Classes
class	CAlignSpanView
	CAlignSpanView. More...

class	CAlignSpanViewFactory
	CAlignSpanViewFactory. More...

class	CAnnotCompareView
	CAnnotCompareView. More...

class	CAnnotCompareViewFactory
	CAnnotCompareViewFactory. More...

class	CBLAST_Dlg_Item

class	CBLAST_DB_Dialog
	CBLAST_DB_Dialog. More...

class	CNetBlastSubmittingJob
	CNetBlastSubmittingJob. More...

class	CNetBlastMonitoringJob

class	CNetBlastLoadingJob
	CNetBlastLoadingJob - an application job for loading RIDs from NCBI Net BLAST server. More...

class	CBLASTSearchOptionsPanel

class	CBLASTParams
	CBLASTParams - save user-specified parameters and preferences. More...

struct	CBLASTParams::SProgInfo
	describes static attributes of a BLAST program More...

struct	CBLASTParams::SProgParams
	describes parameters for a BLAST program More...

class	CBLASTSearchParamsPanel

class	CBlastSearchTask
	TODO. More...

class	CBLASTSeqToolJob
	CBLASTSeqToolJob. More...

class	CBLASTToolManager
	CBLASTToolManager. More...

class	SCleanupAlignmentsParams

class	CCleanupAlignmentsParamsPanel

class	CCleanupAlignmentsToolManager
	CCleanupAlignmentsToolManager. More...

class	CCleanupAlignmentsJob
	CCleanupAlignmentsJob. More...

class	CClustalOmegaTool
	CClustalOmegaTool. More...

class	CClustalOmegaToolJob
	CClustalOmegaToolJob. More...

class	CClustalOmegaToolParams

class	CClustalwTool
	CClustalwTool. More...

class	CClustalwToolJob
	CClustalwToolJob. More...

class	CClustalwToolParams

class	CCreateGeneModelToolManager
	CCreateGeneModelToolManager. More...

class	SGeneCdsmRnaFeats

class	CCreateGeneModelTask
	CCreateGeneModelTask. More...

class	CCrossAlignView
	CCrossAlignView. More...

class	CCrossAlignViewFactory
	CCrossAlignViewFactory. More...

class	CDotMatrixView
	CDotMatrixView. More...

class	CDotMatrixViewFactory
	CDotMatrixViewFactory. More...

class	CFindOverlapPanel

class	CFindOverlapParams

class	CFindOverlapTool
	CFindOverlapTool. More...

class	SGroupAlignmentsParams

class	CGroupAlignmentsParamsPanel
	CGroupAlignmentsParamsPanel. More...

class	CGroupAlignmentsToolManager
	CGroupAlignmentsToolManager. More...

class	CGroupAlignmentsJob
	CGroupAlignmentsJob. More...

class	CKalignTool
	CKalignTool. More...

class	CKalignToolJob
	CKalignToolJob. More...

class	CKalignToolParams

class	CMafftTool
	CMafftTool. More...

class	CMafftToolJob
	CMafftToolJob. More...

class	CMafftToolParams

class	SMergeAlignmentsParams

class	CMergeAlignmentsParamsPanel
	CMergeAlignmentsParamsPanel. More...

class	CMergeAlignmentsToolManager
	CMergeAlignmentsToolManager. More...

class	CMergeAlignmentsJob
	CMergeAlignmentsJob. More...

class	CMPCrossAlignView
	CMPCrossAlignView. More...

class	CMPCrossAlignViewFactory
	CMPCrossAlignViewFactory. More...

class	CMSAToolJob
	CMSAToolJob Provides basic functionality for the integration of third-party multiple sequence alignment tools: More...

class	CMultiAlignView
	CMultiAlignView. More...

class	CMultiAlignViewFactory
	CMultiAlignViewFactory. More...

class	CSelRowHandle

class	CMuscleTool
	CMuscleTool. More...

class	CMuscleToolJob
	CMuscleToolJob. More...

class	CMuscleToolParams

class	CNeedlemanWunschToolParams

class	CNetBlastDMSearchFormPanel

class	CNetBLAST_DMSearchTool
	CNetBLAST_DMSearchTool - a search tool for Data Mining Service that searches and explores Net BLAST Data Source. More...

class	CNetBLAST_DMSearchQuery
	CNetBLAST_DMSearchQuery. More...

class	CNetBLAST_DMSearchForm
	CTestSearchForm. More...

class	CNetBLAST_DMSearchJob
	CNetBLAST_DMSearchJob. More...

class	CNetBlastJobDescriptor
	CNetBlastJobDescriptor. More...

class	CNetBLASTLoadOptionPanel

class	CNetBLASTUIDataSourceEvent

class	CNetBLASTUIDataSource
	CNetBLASTUIDataSource. More...

