource::GetDefaultCommand ()

virtual wxEvtHandler *	CLBLASTUIDataSource::CreateEvtHandler ()

IDataLoaderProvider implementation
virtual string	CLBLASTUIDataSource::AddDataLoader (const objects::CUser_object &obj)
	Add a new data loader to object manager. More...

virtual string	CLBLASTUIDataSource::GetLoaderName (const objects::CUser_object &obj) const
	Get the data loader's name based on input object. More...

IExplorerItemCmdContributor implementation
virtual IExplorerItemCmdContributor::TContribution	CLBLASTUIDataSource::GetMenu (wxTreeCtrl &treeCtrl, PT::TItems &items)
	for the given set of items returns a contribution More...

IUIDataSourceType interface implementation
virtual const IUIObject &	CLBLASTUIDataSourceType::GetDescr ()
	returns UI description of the type (label, icon etc.) More...

virtual IUIDataSource *	CLBLASTUIDataSourceType::CreateDataSource ()
	factory method; create an Data Source instance More...

virtual bool	CLBLASTUIDataSourceType::AutoCreateDefaultDataSource ()
	returns "true" if this type needs to create a default instance of the Data Source at start-up More...

IExtension interface implementation
virtual string	CLBLASTUIDataSourceType::GetExtensionIdentifier () const
	returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this" More...

virtual string	CLBLASTUIDataSourceType::GetExtensionLabel () const
	returns a displayable label for this extension ( please capitalize the key words - "My Extension" ) More...

IUIToolManager interface implementation
virtual void	CLBLASTUILoadManager::SetServiceLocator (IServiceLocator *srv_locator)
	Sets / unsets Service Locator. More...

virtual void	CLBLASTUILoadManager::SetParentWindow (wxWindow *parent)

virtual const IUIObject &	CLBLASTUILoadManager::GetDescriptor () const
	Returns the object describing this tool (UI meta data). More...

virtual void	CLBLASTUILoadManager::InitUI ()
	Initializes the Manager before using it in UI. More...

virtual void	CLBLASTUILoadManager::CleanUI ()
	CleanUI() is called after the host finished using the manager. More...

virtual wxPanel *	CLBLASTUILoadManager::GetCurrentPanel ()
	Return the panel corresponding to the current state of Tool Manager. More...

virtual bool	CLBLASTUILoadManager::CanDo (EAction action)
	Indicates whether given transition is possible in the current state. More...

virtual bool	CLBLASTUILoadManager::IsFinalState ()
	True if Tool Manager has reached its final state, i.e. More...

virtual bool	CLBLASTUILoadManager::IsCompletedState ()
	Manager goes into "Complete" state when "Finish" button is pressed and all input data is gatherred and validated. More...

virtual bool	CLBLASTUILoadManager::DoTransition (EAction action)
	Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false. More...

virtual IAppTask *	CLBLASTUILoadManager::GetTask ()
	Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work. More...

IRegSettings interface implementation
virtual void	CLBLASTUILoadManager::SetRegistryPath (const string &path)

virtual void	CLBLASTUILoadManager::LoadSettings ()

virtual void	CLBLASTUILoadManager::SaveSettings () const

IExtension interface implementation
virtual string	CBamUIDataSource::GetExtensionIdentifier () const
	returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this" More...

virtual string	CBamUIDataSource::GetExtensionLabel () const
	returns a displayable label for this extension ( please capitalize the key words - "My Extension" ) More...

IServiceLocatorConsumer implementation
virtual void	CBamUIDataSource::SetServiceLocator (IServiceLocator *locator)

IUIDataSource interface implementation
virtual IUIDataSourceType &	CBamUIDataSource::GetType () const

virtual const IUIObject &	CBamUIDataSource::GetDescr ()
	returns UI description of the object (label, icon etc.) More...

virtual bool	CBamUIDataSource::IsOpen ()
	a Data source needs to be open before use and closed after. More...

virtual bool	CBamUIDataSource::Open ()
	Prepares Data Source for use, any initialization that can be potentially time-consuming or may require error handling shall be done in this function, not in a constructor. More...

virtual bool	CBamUIDataSource::Close ()

virtual void	CBamUIDataSource::EditProperties ()

virtual IUIToolManager *	CBamUIDataSource::GetLoadManager ()

virtual int	CBamUIDataSource::GetDefaultCommand ()

virtual wxEvtHandler *	CBamUIDataSource::CreateEvtHandler ()

IDataLoaderProvider implementation
virtual string	CBamUIDataSource::AddDataLoader (const objects::CUser_object &obj)
	Add a new data loader to object manager. More...

virtual string	CBamUIDataSource::GetLoaderName (const objects::CUser_object &obj) const
	Get the data loader's name based on input object. More...

IExplorerItemCmdContributor implementation
virtual IExplorerItemCmdContributor::TContribution	CBamUIDataSource::GetMenu (wxTreeCtrl &treeCtrl, PT::TItems &items)
	for the given set of items returns a contribution More...

IUIDataSourceType interface implementation
virtual const IUIObject &	CBamUIDataSourceType::GetDescr ()
	returns UI description of the type (label, icon etc.) More...

virtual IUIDataSource *	CBamUIDataSourceType::CreateDataSource ()
	factory method; create an Data Source instance More...

virtual bool	CBamUIDataSourceType::AutoCreateDefaultDataSource ()
	returns "true" if this type needs to create a default instance of the Data Source at start-up More...

IExtension interface implementation
virtual string	CBamUIDataSourceType::GetExtensionIdentifier () const
	returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this" More...

virtual string	CBamUIDataSourceType::GetExtensionLabel () const
	returns a displayable label for this extension ( please capitalize the key words - "My Extension" ) More...

IUIToolManager interface implementation
virtual void	CBamUILoadManager::SetServiceLocator (IServiceLocator *srv_locator)
	Sets / unsets Service Locator. More...

virtual void	CBamUILoadManager::SetParentWindow (wxWindow *parent)

virtual const IUIObject &	CBamUILoadManager::GetDescriptor () const
	Returns the object describing this tool (UI meta data). More...

virtual void	CBamUILoadManager::InitUI ()
	Initializes the Manager before using it in UI. More...

virtual void	CBamUILoadManager::CleanUI ()
	CleanUI() is called after the host finished using the manager. More...

virtual wxPanel *	CBamUILoadManager::GetCurrentPanel ()
	Return the panel corresponding to the current state of Tool Manager. More...

virtual bool	CBamUILoadManager::CanDo (EAction action)
	Indicates whether given transition is possible in the current state. More...

virtual bool	CBamUILoadManager::IsFinalState ()
	True if Tool Manager has reached its final state, i.e. More...

virtual bool	CBamUILoadManager::IsCompletedState ()
	Manager goes into "Complete" state when "Finish" button is pressed and all input data is gatherred and validated. More...

virtual bool	CBamUILoadManager::DoTransition (EAction action)
	Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false. More...

virtual IAppTask *	CBamUILoadManager::GetTask ()
	Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work. More...

IRegSettings interface implementation
virtual void	CBamUILoadManager::SetRegistryPath (const string &path)

virtual void	CBamUILoadManager::LoadSettings ()

virtual void	CBamUILoadManager::SaveSettings () const

Detailed Description

Typedef Documentation

◆ TBamFiles

typedef set<string> CBamLoadOptionPanel::TBamFiles

Definition at line 82 of file bam_load_option_panel.hpp.

◆ TBamWithIndexFiles

typedef vector<pair<string, string> > CBamLoadOptionPanel::TBamWithIndexFiles

Definition at line 83 of file bam_load_option_panel.hpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Control identifiers.

Enumerator
ID_CBAMLOADOPTIONPANEL
ID_BAM_INPUT
ID_BUTTON

Definition at line 122 of file bam_load_option_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_PARSING_TEXT
ID_PARSING_PROGRESS

Definition at line 129 of file bam_load_option_panel.hpp.

◆ EBamCommands

enum EBamCommands

commands introduced by BAM data source

Enumerator
eCmdLoadBamFile

Definition at line 62 of file bam_ui_data_source.hpp.

◆ ELBLASTCommands

enum ELBLASTCommands

commands introduced by BAM data source

Enumerator
eCmdLoadDB

Definition at line 59 of file lblast_ui_data_source.hpp.

◆ EParseState

enum CBamLoadOptionPanel::EParseState

private

Enumerator
eParseComplete
eParseRunning
eParseCanceling

Definition at line 165 of file bam_load_option_panel.hpp.

◆ EState [1/2]

enum CLBLASTUILoadManager::EState

protected

Enumerator
eInvalid
eSelectDir
eSelectProject
eCompleted

Definition at line 196 of file lblast_ui_data_source.hpp.

◆ EState [2/2]

enum CBamUILoadManager::EState

protected

Enumerator
eInvalid
eSelectBam
eBamIndex
eCoverageGraph
eRefSequences
eSelectProject
eCompleted

Definition at line 212 of file bam_ui_data_source.hpp.

Function Documentation

◆ AddDataLoader() [1/2]

string CLBLASTUIDataSource::AddDataLoader ( const objects::CUser_object & obj )

virtual

Add a new data loader to object manager.

If the data loader exists, return the existing one.

Returns: added data loader's name.

Implements IDataLoaderProvider.

Definition at line 247 of file lblast_ui_data_source.cpp.

References CLBLASTObjectLoader::AddDataLoader().

◆ AddDataLoader() [2/2]

string CBamUIDataSource::AddDataLoader ( const objects::CUser_object & obj )

virtual

Add a new data loader to object manager.

If the data loader exists, return the existing one.

Returns: added data loader's name.

Implements IDataLoaderProvider.

Definition at line 375 of file bam_ui_data_source.cpp.

References NStr::eNocase, CObjectManager::eNonDefault, eUnknown, file, CGencollIdMapperAdapter::GetIdMapper(), CGencollSvc::GetInstance(), CObjectManager::GetInstance(), info, kEmptyStr, kLoaderDataType_CSra_File, kLoaderDataType_File, kLoaderDataType_SRA, kLoaderDataType_SRZ, kLoaderPriority, CBAMDataLoader::SLoaderParams::m_BamFiles, CBAMDataLoader::SLoaderParams::m_DirPath, CBAMDataLoader::SLoaderParams::m_IdMapper, msg(), NCBI_THROW, CBAMDataLoader::RegisterInObjectManager(), CCSRADataLoader::RegisterInObjectManager(), AutoPtr< X, Del >::reset(), CBAMDataLoader::SetSkipEmptyPileupGraphsParamDefault(), NStr::StartsWith(), CBamUIDataSource::x_GetBamInputs(), CBamUIDataSource::x_GetCSraInputs(), CBamUIDataSource::x_GetSraAccession(), and CBamUIDataSource::x_GetSrzAccession().

◆ AddFilenames()

void CBamLoadOptionPanel::AddFilenames ( const wxArrayString & filenames )

Definition at line 672 of file bam_load_option_panel.cpp.

References filenames, i, CBamLoadOptionPanel::m_BamInput, str(), and wxT.

Referenced by CBamLoadOptionPanel::OnButtonClick().

◆ AutoCreateDefaultDataSource() [1/2]

bool CLBLASTUIDataSourceType::AutoCreateDefaultDataSource ( )

virtual

returns "true" if this type needs to create a default instance of the Data Source at start-up

Implements IUIDataSourceType.

Definition at line 281 of file lblast_ui_data_source.cpp.

◆ AutoCreateDefaultDataSource() [2/2]

bool CBamUIDataSourceType::AutoCreateDefaultDataSource ( )

virtual

returns "true" if this type needs to create a default instance of the Data Source at start-up

Implements IUIDataSourceType.

Definition at line 585 of file bam_ui_data_source.cpp.

◆ CanDo() [1/2]

bool CLBLASTUILoadManager::CanDo ( EAction action )

virtual

Indicates whether given transition is possible in the current state.

Implements IUIToolManager.

Definition at line 374 of file lblast_ui_data_source.cpp.

References _ASSERT, IUIToolManager::eBack, CLBLASTUILoadManager::eCompleted, IUIToolManager::eNext, CLBLASTUILoadManager::eSelectDir, CLBLASTUILoadManager::eSelectProject, and CLBLASTUILoadManager::m_State.

◆ CanDo() [2/2]

bool CBamUILoadManager::CanDo ( EAction action )

virtual

Indicates whether given transition is possible in the current state.

Implements IUIToolManager.

Definition at line 715 of file bam_ui_data_source.cpp.

References _ASSERT, IUIToolManager::eBack, CBamUILoadManager::eBamIndex, CBamUILoadManager::eCompleted, CBamUILoadManager::eCoverageGraph, IUIToolManager::eNext, CBamUILoadManager::eRefSequences, CBamUILoadManager::eSelectBam, CBamUILoadManager::eSelectProject, and CBamUILoadManager::m_State.

◆ CBamLoadOptionPanel() [1/2]

CBamLoadOptionPanel::CBamLoadOptionPanel ( )

Definition at line 104 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::Init().

◆ CBamLoadOptionPanel() [2/2]

CBamLoadOptionPanel::CBamLoadOptionPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CBAMLOADOPTIONPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxDefaultSize`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 109 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::Create(), CBamLoadOptionPanel::Init(), and ncbi::grid::netcache::search::fields::size.

◆ CBamUIDataSource()

CBamUIDataSource::CBamUIDataSource ( CBamUIDataSourceType & type )

Definition at line 227 of file bam_ui_data_source.cpp.

◆ CBamUIDataSourceType()

CBamUIDataSourceType::CBamUIDataSourceType ( )

CBamUIDataSourceType.

Definition at line 564 of file bam_ui_data_source.cpp.

References GetDefaultFileArtProvider(), kBAM_DS_Icon, wxFileArtProvider::RegisterFileAlias(), ToWxString(), and wxT.

◆ CBamUILoadManager()

CBamUILoadManager::CBamUILoadManager ( )

CBamUILoadManager.

Definition at line 607 of file bam_ui_data_source.cpp.

References CBamUILoadManager::m_Descriptor, SProjectSelectorParams::m_EnableDecideLater, CBamUILoadManager::m_ProjectParams, and CUIObject::SetLogEvent().

◆ CDropTarget()

CBamLoadOptionPanel::CDropTarget::CDropTarget ( CBamLoadOptionPanel & panel )

Definition at line 65 of file bam_load_option_panel.cpp.

◆ CLBLASTUIDataSource()

CLBLASTUIDataSource::CLBLASTUIDataSource ( CLBLASTUIDataSourceType & type )

Definition at line 100 of file lblast_ui_data_source.cpp.

◆ CLBLASTUIDataSourceType()

CLBLASTUIDataSourceType::CLBLASTUIDataSourceType ( )

CLBLASTUIDataSourceType.

Definition at line 260 of file lblast_ui_data_source.cpp.

References GetDefaultFileArtProvider(), kLBLAST_DS_Icon, wxFileArtProvider::RegisterFileAlias(), ToWxString(), and wxT.

◆ CLBLASTUILoadManager()

CLBLASTUILoadManager::CLBLASTUILoadManager ( )

CLBLASTUILoadManager.

Definition at line 303 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::m_Descriptor, SProjectSelectorParams::m_EnableDecideLater, CLBLASTUILoadManager::m_ProjectParams, and CUIObject::SetLogEvent().

◆ CleanUI() [1/2]

void CLBLASTUILoadManager::CleanUI ( )

virtual

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

This function shall free resources associated with the session and reset internal state.

Implements IUIToolManager.

Definition at line 340 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::eInvalid, CLBLASTUILoadManager::m_ParamsPanel, CLBLASTUILoadManager::m_ProjectSelPanel, and CLBLASTUILoadManager::m_State.