class	CNetBLASTUIDataSourceType
	CNetBLASTUIDataSourceType. More...

class	CNetBLASTUILoadManager
	CNetBLASTUILoadManager. More...

class	CNGAlignJob
	CNGAlignJob. More...

class	CNGAlignParams

class	CNGAlignTool
	CNGAlignTool. More...

class	CPhyTreeView
	CPhyTreeView. More...

class	CPhyTreeViewFactory
	CPhyTreeViewFactory. More...

class	CPhyloTreeJob
	CPhyloTreeJob. More...

class	CProSplignTool
	CProSplignTool. More...

class	CMolTypeValidator

class	CSplignPanel

class	CSplignParams

class	CSplignTool
	CSplignTool. More...

class	CCommonTaxTreeTool
	CCommonTaxTreeTool. More...

class	CTaxTreeToolJob
	CTaxTreeToolJob. More...

class	CTaxTreeToolParams

class	CTreeBuilderPanel

class	CTreeBuilderParams

class	CTreeBuilderTool
	CTreeBuilderTool. More...

class	CDebugMacroToolJob
	CDebugMacroToolJob. More...

class	CTextAlignObjectLoader
	CTextAlignObjectLoader. More...

class	CAdvancedCleanupTool
	CAdvancedCleanupTool. More...

class	CClustalOmegaToolPanel

class	CClustalwToolPanel

class	CCreateNeedlemanWunschToolManager
	CCreateNeedlemanWunschToolManager. More...

class	CCreateNeedlemanWunschJob
	CCreateNeedlemanWunschJob. More...

class	CKalignToolPanel

class	CMafftToolPanel

class	CMuscleToolPanel

class	CNGAlignPanel

class	CPslLoadManager
	CPslLoadManager. More...

class	CPslLoadManager::CPage

class	CTaxTreeToolPanel

class	CTextAlignLoaderManager
	CTextAlignLoaderManager. More...

class	CTextAlignLoaderManager::CPage

Macros
#define	NET_BLAST_DM_TOOL_NAME "NCBI Net BLAST"

#define	NET_BLAST_LOADER_LABEL "RIDs from NCBI Net BLAST"

Typedefs
typedef vector< CConstRef< objects::CSeq_annot > >	CAnnotCompareView::TAnnotVector

typedef vector< CConstRef< objects::CSeq_align > >	CAnnotCompareView::TAlignVector

typedef map< wxString, CRef< CBLAST_Dlg_Item > >	CBLAST_Dlg_Item::TNameToItemMap

typedef CBLASTDatabases::TDbMap	CBLAST_DB_Dialog::TDbMap

typedef deque< CBLAST_Dlg_Item * >	CBLAST_DB_Dialog::TItemDeque

typedef vector< CRef< CNetBlastJobDescriptor > >	CNetBlastSubmittingJob::TDescriptors

typedef vector< CRef< CNetBlastJobDescriptor > >	CNetBlastMonitoringJob::TDescriptors

typedef vector< CRef< CNetBlastJobDescriptor > >	CNetBlastLoadingJob::TDescriptors

typedef CMRUList< string >	CBLASTParams::TMRUDatabases

typedef CMRUList< string >	CBLASTParams::TMRUQueries

typedef set< string, PNocase >	CBLASTParams::TRepeatLibs

typedef map< blast::EProgram, const SProgInfo * >	CBLASTParams::TProgramAttrMap

typedef map< blast::EProgram, SProgParams >	CBLASTParams::TProgramParamsMap

typedef vector< CRef< CNetBlastJobDescriptor > >	CBlastSearchTask::TDescriptors

typedef map< string, TConstScopedObjects >	CClustalOmegaTool::TObjects

typedef map< string, TConstScopedObjects >	CClustalwTool::TObjects

typedef CRef< objects::CLoaderDescriptor >	CCreateGeneModelTask::TLoaderRef

typedef CRef< objects::CProjectItem >	CCreateGeneModelTask::TItemRef

typedef list< SGeneCdsmRnaFeats >	CCreateGeneModelTask::TGeneCDSmRNAList
	a loader might be tied with a specific project item. More...