◆ CleanUI() [2/2]

void CBamUILoadManager::CleanUI ( )

virtual

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

This function shall free resources associated with the session and reset internal state.

Implements IUIToolManager.

Definition at line 647 of file bam_ui_data_source.cpp.

References CBamUILoadManager::eInvalid, CBamLoadOptionPanel::GetInput(), CBamIndexingPanel::GetSamtoolsPath(), CBamUILoadManager::m_GraphPanel, CBamUILoadManager::m_IndexingPanel, CBamUILoadManager::m_OptionPanel, CBamUILoadManager::m_ProjectSelPanel, CBamUILoadManager::m_RefSequencesPanel, CBamUILoadManager::m_SamtoolsPath, CBamUILoadManager::m_SavedInput, CBamUILoadManager::m_State, and NULL.

◆ Close() [1/2]

bool CLBLASTUIDataSource::Close ( void )

virtual

Implements IUIDataSource.

Definition at line 208 of file lblast_ui_data_source.cpp.

References CExtensionRegistry::GetInstance(), kAppExpCmdExtPoint, and CLBLASTUIDataSource::m_Open.

◆ Close() [2/2]

bool CBamUIDataSource::Close ( void )

virtual

Implements IUIDataSource.

Definition at line 335 of file bam_ui_data_source.cpp.

References CExtensionRegistry::GetInstance(), kAppExpCmdExtPoint, and CBamUIDataSource::m_Open.

◆ Create()

bool CBamLoadOptionPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CBAMLOADOPTIONPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxDefaultSize`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 116 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::CreateControls(), and ncbi::grid::netcache::search::fields::size.

Referenced by CBamLoadOptionPanel::CBamLoadOptionPanel().

◆ CreateControls()

void CBamLoadOptionPanel::CreateControls ( )

Definition at line 151 of file bam_load_option_panel.cpp.

References _, CBamLoadOptionPanel::ID_BAM_INPUT, CBamLoadOptionPanel::ID_BUTTON, CBamLoadOptionPanel::ID_PARSING_PROGRESS, CBamLoadOptionPanel::ID_PARSING_TEXT, CBamLoadOptionPanel::m_BamInput, CBamLoadOptionPanel::m_DefStyle, CBamLoadOptionPanel::m_ErrStyle, CBamLoadOptionPanel::m_MainSizer, CBamLoadOptionPanel::m_ParseProgressSizer, wxID_ANY, and wxT.

Referenced by CBamLoadOptionPanel::Create().

◆ CreateDataSource() [1/2]

IUIDataSource * CLBLASTUIDataSourceType::CreateDataSource ( )

virtual

factory method; create an Data Source instance

Implements IUIDataSourceType.

Definition at line 275 of file lblast_ui_data_source.cpp.

◆ CreateDataSource() [2/2]

IUIDataSource * CBamUIDataSourceType::CreateDataSource ( )

virtual

factory method; create an Data Source instance

Implements IUIDataSourceType.

Definition at line 579 of file bam_ui_data_source.cpp.

◆ CreateEvtHandler() [1/2]

wxEvtHandler * CLBLASTUIDataSource::CreateEvtHandler ( )

virtual

Reimplemented from IUIDataSource.

Definition at line 239 of file lblast_ui_data_source.cpp.

References CLBLASTUIDataSource::m_SrvLocator.

◆ CreateEvtHandler() [2/2]

wxEvtHandler * CBamUIDataSource::CreateEvtHandler ( )

virtual

Reimplemented from IUIDataSource.

Definition at line 366 of file bam_ui_data_source.cpp.

References CBamUIDataSource::m_SrvLocator.

◆ DoTransition() [1/2]

bool CLBLASTUILoadManager::DoTransition ( EAction action )

virtual

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Implements IUIToolManager.

Definition at line 402 of file lblast_ui_data_source.cpp.

References _ASSERT, IUIToolManager::eBack, CLBLASTUILoadManager::eCompleted, IUIToolManager::eNext, CLBLASTUILoadManager::eSelectDir, CLBLASTUILoadManager::eSelectProject, CLBLASTParamsPanel::GetData(), CLBLASTUILoadManager::m_LBLASTParams, CLBLASTUILoadManager::m_ParamsPanel, CLBLASTUILoadManager::m_ProjectSelPanel, CLBLASTUILoadManager::m_State, CProjectSelectorPanel::TransferDataFromWindow(), and CLBLASTParamsPanel::TransferDataFromWindow().

◆ DoTransition() [2/2]

bool CBamUILoadManager::DoTransition ( EAction action )

virtual

Performs transition if possible and returns true, otherwise the function shall warn the user about the problem preventing the transition (such as insufficient or invalid input) and return false.

Typically this function would take user input from the current panel, validate the input and go to the next state creating new UI panel if needed.

Implements IUIToolManager.

Definition at line 746 of file bam_ui_data_source.cpp.

◆ EditProperties() [1/2]

void CLBLASTUIDataSource::EditProperties ( )

virtual

Definition at line 223 of file lblast_ui_data_source.cpp.

◆ EditProperties() [2/2]

void CBamUIDataSource::EditProperties ( )

virtual

Definition at line 350 of file bam_ui_data_source.cpp.

◆ GetBamFilePath()

string CBamLoadOptionPanel::GetBamFilePath ( ) const

Definition at line 574 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_BamFiles, and CDirEntry::SplitPath().

Referenced by CBamUILoadManager::GetCurrentPanel().

◆ GetBamFiles()

const CBamLoadOptionPanel::TBamWithIndexFiles & CBamLoadOptionPanel::GetBamFiles ( ) const

Definition at line 585 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_BamFiles.

Referenced by CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), and CBamUILoadManager::GetTask().

◆ GetBitmapResource()

wxBitmap CBamLoadOptionPanel::GetBitmapResource ( const wxString & name )

Retrieves bitmap resources.

Definition at line 618 of file bam_load_option_panel.cpp.

◆ GetCSraFiles()

const CBamLoadOptionPanel::TBamFiles & CBamLoadOptionPanel::GetCSraFiles ( ) const

Definition at line 592 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_CSraFiles.

Referenced by CBamUILoadManager::DoTransition(), and CBamUILoadManager::GetTask().

◆ GetCurrentPanel() [1/2]

wxPanel * CLBLASTUILoadManager::GetCurrentPanel ( )

virtual

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

Implements IUIToolManager.

Definition at line 348 of file lblast_ui_data_source.cpp.

◆ GetCurrentPanel() [2/2]

wxPanel * CBamUILoadManager::GetCurrentPanel ( )

virtual

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

Implements IUIToolManager.

Definition at line 664 of file bam_ui_data_source.cpp.

◆ GetDefaultCommand() [1/2]

int CLBLASTUIDataSource::GetDefaultCommand ( void )

virtual

Reimplemented from IUIDataSource.

Definition at line 235 of file lblast_ui_data_source.cpp.

References eCmdLoadDB.

◆ GetDefaultCommand() [2/2]

int CBamUIDataSource::GetDefaultCommand ( void )

virtual

Reimplemented from IUIDataSource.

Definition at line 362 of file bam_ui_data_source.cpp.

References eCmdLoadBamFile.

◆ GetDescr() [1/4]

const IUIObject & CLBLASTUIDataSource::GetDescr ( )

virtual

returns UI description of the object (label, icon etc.)

Implements IUIDataSource.

Definition at line 174 of file lblast_ui_data_source.cpp.

References CLBLASTUIDataSource::m_Descr.

◆ GetDescr() [2/4]

const IUIObject & CLBLASTUIDataSourceType::GetDescr ( )

virtual

returns UI description of the type (label, icon etc.)

Implements IUIDataSourceType.

Definition at line 269 of file lblast_ui_data_source.cpp.

References CLBLASTUIDataSourceType::m_Descr.

◆ GetDescr() [3/4]

const IUIObject & CBamUIDataSource::GetDescr ( )

virtual

returns UI description of the object (label, icon etc.)