typedef map< objects::CSeq_id_Handle, TGeneCDSmRNAList >	CCreateGeneModelTask::TGeneModelMap

typedef vector< CConstRef< objects::CSeq_align > >	CDotMatrixView::TAlignVector

typedef map< string, TConstScopedObjects >	CKalignTool::TObjects

typedef map< string, TConstScopedObjects >	CMafftTool::TObjects

typedef vector< CIRef< IProjectView > >	CMPCrossAlignView::TViews

typedef pair< CConstRef< objects::CSeq_loc >, CRef< objects::CScope > >	CMSAToolJob::TLocPair

typedef map< string, TLocPair >	CMSAToolJob::TIdMap

typedef map< objects::CSeq_id_Handle, bool >	CMSAToolJob::TSeqTypeMap

typedef map< string, TConstScopedObjects >	CMuscleTool::TObjects

typedef set< CNetBlastJobDescriptor::EState >	CNetBLAST_DMSearchQuery::TStates

typedef pair< const char , const char >	CNetBLAST_DMSearchJob::TPair

typedef vector< CRef< CNetBlastJobDescriptor > >	CNetBLASTUIDataSource::TJobDescrVec

typedef map< int, string >	CNetBLASTUIDataSource::TTaxIdLabelMap

typedef list< CConstRef< objects::CUser_field > >	CNetBLASTUIDataSource::TUserFields

typedef map< string, TConstScopedObjects >	CProSplignTool::TObjects

typedef map< string, TConstScopedObjects >	CSplignTool::TObjects

typedef map< string, TConstScopedObjects >	CCommonTaxTreeTool::TObjects

Enumerations
enum	{ CBLAST_DB_Dialog::ID_CBLAST_DB_DIALOG = 10012 , CBLAST_DB_Dialog::ID_SEARCH = 10015 , CBLAST_DB_Dialog::ID_RESET_BTN = 10016 , CBLAST_DB_Dialog::wxID_STATUS = 10017 , CBLAST_DB_Dialog::ID_TREECTRL = 10014 }

enum	{ CBLASTSearchOptionsPanel::ID_CBLASTSEARCHOPTIONSPANEL = 10000 , CBLASTSearchOptionsPanel::ID_NUC_RADIO = 10001 , CBLASTSearchOptionsPanel::ID_PROT_RADIO = 10002 , CBLASTSearchOptionsPanel::ID_QUERY_SEQ_SET = 10042 , CBLASTSearchOptionsPanel::ID_LIST = 10003 , CBLASTSearchOptionsPanel::ID_PROGRAM_COMBO = 10004 , CBLASTSearchOptionsPanel::ID_RADIOBUTTON = 10040 , CBLASTSearchOptionsPanel::ID_RADIOBUTTON2 = 10010 , CBLASTSearchOptionsPanel::ID_RADIOBUTTON1 = 10041 , CBLASTSearchOptionsPanel::ID_SUBJECT_SEQ_SET = 10043 , CBLASTSearchOptionsPanel::ID_SUBJ_LIST = 10012 , CBLASTSearchOptionsPanel::ID_DB_COMBO = 10005 , CBLASTSearchOptionsPanel::ID_SELECT_NCBI_DB = 10006 , CBLASTSearchOptionsPanel::ID_ENTREZ_COMBO = 10007 , CBLASTSearchOptionsPanel::ID_TEXTCTRL = 10011 , CBLASTSearchOptionsPanel::ID_SELECT_LOCAL_DB_BTN = 10026 , CBLASTSearchOptionsPanel::ID_CHECKBOX = 10039 }

enum	{ CBLASTSearchOptionsPanel::ID_DBS_LOADING_TEXT = 10030 , CBLASTSearchOptionsPanel::ID_DBS_LOADING_PROGRESS = 10031 , CBLASTSearchOptionsPanel::ID_DBS_FAILED = 10032 , CBLASTSearchOptionsPanel::ID_DBS_TRY_AGAIN = 10033 }

enum	CBLASTParams::ESubjectType { CBLASTParams::eSequences , CBLASTParams::eNCBIDB , CBLASTParams::eLocalDB }

enum	{ CBLASTSearchParamsPanel::ID_CBLASTSEARCHPARAMSPANEL = 10000 , CBLASTSearchParamsPanel::ID_WORDSIZE = 10019 , CBLASTSearchParamsPanel::ID_E_VALUE = 10020 , CBLASTSearchParamsPanel::ID_THRESHOLD = 10018 , CBLASTSearchParamsPanel::ID_GEN_CODE = 10024 , CBLASTSearchParamsPanel::ID_COMBOBOX = 10003 , CBLASTSearchParamsPanel::ID_LOW_COMPLEXITY = 10021 , CBLASTSearchParamsPanel::ID_STATIC_REPEAT_TYPE = 10037 , CBLASTSearchParamsPanel::ID_REPEAT_TYPE = 10032 , CBLASTSearchParamsPanel::ID_MASK_LOWERCASE = 10002 , CBLASTSearchParamsPanel::ID_MASK_REPEATS = 10001 , CBLASTSearchParamsPanel::ID_WMTI_CHOICE = 10035 , CBLASTSearchParamsPanel::ID_BUTTON = 10036 , CBLASTSearchParamsPanel::ID_ADV_TEXT = 10008 , CBLASTSearchParamsPanel::ID_COMPARTMENTS = 10038 , CBLASTSearchParamsPanel::ID_TITLE_TEXT = 10009 , CBLASTSearchParamsPanel::ID_STANDALONE = 10033 }