Implements IUIDataSource.

Definition at line 301 of file bam_ui_data_source.cpp.

References CBamUIDataSource::m_Descr.

◆ GetDescr() [4/4]

const IUIObject & CBamUIDataSourceType::GetDescr ( )

virtual

returns UI description of the type (label, icon etc.)

Implements IUIDataSourceType.

Definition at line 573 of file bam_ui_data_source.cpp.

References CBamUIDataSourceType::m_Descr.

◆ GetDescriptor() [1/2]

const IUIObject & CLBLASTUILoadManager::GetDescriptor ( ) const

virtual

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

Implements IUIToolManager.

Definition at line 328 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::m_Descriptor.

◆ GetDescriptor() [2/2]

const IUIObject & CBamUILoadManager::GetDescriptor ( ) const

virtual

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

Implements IUIToolManager.

Definition at line 635 of file bam_ui_data_source.cpp.

References CBamUILoadManager::m_Descriptor.

◆ GetExtensionIdentifier() [1/4]

string CLBLASTUIDataSource::GetExtensionIdentifier ( ) const

virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 113 of file lblast_ui_data_source.cpp.

◆ GetExtensionIdentifier() [2/4]

string CLBLASTUIDataSourceType::GetExtensionIdentifier ( ) const

virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 287 of file lblast_ui_data_source.cpp.

◆ GetExtensionIdentifier() [3/4]

string CBamUIDataSource::GetExtensionIdentifier ( ) const

virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 240 of file bam_ui_data_source.cpp.

◆ GetExtensionIdentifier() [4/4]

string CBamUIDataSourceType::GetExtensionIdentifier ( ) const

virtual

returns the unique human-readable identifier for the extension the id should use lowercase letters separated by underscores - "like_this"

Implements IExtension.

Definition at line 591 of file bam_ui_data_source.cpp.

Referenced by CBamLoadingJob::x_CreateDataLoader(), and CBamLoadingJob::x_CreateProjectItems().

◆ GetExtensionLabel() [1/4]

string CLBLASTUIDataSource::GetExtensionLabel ( ) const

virtual

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

Implements IExtension.

Definition at line 119 of file lblast_ui_data_source.cpp.

◆ GetExtensionLabel() [2/4]

string CLBLASTUIDataSourceType::GetExtensionLabel ( ) const

virtual

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

Implements IExtension.

Definition at line 294 of file lblast_ui_data_source.cpp.

References CUIObject::GetLabel(), and CLBLASTUIDataSourceType::m_Descr.

◆ GetExtensionLabel() [3/4]

string CBamUIDataSource::GetExtensionLabel ( ) const

virtual

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

Implements IExtension.

Definition at line 246 of file bam_ui_data_source.cpp.

◆ GetExtensionLabel() [4/4]

string CBamUIDataSourceType::GetExtensionLabel ( ) const

virtual

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

Implements IExtension.

Definition at line 598 of file bam_ui_data_source.cpp.

References CUIObject::GetLabel(), and CBamUIDataSourceType::m_Descr.

◆ GetIconResource()

wxIcon CBamLoadOptionPanel::GetIconResource ( const wxString & name )

Retrieves icon resources.

Definition at line 628 of file bam_load_option_panel.cpp.

◆ GetInput()

string CBamLoadOptionPanel::GetInput ( ) const

Definition at line 202 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_BamInput, and string.

Referenced by CBamUILoadManager::CleanUI(), and CBamUILoadManager::SaveSettings().

◆ GetLoaderName() [1/2]

string CLBLASTUIDataSource::GetLoaderName ( const objects::CUser_object & obj ) const

virtual

Get the data loader's name based on input object.

Implements IDataLoaderProvider.

Definition at line 252 of file lblast_ui_data_source.cpp.

References CLBLASTObjectLoader::GetLoaderName().

◆ GetLoaderName() [2/2]

string CBamUIDataSource::GetLoaderName ( const objects::CUser_object & obj ) const

virtual

Get the data loader's name based on input object.

Implements IDataLoaderProvider.

Definition at line 465 of file bam_ui_data_source.cpp.

References file, CBAMDataLoader::GetLoaderNameFromArgs(), CCSRADataLoader::GetLoaderNameFromArgs(), kLoaderDataType_CSra_File, kLoaderDataType_File, kLoaderDataType_SRA, kLoaderDataType_SRZ, CBamUIDataSource::x_GetBamInputs(), CBamUIDataSource::x_GetCSraInputs(), CBamUIDataSource::x_GetSraAccession(), and CBamUIDataSource::x_GetSrzAccession().

◆ GetLoadManager() [1/2]

IUIToolManager * CLBLASTUIDataSource::GetLoadManager ( )

virtual

Implements IUIDataSource.

Definition at line 229 of file lblast_ui_data_source.cpp.

◆ GetLoadManager() [2/2]

IUIToolManager * CBamUIDataSource::GetLoadManager ( )

virtual

Implements IUIDataSource.

Definition at line 356 of file bam_ui_data_source.cpp.

◆ GetMenu() [1/2]

IExplorerItemCmdContributor::TContribution CLBLASTUIDataSource::GetMenu	(	wxTreeCtrl &	treeCtrl,
		PT::TItems &	items
	)

virtual

for the given set of items returns a contribution

Implements IExplorerItemCmdContributor.

Definition at line 131 of file lblast_ui_data_source.cpp.

References CUICommandRegistry::AppendMenuItem(), eCmdLoadDB, PT::eDataSource, PT::TPTItem< TData, Type >::GetData(), CUICommandRegistry::GetInstance(), CRef< C, Locker >::GetPointer(), PT::CItem::GetType(), CLBLASTUIDataSource::m_SrvLocator, NULL, and wxT.

◆ GetMenu() [2/2]

IExplorerItemCmdContributor::TContribution CBamUIDataSource::GetMenu	(	wxTreeCtrl &	treeCtrl,
		PT::TItems &	items
	)

virtual

for the given set of items returns a contribution

Implements IExplorerItemCmdContributor.

Definition at line 258 of file bam_ui_data_source.cpp.

References CUICommandRegistry::AppendMenuItem(), eCmdLoadBamFile, PT::eDataSource, PT::TPTItem< TData, Type >::GetData(), CUICommandRegistry::GetInstance(), CRef< C, Locker >::GetPointer(), PT::CItem::GetType(), CBamUIDataSource::m_SrvLocator, NULL, and wxT.

◆ GetSraAccs()

const CBamLoadOptionPanel::TBamFiles & CBamLoadOptionPanel::GetSraAccs ( ) const

Definition at line 606 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_SraAccs.

Referenced by CBamUILoadManager::DoTransition(), and CBamUILoadManager::GetTask().

◆ GetSrzAccs()

const CBamLoadOptionPanel::TBamFiles & CBamLoadOptionPanel::GetSrzAccs ( ) const

Definition at line 599 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_SrzAccs.

Referenced by CBamUILoadManager::DoTransition(), and CBamUILoadManager::GetTask().

◆ GetTask() [1/2]

IAppTask * CLBLASTUILoadManager::GetTask ( )

virtual

Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work.

Implements IUIToolManager.

Definition at line 436 of file lblast_ui_data_source.cpp.

References CProjectSelectorPanel::GetParams(), IServiceLocator::GetServiceByType(), SProjectSelectorParams::m_CreateFolder, SProjectSelectorParams::m_FolderName, CLBLASTUILoadManager::m_LBLASTParams, CLBLASTUILoadManager::m_ProjectParams, CLBLASTUILoadManager::m_ProjectSelPanel, CLBLASTUILoadManager::m_SrvLocator, and SProjectSelectorParams::ToLoadingOptions().

◆ GetTask() [2/2]

IAppTask * CBamUILoadManager::GetTask ( )

virtual

Once parameters are gathered and validated this function is called to produce the final Task object that will be executed to do the actual computational work.

Implements IUIToolManager.

Definition at line 835 of file bam_ui_data_source.cpp.

◆ GetType() [1/2]

IUIDataSourceType & CLBLASTUIDataSource::GetType ( void ) const

virtual

Implements IUIDataSource.

Definition at line 168 of file lblast_ui_data_source.cpp.

References CLBLASTUIDataSource::m_Type.

◆ GetType() [2/2]

IUIDataSourceType & CBamUIDataSource::GetType ( void ) const

virtual

Implements IUIDataSource.

Definition at line 295 of file bam_ui_data_source.cpp.

References CBamUIDataSource::m_Type.

◆ HasBamFile()

bool CBamLoadOptionPanel::HasBamFile ( ) const

Definition at line 256 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_BamFiles.

Referenced by CBamUILoadManager::DoTransition().

◆ Init()

void CBamLoadOptionPanel::Init ( void )

Definition at line 139 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_BamInput, CBamLoadOptionPanel::m_ErrNum, CBamLoadOptionPanel::m_InputNum, CBamLoadOptionPanel::m_MainSizer, CBamLoadOptionPanel::m_ParseProgressSizer, and NULL.

Referenced by CBamLoadOptionPanel::CBamLoadOptionPanel().

◆ InitUI() [1/2]

void CLBLASTUILoadManager::InitUI ( )

virtual

Initializes the Manager before using it in UI.

This function shall reset Internal state of the tool.

Implements IUIToolManager.

Definition at line 334 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::eSelectDir, and CLBLASTUILoadManager::m_State.

◆ InitUI() [2/2]

void CBamUILoadManager::InitUI ( )

virtual

Initializes the Manager before using it in UI.

This function shall reset Internal state of the tool.

Implements IUIToolManager.

Definition at line 641 of file bam_ui_data_source.cpp.

References CBamUILoadManager::eSelectBam, and CBamUILoadManager::m_State.

◆ IsCompletedState() [1/2]

bool CLBLASTUILoadManager::IsCompletedState ( )

virtual

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

Typically this is the last state after Final state. This state does not have an associated UI panel. When manager reaches the �Completed� state the framework hides the dialog and calls GetTask() function.

Implements IUIToolManager.

Definition at line 396 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::eCompleted, and CLBLASTUILoadManager::m_State.

◆ IsCompletedState() [2/2]

bool CBamUILoadManager::IsCompletedState ( )

virtual

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

Typically this is the last state after Final state. This state does not have an associated UI panel. When manager reaches the �Completed� state the framework hides the dialog and calls GetTask() function.

Implements IUIToolManager.

Definition at line 740 of file bam_ui_data_source.cpp.

References CBamUILoadManager::eCompleted, and CBamUILoadManager::m_State.

◆ IsFinalState() [1/2]

bool CLBLASTUILoadManager::IsFinalState ( )

virtual

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

the last page (panel) in the sequence is displayed and "Finish" button is shown. The framework calls this function to decide whether �Finish� or �Next� button needs to be shown.

Implements IUIToolManager.

Definition at line 390 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::eSelectProject, and CLBLASTUILoadManager::m_State.

◆ IsFinalState() [2/2]

bool CBamUILoadManager::IsFinalState ( )

virtual

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

the last page (panel) in the sequence is displayed and "Finish" button is shown. The framework calls this function to decide whether �Finish� or �Next� button needs to be shown.

Implements IUIToolManager.

Definition at line 734 of file bam_ui_data_source.cpp.

References CBamUILoadManager::eSelectProject, and CBamUILoadManager::m_State.

◆ IsInputValid()

bool CBamLoadOptionPanel::IsInputValid ( )

Definition at line 222 of file bam_load_option_panel.cpp.

References BAM_LOADER_ERR, EMPTY_INPUT, CBamLoadOptionPanel::eParseCanceling, CBamLoadOptionPanel::eParseRunning, INVALID_INPUT, CBamLoadOptionPanel::m_ErrNum, CBamLoadOptionPanel::m_InputNum, CBamLoadOptionPanel::m_State, NStr::SizetToString(), ToWxString(), and wxT.

Referenced by CBamUILoadManager::DoTransition().

◆ IsOpen() [1/2]

bool CLBLASTUIDataSource::IsOpen ( )

virtual

a Data source needs to be open before use and closed after.

Implements IUIDataSource.

Definition at line 180 of file lblast_ui_data_source.cpp.

References CLBLASTUIDataSource::m_Open.

◆ IsOpen() [2/2]

bool CBamUIDataSource::IsOpen ( )

virtual

a Data source needs to be open before use and closed after.

Implements IUIDataSource.

Definition at line 307 of file bam_ui_data_source.cpp.

References CBamUIDataSource::m_Open.

◆ LoadSettings() [1/2]

void CLBLASTUILoadManager::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 474 of file lblast_ui_data_source.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kProjectParamsTag, CLBLASTLoadParams::LoadSettings(), SProjectSelectorParams::LoadSettings(), CLBLASTUILoadManager::m_LBLASTParams, CLBLASTUILoadManager::m_ProjectParams, and CLBLASTUILoadManager::m_RegPath.

◆ LoadSettings() [2/2]

void CBamUILoadManager::LoadSettings ( )

virtual

◆ OnBamInputTextUpdated()

void CBamLoadOptionPanel::OnBamInputTextUpdated ( wxCommandEvent & event )

wxEVT_COMMAND_TEXT_UPDATED event handler for ID_BAM_INPUT

Definition at line 689 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::m_BamInput, CBamLoadOptionPanel::m_TextChanged, CBamLoadOptionPanel::m_Timer, CBamLoadOptionPanel::m_UpdatingStyle, and CRichTextCtrl::RemoveFormatting().

◆ OnButtonClick()

void CBamLoadOptionPanel::OnButtonClick ( wxCommandEvent & event )

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON

Definition at line 642 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::AddFilenames(), filenames, CBamLoadOptionPanel::m_BamInput, CDirEntry::SplitPath(), and wxT.

◆ OnData()

wxDragResult CBamLoadOptionPanel::CDropTarget::OnData	(	wxCoord	x,
		wxCoord	y,
		wxDragResult	def
	)

virtual

Definition at line 72 of file bam_load_option_panel.cpp.

References filenames.

◆ OnTimer()

void CBamLoadOptionPanel::OnTimer ( wxTimerEvent & event )

Definition at line 709 of file bam_load_option_panel.cpp.

References CBamLoadOptionPanel::x_ValidateInput().

◆ Open() [1/2]

bool CLBLASTUIDataSource::Open ( )

virtual

Prepares Data Source for use, any initialization that can be potentially time-consuming or may require error handling shall be done in this function, not in a constructor.

Is initialization takes more than 1-2 sec it shall be done on a background thread (see App Job Dispatcher).

Implements IUIDataSource.

Definition at line 188 of file lblast_ui_data_source.cpp.

References Error(), CExtensionRegistry::GetInstance(), kAppExpCmdExtPoint, LOG_POST, CLBLASTUIDataSource::m_Open, CStopWatch::Start(), and sw.

◆ Open() [2/2]

bool CBamUIDataSource::Open ( )

virtual

Prepares Data Source for use, any initialization that can be potentially time-consuming or may require error handling shall be done in this function, not in a constructor.

Is initialization takes more than 1-2 sec it shall be done on a background thread (see App Job Dispatcher).

Implements IUIDataSource.

Definition at line 315 of file bam_ui_data_source.cpp.

References Error(), CExtensionRegistry::GetInstance(), kAppExpCmdExtPoint, LOG_POST, CBamUIDataSource::m_Open, CStopWatch::Start(), and sw.

◆ SaveSettings() [1/2]

void CLBLASTUILoadManager::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 462 of file lblast_ui_data_source.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kProjectParamsTag, CLBLASTUILoadManager::m_LBLASTParams, CLBLASTUILoadManager::m_ProjectParams, CLBLASTUILoadManager::m_RegPath, CLBLASTLoadParams::SaveSettings(), and SProjectSelectorParams::SaveSettings().