enum	{ CBLASTSearchParamsPanel::ID_LOADING_TEXT = 10100 , CBLASTSearchParamsPanel::ID_LOADING_PROGRESS = 10101 }

enum	CBlastSearchTask::ECommand { CBlastSearchTask::eInvalid = -1 , CBlastSearchTask::eSubmit , CBlastSearchTask::eMonitor , CBlastSearchTask::eRetrieve , CBlastSearchTask::eFinished }

enum	CBLASTToolManager::EState { CBLASTToolManager::eInvalid = -1 , CBLASTToolManager::eOptions , CBLASTToolManager::eParams , CBLASTToolManager::eCompleted }

enum	SCleanupAlignmentsParams::EAlgorithm { SCleanupAlignmentsParams::eHitFilter , SCleanupAlignmentsParams::eAlignmentManager }
	which algorithm are we using? More...

enum	{ CCleanupAlignmentsParamsPanel::ID_CCLEANUPALIGNMENTSPARAMSPANEL = 10013 , CCleanupAlignmentsParamsPanel::ID_LISTCTRL2 = 10014 , CCleanupAlignmentsParamsPanel::ID_COMBOBOX = 10015 , CCleanupAlignmentsParamsPanel::ID_TEXTCTRL1 = 10017 , CCleanupAlignmentsParamsPanel::ID_TEXTCTRL = 10016 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX1 = 10019 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX2 = 10020 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX = 10018 , CCleanupAlignmentsParamsPanel::ID_CHECKBOX5 = 10033 }

enum	{ CFindOverlapPanel::ID_CFINDOVERLAPPANEL = 10021 , CFindOverlapPanel::ID_LISTCTRL3 = 10022 , CFindOverlapPanel::ID_LISTCTRL4 = 10023 , CFindOverlapPanel::ID_TEXTCTRL2 = 10024 , CFindOverlapPanel::ID_TEXTCTRL4 = 10026 , CFindOverlapPanel::ID_TEXTCTRL5 = 10027 }

enum	{ CGroupAlignmentsParamsPanel::ID_CGROUPALIGNMENTSPARAMSPANEL = 10002 , CGroupAlignmentsParamsPanel::ID_LISTCTRL = 10004 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_SEQID = 10005 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_STRAND = 10006 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_TAXID = 10000 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_SIMILAR_TAXID = 10001 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_REFSEQ = 10007 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_EST = 10008 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_REFSEQ_PREDICTED = 10009 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_GENBANK = 10010 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_WGS = 10011 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_HTGS = 10012 , CGroupAlignmentsParamsPanel::ID_CHECKBOX_PATENT = 10003 }

enum	{ CMergeAlignmentsParamsPanel::ID_CBLASTSEARCHOPTIONSPANEL = 10000 , CMergeAlignmentsParamsPanel::ID_LISTCTRL1 = 10003 , CMergeAlignmentsParamsPanel::ID_CHECKBOX6 = 10071 , CMergeAlignmentsParamsPanel::ID_CHECKBOX7 = 10072 , CMergeAlignmentsParamsPanel::ID_CHECKBOX8 = 10073 , CMergeAlignmentsParamsPanel::ID_CHECKBOX9 = 10074 , CMergeAlignmentsParamsPanel::ID_CHECKBOX10 = 10075 }

enum	CNeedlemanWunschToolParams::EFreeEndType { CNeedlemanWunschToolParams::eNone , CNeedlemanWunschToolParams::eLeft , CNeedlemanWunschToolParams::eRight , CNeedlemanWunschToolParams::eBoth }

enum	{ CNetBlastDMSearchFormPanel::ID_CNETBLASTDMSEARCHFORM = 10023 , CNetBlastDMSearchFormPanel::ID_FILTER_INPUT = 10025 , CNetBlastDMSearchFormPanel::ID_SUBMITTED_CHECK = 10027 , CNetBlastDMSearchFormPanel::ID_COMPLETED_CHECK = 10028 , CNetBlastDMSearchFormPanel::ID_FAILED_CHECK = 10029 , CNetBlastDMSearchFormPanel::ID_RETRIEVED_CHECK = 10030 , CNetBlastDMSearchFormPanel::ID_EXPIRED_CHECK = 10031 }