◆ SaveSettings() [2/2]

void CBamUILoadManager::SaveSettings ( ) const

virtual

◆ SetFilenames()

void CBamLoadOptionPanel::SetFilenames ( const wxArrayString & filenames )

Definition at line 660 of file bam_load_option_panel.cpp.

References filenames, i, CBamLoadOptionPanel::m_BamInput, str(), and wxT.

◆ SetIndexFiles()

bool CBamLoadOptionPanel::SetIndexFiles ( )

Definition at line 304 of file bam_load_option_panel.cpp.

References NStr::eNocase, file, CBamLoadOptionPanel::m_BamFiles, CDirEntry::SplitPath(), NStr::StartsWith(), and x_IsUrlAccessible().

Referenced by CBamUILoadManager::DoTransition().

◆ SetInput()

void CBamLoadOptionPanel::SetInput ( const string & input )

Definition at line 208 of file bam_load_option_panel.cpp.

References _ASSERT, input(), and CBamLoadOptionPanel::m_BamInput.

Referenced by CBamUILoadManager::GetCurrentPanel().

◆ SetParentWindow() [1/2]

void CLBLASTUILoadManager::SetParentWindow ( wxWindow * parent )

virtual

Implements IUIToolManager.

Definition at line 322 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::m_ParentWindow.

◆ SetParentWindow() [2/2]

void CBamUILoadManager::SetParentWindow ( wxWindow * parent )

virtual

Implements IUIToolManager.

Definition at line 629 of file bam_ui_data_source.cpp.

References CBamUILoadManager::m_ParentWindow.

◆ SetRegistryPath() [1/2]

void CLBLASTUILoadManager::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 450 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::m_LBLASTParams, CLBLASTUILoadManager::m_RegPath, and CLBLASTLoadParams::SetRegistryPath().

◆ SetRegistryPath() [2/2]

void CBamUILoadManager::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 876 of file bam_ui_data_source.cpp.

References CBamUILoadManager::m_RegPath.

◆ SetServiceLocator() [1/4]

void CLBLASTUIDataSource::SetServiceLocator ( IServiceLocator * locator )

virtual

Implements IServiceLocatorConsumer.

Definition at line 125 of file lblast_ui_data_source.cpp.

References CLBLASTUIDataSource::m_SrvLocator.

◆ SetServiceLocator() [2/4]

void CBamUIDataSource::SetServiceLocator ( IServiceLocator * locator )

virtual

Implements IServiceLocatorConsumer.

Definition at line 252 of file bam_ui_data_source.cpp.

References CBamUIDataSource::m_SrvLocator.

◆ SetServiceLocator() [3/4]

void CLBLASTUILoadManager::SetServiceLocator ( IServiceLocator * srv_locator )

virtual

Sets / unsets Service Locator.

Tool Manager can use the locator to obtain the services necessary services.

Implements IUIToolManager.

Definition at line 316 of file lblast_ui_data_source.cpp.

References CLBLASTUILoadManager::m_SrvLocator.

◆ SetServiceLocator() [4/4]

void CBamUILoadManager::SetServiceLocator ( IServiceLocator * srv_locator )

virtual

Sets / unsets Service Locator.

Tool Manager can use the locator to obtain the services necessary services.

Implements IUIToolManager.

Definition at line 623 of file bam_ui_data_source.cpp.

References CBamUILoadManager::m_SrvLocator.

◆ ShowToolTips()

bool CBamLoadOptionPanel::ShowToolTips ( )

static

Definition at line 612 of file bam_load_option_panel.cpp.

◆ x_GetBamInputs()

bool CBamUIDataSource::x_GetBamInputs	(	const objects::CUser_object &	obj,
		string &	path,
		string &	files,
		string &	idx,
		string &	target_assm
	)		const

private

Definition at line 502 of file bam_ui_data_source.cpp.

References file, CUser_field_Base::GetData(), CUser_field_Base::C_Data::GetStr(), kBamFile, kBamIndexFile, kBamPath, and kTargetAssm.

Referenced by CBamUIDataSource::AddDataLoader(), and CBamUIDataSource::GetLoaderName().

◆ x_GetBamRefSeqs()

void CBamUILoadManager::x_GetBamRefSeqs	(	const CBamLoadOptionPanel::TBamWithIndexFiles &	files,
		const string &	mappedAcc
	)

protected

Definition at line 945 of file bam_ui_data_source.cpp.

References CRef< C, Locker >::Empty(), eNoOwnership, CGencollIdMapperAdapter::GetIdMapper(), CGencollSvc::GetInstance(), CBamDb::GetRefSeq_id(), CSeq_id::GetSeqIdString(), set< Key, Compare >::insert(), CBamUILoadManager::m_RefSeqIds, and CBamDb::SetIdMapper().

Referenced by CBamUILoadManager::DoTransition().

◆ x_GetCSraInputs()

bool CBamUIDataSource::x_GetCSraInputs	(	const objects::CUser_object &	obj,
		string &	file
	)		const

private

Definition at line 536 of file bam_ui_data_source.cpp.

References file, CUser_field_Base::GetData(), CUser_field_Base::C_Data::GetStr(), and kCSraFile.

Referenced by CBamUIDataSource::AddDataLoader(), and CBamUIDataSource::GetLoaderName().

◆ x_GetCSraRefSeqs()

void CBamUILoadManager::x_GetCSraRefSeqs ( const CBamLoadOptionPanel::TBamFiles & accessions )

protected

Definition at line 975 of file bam_ui_data_source.cpp.

References CRef< C, Locker >::Empty(), ITERATE, CBamUILoadManager::m_RefSeqIds, and s_GetRefSeq_id().

Referenced by CBamUILoadManager::DoTransition().

◆ x_GetSraAccession()

bool CBamUIDataSource::x_GetSraAccession	(	const objects::CUser_object &	obj,
		string &	sra
	)		const

private

Definition at line 551 of file bam_ui_data_source.cpp.

References CUser_field_Base::GetData(), CUser_field_Base::C_Data::GetStr(), and kSraAccession.

Referenced by CBamUIDataSource::AddDataLoader(), and CBamUIDataSource::GetLoaderName().

◆ x_GetSrzAccession()

bool CBamUIDataSource::x_GetSrzAccession	(	const objects::CUser_object &	obj,
		string &	srz
	)		const

private

Definition at line 524 of file bam_ui_data_source.cpp.

References CUser_field_Base::GetData(), CUser_field_Base::C_Data::GetStr(), and kSrzAccession.

Referenced by CBamUIDataSource::AddDataLoader(), and CBamUIDataSource::GetLoaderName().

◆ x_GetSrzRefSeqs()

void CBamUILoadManager::x_GetSrzRefSeqs ( const CBamLoadOptionPanel::TBamFiles & accessions )

protected

Definition at line 989 of file bam_ui_data_source.cpp.

References CSeq_id_Base::e_Local, CSrzPath::FindAccPath(), in(), ITERATE, CBamUILoadManager::m_RefSeqIds, CDirEntry::MakePath(), NStr::Split(), and SRZ_CONFIG_NAME.

Referenced by CBamUILoadManager::DoTransition().

◆ x_ValidateInput()

void CBamLoadOptionPanel::x_ValidateInput ( )

protected

Definition at line 470 of file bam_load_option_panel.cpp.

Referenced by CBamLoadOptionPanel::OnTimer().

◆ ~CBamLoadOptionPanel()

CBamLoadOptionPanel::~CBamLoadOptionPanel ( )

Definition at line 132 of file bam_load_option_panel.cpp.

◆ ~CBamUIDataSource()

CBamUIDataSource::~CBamUIDataSource ( )

Definition at line 235 of file bam_ui_data_source.cpp.

◆ ~CLBLASTUIDataSource()

CLBLASTUIDataSource::~CLBLASTUIDataSource ( )

Definition at line 108 of file lblast_ui_data_source.cpp.