enum	CNetBlastJobDescriptor::EState { CNetBlastJobDescriptor::eInvalidState = -1 , CNetBlastJobDescriptor::eInitial , CNetBlastJobDescriptor::eSubmitted , CNetBlastJobDescriptor::eCompleted , CNetBlastJobDescriptor::eFailed , CNetBlastJobDescriptor::eRetrieved , CNetBlastJobDescriptor::eExpired }

enum	{ CNetBLASTLoadOptionPanel::ID_NETBLASTLOADOPTIONPANEL = 10013 , CNetBLASTLoadOptionPanel::ID_TEXTCTRL1 = 10044 }

enum	ENetBlastCommands { eCmdRetriveBlastJobs = 12200 , eCmdMonitorBlastJobs , eCmdDeleteBlastJobs , eCmdExploreNetBLAST , eCmdLoadRIDs , eCmdBlastWinMask }
	commands introduced by Net BLAST data source More...

enum	CNetBLASTUIDataSourceEvent::EEventId { CNetBLASTUIDataSourceEvent::eJobDescrChanged }

enum	CNetBLASTUILoadManager::EState { CNetBLASTUILoadManager::eInvalid = -1 , CNetBLASTUILoadManager::eSelectRID , CNetBLASTUILoadManager::eSelectProject , CNetBLASTUILoadManager::eCompleted }

enum	{ CPhyTreeView::kQueryPanelID = 6000 , CPhyTreeView::kPhylpWidgetID = 6001 }

enum	CMolTypeValidator::MolType { CMolTypeValidator::kGenomic , CMolTypeValidator::kCDNA , CMolTypeValidator::kProtein , CMolTypeValidator::kNucleotide }

enum	{ CSplignPanel::ID_CSPLIGNPANEL = 10028 , CSplignPanel::ID_PANEL1 = 10029 , CSplignPanel::ID_PANEL2 = 10030 , CSplignPanel::ID_CHOICE3 = 10040 , CSplignPanel::ID_CHOICE4 = 10076 , CSplignPanel::ID_CHECKBOX3 = 10034 , CSplignPanel::ID_CHECKBOX4 = 10035 , CSplignPanel::ID_TEXTCTRL7 = 10037 , CSplignPanel::ID_TEXTCTRL6 = 10036 , CSplignPanel::ID_TEXTCTRL8 = 10038 , CSplignPanel::ID_TEXTCTRL9 = 10039 , CSplignPanel::ID_TEXTCTRL13 = 10043 }

enum	{ CTreeBuilderPanel::ID_CTreeBuilderPanel = 10021 , CTreeBuilderPanel::ID_LISTCTRL3 = 10022 , CTreeBuilderPanel::ID_LISTCTRL4 = 10023 , CTreeBuilderPanel::ID_TEXTCTRL2 = 10024 , CTreeBuilderPanel::ID_TEXTCTRL3 = 10025 , CTreeBuilderPanel::ID_TEXTCTRL4 = 10026 , CTreeBuilderPanel::ID_TEXTCTRL5 = 10027 }

enum	{ CMuscleToolPanel::ID_CMUSCLEPANEL = 10050 , CMuscleToolPanel::ID_PANEL = 10051 , CMuscleToolPanel::ID_CHOICE2 = 10054 , CMuscleToolPanel::ID_CHECKBOX12 = 10053 , CMuscleToolPanel::ID_TEXTCTRL11 = 10052 , CMuscleToolPanel::ID_TEXTCTRL12 = 10055 , CMuscleToolPanel::ID_BITMAPBUTTON1 = 10056 }

enum	{ CNGAlignPanel::ID_CNGALIGNPANEL = 10047 , CNGAlignPanel::ID_QUERY_LIST = 10060 , CNGAlignPanel::ID_SUBJ_LIST = 10061 }

enum	CPslLoadManager::EState { CPslLoadManager::eInvalid = -1 , CPslLoadManager::eParams , CPslLoadManager::eCompleted }

enum	{ CTaxTreeToolPanel::ID_CTAXTREETOOLPANEL = 10057 , CTaxTreeToolPanel::ID_PANEL3 = 10058 }

enum	CTextAlignLoaderManager::EState { CTextAlignLoaderManager::eInvalid = -1 , CTextAlignLoaderManager::eParams , CTextAlignLoaderManager::eCompleted }

Functions
	CAlignSpanView::CAlignSpanView ()

void	CAlignSpanView::x_InitMenuResources ()

void	CAlignSpanView::x_InitWidget ()

virtual void	CAlignSpanView::x_UpdateStatusMessage ()

virtual void	CAlignSpanView::x_Update ()

	CAnnotCompareView::CAnnotCompareView ()

virtual void	CAnnotCompareView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual const CObject *	CAnnotCompareView::x_GetOrigObject () const

void	CAnnotCompareView::x_InitWidget ()

	CBLAST_Dlg_Item::CBLAST_Dlg_Item ()

	CBLAST_Dlg_Item::CBLAST_Dlg_Item (const string &label, const string &path, bool is_database=false)

	CBLAST_Dlg_Item::~CBLAST_Dlg_Item ()

wxString	CBLAST_Dlg_Item::GetLabel () const

const string &	CBLAST_Dlg_Item::GetPath () const

bool	CBLAST_Dlg_Item::IsDatabase () const

bool	CBLAST_Dlg_Item::IsVisible () const

void	CBLAST_Dlg_Item::SetVisible (bool visible)

bool	CBLAST_Dlg_Item::IsExpanded () const

void	CBLAST_Dlg_Item::Expand (bool expand)

CBLAST_Dlg_Item *	CBLAST_Dlg_Item::GetParent ()

TNameToItemMap *	CBLAST_Dlg_Item::GetChildItems ()

CBLAST_Dlg_Item *	CBLAST_Dlg_Item::GetChildByLabel (const string &label)

void	CBLAST_Dlg_Item::AddChild (CBLAST_Dlg_Item &item)

const wxTreeItemId &	CBLAST_Dlg_Item::GetId () const

void	CBLAST_Dlg_Item::SetId (const wxTreeItemId &id)

	CBLAST_DB_Dialog::CBLAST_DB_Dialog ()

	CBLAST_DB_Dialog::CBLAST_DB_Dialog (wxWindow *parent, wxWindowID id=ID_CBLAST_DB_DIALOG, const wxString &caption=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL)

bool	CBLAST_DB_Dialog::Create (wxWindow *parent, wxWindowID id=ID_CBLAST_DB_DIALOG, const wxString &caption=wxEmptyString, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL)

	CBLAST_DB_Dialog::~CBLAST_DB_Dialog ()

void	CBLAST_DB_Dialog::Init ()

void	CBLAST_DB_Dialog::CreateControls ()

void	CBLAST_DB_Dialog::OnInitDialog (wxInitDialogEvent &event)

void	CBLAST_DB_Dialog::OnSearchTextUpdated (wxCommandEvent &event)

void	CBLAST_DB_Dialog::OnResetBtnClick (wxCommandEvent &event)

void	CBLAST_DB_Dialog::OnTreectrlSelChanged (wxTreeEvent &event)

void	CBLAST_DB_Dialog::OnTreectrlItemActivated (wxTreeEvent &event)

void	CBLAST_DB_Dialog::OnTreectrlItemCollapsed (wxTreeEvent &event)

void	CBLAST_DB_Dialog::OnTreectrlItemExpanded (wxTreeEvent &event)

void	CBLAST_DB_Dialog::OnOkClick (wxCommandEvent &event)

wxBitmap	CBLAST_DB_Dialog::GetBitmapResource (const wxString &name)

wxIcon	CBLAST_DB_Dialog::GetIconResource (const wxString &name)

static bool	CBLAST_DB_Dialog::ShowToolTips ()

void	CBLAST_DB_Dialog::SetToolName (const string &tool)

void	CBLAST_DB_Dialog::SetDBMap (const TDbMap &map)

void	CBLAST_DB_Dialog::SelectDatabases (vector< string > &databases)

void	CBLAST_DB_Dialog::GetSelectedDatabases (vector< string > &databases)

void	CBLAST_DB_Dialog::x_CreateItems ()

void	CBLAST_DB_Dialog::x_BuildTreeItems (CBLAST_Dlg_Item &item)

void	CBLAST_DB_Dialog::x_CreateTreeItems ()

void	CBLAST_DB_Dialog::x_FilterItems (const string &query)

void	CBLAST_DB_Dialog::x_UpdateCollapsedState (wxTreeItemId id)

void	CBLAST_DB_Dialog::x_UpdateFilterStatusText (bool reset, int n)

CBLAST_Dlg_Item *	CBLAST_DB_Dialog::x_GetSelectedDBItem ()

void	CBLAST_DB_Dialog::x_OnDatabaseSelected ()

	CNetBlastSubmittingJob::CNetBlastSubmittingJob (string tool_name, const CBLASTParams &params, CNetBLASTUIDataSource &ds)
	CNetBlastSubmittingJob. More...

void	CNetBlastSubmittingJob::GetDescriptors (TDescriptors &descriptors)

void	CNetBlastSubmittingJob::GetErrors (vector< string > &errors) const

void	CNetBlastSubmittingJob::x_Run ()
	this fucntions performs real work More...

void	CNetBlastSubmittingJob::x_SetStatusText (const string &text)

void	CNetBlastSubmittingJob::x_ResetState ()

void	CNetBlastSubmittingJob::x_AddError (const string &error)