Variable Documentation

◆ m_AssmAcc [1/2]

string CLBLASTUILoadManager::m_AssmAcc

protected

Definition at line 212 of file lblast_ui_data_source.hpp.

◆ m_AssmAcc [2/2]

string CBamUILoadManager::m_AssmAcc

protected

Definition at line 237 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::DoTransition(), and CBamUILoadManager::GetTask().

◆ m_BamFiles

TBamWithIndexFiles CBamLoadOptionPanel::m_BamFiles

private

Definition at line 180 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::GetBamFilePath(), CBamLoadOptionPanel::GetBamFiles(), CBamLoadOptionPanel::HasBamFile(), CBamLoadOptionPanel::SetIndexFiles(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_BamInput

CRichTextCtrl* CBamLoadOptionPanel::m_BamInput

Definition at line 119 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::AddFilenames(), CBamLoadOptionPanel::CreateControls(), CBamLoadOptionPanel::GetInput(), CBamLoadOptionPanel::Init(), CBamLoadOptionPanel::OnBamInputTextUpdated(), CBamLoadOptionPanel::OnButtonClick(), CBamLoadOptionPanel::SetFilenames(), CBamLoadOptionPanel::SetInput(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_CSraFiles

TBamFiles CBamLoadOptionPanel::m_CSraFiles

private

Definition at line 181 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::GetCSraFiles(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_DefStyle

wxTextAttr CBamLoadOptionPanel::m_DefStyle

private

Definition at line 176 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::CreateControls(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_Descr [1/4]

CUIObject CLBLASTUIDataSource::m_Descr

protected

Definition at line 125 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUIDataSource::GetDescr().

◆ m_Descr [2/4]

CUIObject CLBLASTUIDataSourceType::m_Descr

protected

Definition at line 158 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUIDataSourceType::GetDescr(), and CLBLASTUIDataSourceType::GetExtensionLabel().

◆ m_Descr [3/4]

CUIObject CBamUIDataSource::m_Descr

protected

Definition at line 136 of file bam_ui_data_source.hpp.

Referenced by CBamUIDataSource::GetDescr().

◆ m_Descr [4/4]

CUIObject CBamUIDataSourceType::m_Descr

protected

Definition at line 169 of file bam_ui_data_source.hpp.

Referenced by CBamUIDataSourceType::GetDescr(), and CBamUIDataSourceType::GetExtensionLabel().

◆ m_Descriptor [1/2]

CUIObject CLBLASTUILoadManager::m_Descriptor

protected

Definition at line 207 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::CLBLASTUILoadManager(), and CLBLASTUILoadManager::GetDescriptor().

◆ m_Descriptor [2/2]

CUIObject CBamUILoadManager::m_Descriptor

protected

Definition at line 231 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CBamUILoadManager(), and CBamUILoadManager::GetDescriptor().

◆ m_ErrNum

size_t CBamLoadOptionPanel::m_ErrNum

private

number of token with errors

Definition at line 179 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::Init(), CBamLoadOptionPanel::IsInputValid(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_ErrStyle

wxTextAttr CBamLoadOptionPanel::m_ErrStyle

private

Definition at line 177 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::CreateControls(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_GraphPanel

CBamCoverageGraphPanel* CBamUILoadManager::m_GraphPanel

protected

Definition at line 243 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::LoadSettings(), and CBamUILoadManager::SaveSettings().

◆ m_IndexingPanel

CBamIndexingPanel* CBamUILoadManager::m_IndexingPanel

protected

Definition at line 241 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::GetTask(), and CBamUILoadManager::SaveSettings().

◆ m_InputNum

size_t CBamLoadOptionPanel::m_InputNum

private

total number of valid inputs

Definition at line 178 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::Init(), CBamLoadOptionPanel::IsInputValid(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_LBLASTParams

CLBLASTLoadParams CLBLASTUILoadManager::m_LBLASTParams

protected

Definition at line 219 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::DoTransition(), CLBLASTUILoadManager::GetCurrentPanel(), CLBLASTUILoadManager::GetTask(), CLBLASTUILoadManager::LoadSettings(), CLBLASTUILoadManager::SaveSettings(), and CLBLASTUILoadManager::SetRegistryPath().

◆ m_MainSizer

wxBoxSizer* CBamLoadOptionPanel::m_MainSizer

Definition at line 118 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::CreateControls(), CBamLoadOptionPanel::Init(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_Open [1/2]

bool CLBLASTUIDataSource::m_Open

protected

Definition at line 129 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUIDataSource::Close(), CLBLASTUIDataSource::IsOpen(), and CLBLASTUIDataSource::Open().

◆ m_Open [2/2]

bool CBamUIDataSource::m_Open

protected

Definition at line 140 of file bam_ui_data_source.hpp.

Referenced by CBamUIDataSource::Close(), CBamUIDataSource::IsOpen(), and CBamUIDataSource::Open().

◆ m_OptionPanel

CBamLoadOptionPanel* CBamUILoadManager::m_OptionPanel

protected

Definition at line 240 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::GetTask(), and CBamUILoadManager::SaveSettings().

◆ m_Panel

CBamLoadOptionPanel& CBamLoadOptionPanel::CDropTarget::m_Panel

protected

Definition at line 161 of file bam_load_option_panel.hpp.

◆ m_ParamsPanel

CLBLASTParamsPanel* CLBLASTUILoadManager::m_ParamsPanel

protected

Definition at line 215 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::CleanUI(), CLBLASTUILoadManager::DoTransition(), and CLBLASTUILoadManager::GetCurrentPanel().

◆ m_ParentWindow [1/2]

wxWindow* CLBLASTUILoadManager::m_ParentWindow

protected

Definition at line 205 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::GetCurrentPanel(), and CLBLASTUILoadManager::SetParentWindow().

◆ m_ParentWindow [2/2]

wxWindow* CBamUILoadManager::m_ParentWindow

protected

Definition at line 229 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::GetCurrentPanel(), and CBamUILoadManager::SetParentWindow().

◆ m_ParseProgressSizer

wxBoxSizer* CBamLoadOptionPanel::m_ParseProgressSizer

Definition at line 120 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::CreateControls(), CBamLoadOptionPanel::Init(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_ProjectParams [1/2]

SProjectSelectorParams CLBLASTUILoadManager::m_ProjectParams

protected

Definition at line 217 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::CLBLASTUILoadManager(), CLBLASTUILoadManager::GetCurrentPanel(), CLBLASTUILoadManager::GetTask(), CLBLASTUILoadManager::LoadSettings(), and CLBLASTUILoadManager::SaveSettings().

◆ m_ProjectParams [2/2]

SProjectSelectorParams CBamUILoadManager::m_ProjectParams

protected

Definition at line 245 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CBamUILoadManager(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::GetTask(), CBamUILoadManager::LoadSettings(), and CBamUILoadManager::SaveSettings().

◆ m_ProjectSelPanel [1/2]

CProjectSelectorPanel* CLBLASTUILoadManager::m_ProjectSelPanel

protected

Definition at line 216 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::CleanUI(), CLBLASTUILoadManager::DoTransition(), CLBLASTUILoadManager::GetCurrentPanel(), and CLBLASTUILoadManager::GetTask().

◆ m_ProjectSelPanel [2/2]

CProjectSelectorPanel* CBamUILoadManager::m_ProjectSelPanel

protected

Definition at line 244 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), and CBamUILoadManager::GetTask().

◆ m_RefSeqIds [1/2]

vector<CRef<objects::CSeq_id> > CLBLASTUILoadManager::m_RefSeqIds

protected

Definition at line 213 of file lblast_ui_data_source.hpp.

◆ m_RefSeqIds [2/2]

vector<CConstRef<objects::CSeq_id> > CBamUILoadManager::m_RefSeqIds

protected

Definition at line 238 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::GetTask(), CBamUILoadManager::x_GetBamRefSeqs(), CBamUILoadManager::x_GetCSraRefSeqs(), and CBamUILoadManager::x_GetSrzRefSeqs().

◆ m_RefSequencesPanel

CBamRefSequencesPanel* CBamUILoadManager::m_RefSequencesPanel

protected

Definition at line 242 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::GetCurrentPanel(), and CBamUILoadManager::GetTask().

◆ m_RegPath [1/2]

string CLBLASTUILoadManager::m_RegPath

protected

Definition at line 210 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::LoadSettings(), CLBLASTUILoadManager::SaveSettings(), and CLBLASTUILoadManager::SetRegistryPath().

◆ m_RegPath [2/2]

string CBamUILoadManager::m_RegPath

protected

Definition at line 234 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::LoadSettings(), CBamUILoadManager::SaveSettings(), and CBamUILoadManager::SetRegistryPath().

◆ m_SamtoolsPath

string CBamUILoadManager::m_SamtoolsPath

mutableprotected

Definition at line 236 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::LoadSettings(), and CBamUILoadManager::SaveSettings().

◆ m_SavedInput [1/2]

string CLBLASTUILoadManager::m_SavedInput

mutableprotected

Definition at line 211 of file lblast_ui_data_source.hpp.

◆ m_SavedInput [2/2]

string CBamUILoadManager::m_SavedInput

mutableprotected

Definition at line 235 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CleanUI(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::LoadSettings(), and CBamUILoadManager::SaveSettings().

◆ m_SraAccs

TBamFiles CBamLoadOptionPanel::m_SraAccs

private

Definition at line 183 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::GetSraAccs(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_SrvLocator [1/4]

IServiceLocator* CLBLASTUIDataSource::m_SrvLocator

protected

Definition at line 127 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUIDataSource::CreateEvtHandler(), CLBLASTUIDataSource::GetMenu(), and CLBLASTUIDataSource::SetServiceLocator().

◆ m_SrvLocator [2/4]

IServiceLocator* CLBLASTUILoadManager::m_SrvLocator

protected

Definition at line 204 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::GetCurrentPanel(), CLBLASTUILoadManager::GetTask(), and CLBLASTUILoadManager::SetServiceLocator().

◆ m_SrvLocator [3/4]

IServiceLocator* CBamUIDataSource::m_SrvLocator

protected

Definition at line 138 of file bam_ui_data_source.hpp.

Referenced by CBamUIDataSource::CreateEvtHandler(), CBamUIDataSource::GetMenu(), and CBamUIDataSource::SetServiceLocator().

◆ m_SrvLocator [4/4]

IServiceLocator* CBamUILoadManager::m_SrvLocator

protected

Definition at line 228 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::GetTask(), and CBamUILoadManager::SetServiceLocator().

◆ m_SrzAccs

TBamFiles CBamLoadOptionPanel::m_SrzAccs

private

Definition at line 182 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::GetSrzAccs(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_State [1/3]

EState CLBLASTUILoadManager::m_State

protected

Definition at line 208 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUILoadManager::CanDo(), CLBLASTUILoadManager::CleanUI(), CLBLASTUILoadManager::DoTransition(), CLBLASTUILoadManager::GetCurrentPanel(), CLBLASTUILoadManager::InitUI(), CLBLASTUILoadManager::IsCompletedState(), and CLBLASTUILoadManager::IsFinalState().

◆ m_State [2/3]

EState CBamUILoadManager::m_State

protected

Definition at line 232 of file bam_ui_data_source.hpp.

Referenced by CBamUILoadManager::CanDo(), CBamUILoadManager::CleanUI(), CBamUILoadManager::DoTransition(), CBamUILoadManager::GetCurrentPanel(), CBamUILoadManager::InitUI(), CBamUILoadManager::IsCompletedState(), and CBamUILoadManager::IsFinalState().

◆ m_State [3/3]

EParseState CBamLoadOptionPanel::m_State = eParseComplete

private

Definition at line 173 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::IsInputValid(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_TextChanged

bool CBamLoadOptionPanel::m_TextChanged = false

private

Definition at line 174 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::OnBamInputTextUpdated(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_Timer

wxTimer CBamLoadOptionPanel::m_Timer

private

Definition at line 185 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::OnBamInputTextUpdated(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_Type [1/2]

CRef<CLBLASTUIDataSourceType> CLBLASTUIDataSource::m_Type

mutableprotected

Definition at line 123 of file lblast_ui_data_source.hpp.

Referenced by CLBLASTUIDataSource::GetType().

◆ m_Type [2/2]

CRef<CBamUIDataSourceType> CBamUIDataSource::m_Type

mutableprotected

Definition at line 134 of file bam_ui_data_source.hpp.

Referenced by CBamUIDataSource::GetType().

◆ m_UpdatingStyle

bool CBamLoadOptionPanel::m_UpdatingStyle = false

private

Definition at line 172 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::OnBamInputTextUpdated(), and CBamLoadOptionPanel::x_ValidateInput().

◆ m_ValidateJob

std::unique_ptr<async_job> CBamLoadOptionPanel::m_ValidateJob

private

Definition at line 187 of file bam_load_option_panel.hpp.

Referenced by CBamLoadOptionPanel::x_ValidateInput().

Classes

Typedefs

Enumerations

Functions

Variables

IExtension interface implementation

IServiceLocatorConsumer implementation

IUIDataSource interface implementation

IDataLoaderProvider implementation

IExplorerItemCmdContributor implementation

IUIDataSourceType interface implementation

IExtension interface implementation

IUIToolManager interface implementation

IRegSettings interface implementation

IExtension interface implementation

IServiceLocatorConsumer implementation

IUIDataSource interface implementation

IDataLoaderProvider implementation

IExplorerItemCmdContributor implementation

IUIDataSourceType interface implementation

IExtension interface implementation

IUIToolManager interface implementation

IRegSettings interface implementation

Detailed Description

Typedef Documentation

◆ TBamFiles

◆ TBamWithIndexFiles

Enumeration Type Documentation

◆ anonymous enum

◆ anonymous enum

◆ EBamCommands

◆ ELBLASTCommands

◆ EParseState

◆ EState [1/2]

◆ EState [2/2]

Function Documentation

◆ AddDataLoader() [1/2]

◆ AddDataLoader() [2/2]

◆ AddFilenames()

◆ AutoCreateDefaultDataSource() [1/2]

◆ AutoCreateDefaultDataSource() [2/2]

◆ CanDo() [1/2]

◆ CanDo() [2/2]

◆ CBamLoadOptionPanel() [1/2]

◆ CBamLoadOptionPanel() [2/2]

◆ CBamUIDataSource()

◆ CBamUIDataSourceType()

◆ CBamUILoadManager()

◆ CDropTarget()

◆ CLBLASTUIDataSource()

◆ CLBLASTUIDataSourceType()

◆ CLBLASTUILoadManager()

◆ CleanUI() [1/2]

◆ CleanUI() [2/2]

◆ Close() [1/2]

◆ Close() [2/2]

◆ Create()

◆ CreateControls()

◆ CreateDataSource() [1/2]

◆ CreateDataSource() [2/2]

◆ CreateEvtHandler() [1/2]

◆ CreateEvtHandler() [2/2]

◆ DoTransition() [1/2]

◆ DoTransition() [2/2]

◆ EditProperties() [1/2]

◆ EditProperties() [2/2]

◆ GetBamFilePath()

◆ GetBamFiles()

◆ GetBitmapResource()

◆ GetCSraFiles()

◆ GetCurrentPanel() [1/2]

◆ GetCurrentPanel() [2/2]

◆ GetDefaultCommand() [1/2]

◆ GetDefaultCommand() [2/2]

◆ GetDescr() [1/4]

◆ GetDescr() [2/4]

◆ GetDescr() [3/4]

◆ GetDescr() [4/4]

◆ GetDescriptor() [1/2]

◆ GetDescriptor() [2/2]