	CNetBlastMonitoringJob::CNetBlastMonitoringJob (CNetBLASTUIDataSource &ds, IServiceLocator *srv_locator, const string &tool_name, TDescriptors &descriptors)
	CNetBlastSubmittingJob. More...

virtual void	CNetBlastMonitoringJob::SetLoadingOptions (CSelectProjectOptions &options)

EJobState	CNetBlastMonitoringJob::x_Run ()
	this functions performs real work every call to this function does pools each job once, then functions exits if some of jobs are still pending it returns eRunning state, so that it can be executed one more time More...

void	CNetBlastMonitoringJob::x_SetStatusText (const string &text)

void	CNetBlastMonitoringJob::x_ResetState ()

void	CNetBlastMonitoringJob::x_StartRetrivingTask (const vector< string > &RIDs)

	CNetBlastLoadingJob::CNetBlastLoadingJob (CNetBLASTUIDataSource &ds, const vector< string > RIDs=NULL, CScope scope=NULL)
	CNetBlastLoadingJob. More...

void	CNetBlastLoadingJob::SetRIDs (CNetBLASTUIDataSource &ds, const vector< string > &RIDs)

bool	CNetBlastLoadingJob::HasErrors () const

void	CNetBlastLoadingJob::GetErrors (vector< string > &errors) const

virtual void	CNetBlastLoadingJob::x_CreateProjectItems ()
	iterates on the given RIDs and creates Project Items or accumulates error More...

void	CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult (objects::CSeq_align_set &results, CRef< blast::CRemoteBlast > RemoteBlast)

	CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel ()

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

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

	CBLASTSearchOptionsPanel::~CBLASTSearchOptionsPanel ()

void	CBLASTSearchOptionsPanel::Init ()

void	CBLASTSearchOptionsPanel::CreateControls ()

bool	CBLASTSearchOptionsPanel::TransferDataToWindow ()

bool	CBLASTSearchOptionsPanel::TransferDataFromWindow ()

void	CBLASTSearchOptionsPanel::OnNucRadioSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnProtRadioSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnQuerySequenceSetSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnProgramComboSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnSubjectSequencesSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnSubjectNCBIDBSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnSubjectLocalDBSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnSubjectSequenceSetSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnDatabaseComboSelected (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnBrowseDatabases (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnSelectLocalDB (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnLocalDBLoaderClick (wxCommandEvent &event)

wxBitmap	CBLASTSearchOptionsPanel::GetBitmapResource (const wxString &name)

wxIcon	CBLASTSearchOptionsPanel::GetIconResource (const wxString &name)

static bool	CBLASTSearchOptionsPanel::ShowToolTips ()

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

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

void	CBLASTSearchOptionsPanel::SelectInputType ()

bool	CBLASTSearchOptionsPanel::CanDoNext ()

void	CBLASTSearchOptionsPanel::x_OnInputTypeChanged (bool nuc_input)

void	CBLASTSearchOptionsPanel::x_OnSubjInputTypeChanged ()

void	CBLASTSearchOptionsPanel::x_UpdateDBCombo ()

void	CBLASTSearchOptionsPanel::x_CheckDBLoaded ()

void	CBLASTSearchOptionsPanel::x_UpdateSubjects ()

void	CBLASTSearchOptionsPanel::OnTryAgain (wxCommandEvent &event)

void	CBLASTSearchOptionsPanel::OnTimer (wxTimerEvent &event)

void	CBLASTSearchOptionsPanel::x_UpdateSubjectType ()

void	CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet ()

void	CBLASTSearchOptionsPanel::x_FillQueryList ()

void	CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet ()

void	CBLASTSearchOptionsPanel::x_FillSubjectList ()

	CBLASTParams::SProgParams::SProgParams ()

	CBLASTParams::SProgParams::SProgParams (int thresh, int word, double ev, bool low_c, int query_gen_code, int db_gen_code)

	CBLASTParams::CBLASTParams ()

bool &	CBLASTParams::IsNucInput ()

bool	CBLASTParams::IsNucInput () const

TConstScopedObjects &	CBLASTParams::GetSeqLocs ()

const TConstScopedObjects &	CBLASTParams::GetSeqLocs () const

blast::EProgram &	CBLASTParams::GetCurrProgram ()
	returns the current program for the currently selected input type More...

const blast::EProgram	CBLASTParams::GetCurrProgram () const

blast::EProgram &	CBLASTParams::GetProgram (bool nuc)
	returns the selected programs for the given input type More...

const blast::EProgram	CBLASTParams::GetProgram (bool nuc) const

string &	CBLASTParams::GetCurrDatabase ()
	returns the current database for the current program More...

const string &	CBLASTParams::GetCurrDatabase () const

string &	CBLASTParams::GetDatabase (bool nuc_db)
	returns the database of the specified type More...

const string &	CBLASTParams::GetDatabase (bool nuc_db) const

TMRUDatabases &	CBLASTParams::GetCurrMRUDatabases ()
	returns MRU databases for the current program More...

TMRUDatabases &	CBLASTParams::GetMRUDatabases (bool nuc_db)

string &	CBLASTParams::GetEntrezQuery ()

string	CBLASTParams::GetEntrezQuery () const

bool	CBLASTParams::IsSubjNucInput () const

TConstScopedObjects &	CBLASTParams::GetSubjSeqLocs ()

const TConstScopedObjects &	CBLASTParams::GetSubjSeqLocs () const

SProgParams &	CBLASTParams::GetCurrParams ()
	returns params for the current program More...

const SProgParams &	CBLASTParams::GetCurrParams () const

void	CBLASTParams::ResetCurrParams ()

string &	CBLASTParams::GetAdvancedParams ()

string	CBLASTParams::GetAdvancedParams () const

static TRepeatLibs	CBLASTParams::GetAllRepeatLibs ()

static string	CBLASTParams::GetRepeatLib (const string &repeat_db)

static string	CBLASTParams::GetRepeatDb (const string &repeat_lib)

string &	CBLASTParams::GetJobTitle ()

string	CBLASTParams::GetJobTitle () const

bool	CBLASTParams::IsStandaloneRequested () const

void	CBLASTParams::StandaloneRequested (bool req)

bool	CBLASTParams::IsCompartmentsRequested () const

void	CBLASTParams::FindCompartments (bool req)

void	CBLASTParams::SetWM_Dir (const string &wm_dir_path)

const string &	CBLASTParams::GetWmDir () const

vector< string > &	CBLASTParams::ToArgVec (vector< string > &arg_vec) const

CArgs *	CBLASTParams::ToArgs (vector< string > &argv) const

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

CRef< blast::CBlastOptionsHandle >	CBLASTParams::ToArgVecBlastOptions (vector< string > &arg_vec, bool local=true) const

objects::CUser_object *	CBLASTParams::ToUserObject () const

void	CBLASTParams::FromUserObject (const objects::CUser_object &user_obj)

static void	CBLASTParams::GetProgramLabels (bool nuc_input, vector< string > &labels)

static string	CBLASTParams::GetProgramLabel (blast::EProgram program)

static blast::EProgram	CBLASTParams::GetProgramByLabel (const string &str)

static bool	CBLASTParams::IsNucInput (blast::EProgram program)

static bool	CBLASTParams::IsNucDatabase (blast::EProgram program)

static bool	CBLASTParams::UseDustFilter (blast::EProgram program)

static bool	CBLASTParams::NeedsThreshold (blast::EProgram program)

static bool	CBLASTParams::NeedsDbGeneticCode (blast::EProgram program)

static bool	CBLASTParams::NeedsQueryGeneticCode (blast::EProgram program)

static int	CBLASTParams::GetGeneticCodeByLabel (const string &label)

static string	CBLASTParams::GetGeneticCodeLabel (int code_id)

static void	CBLASTParams::GetGeneticCodeLabels (vector< string > &labels)

void	CBLASTParams::PrintParams (const string &log_title) const
	LOG_POST params for forensic purposes. More...

string	CBLASTParams::GetLocalNucDB () const

void	CBLASTParams::SetLocalNucDB (const string &value)

string	CBLASTParams::GetLocalProtDB () const

void	CBLASTParams::SetLocalProtDB (const string &value)

ESubjectType	CBLASTParams::GetSubjectType () const

void	CBLASTParams::SetSubjectType (ESubjectType subjectType)

bool	CBLASTParams::GetLocalDBLoader () const

void	CBLASTParams::SetLocalDBLoader (bool value)

void	CBLASTParams::x_AddProgramParams (blast::EProgram program, int thresh, int word, int ev)

void	CBLASTParams::x_ArgsToBlastOptions (const string &cmd_line, blast::CBlastOptions &opts) const

static objects::CUser_object *	CBLASTParams::x_ToUserObject (blast::EProgram prg, const SProgParams &params)
	converts SProgParams into CUser_object More...

static void	CBLASTParams::x_FromUserObject (const objects::CUser_object &user_obj, blast::EProgram prg, SProgParams &params)
	reads SProgParams fields from CUser_object More...

	CBLASTSearchParamsPanel::CBLASTSearchParamsPanel ()

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

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

	CBLASTSearchParamsPanel::~CBLASTSearchParamsPanel ()

void	CBLASTSearchParamsPanel::Init ()

void	CBLASTSearchParamsPanel::CreateControls ()

bool	CBLASTSearchParamsPanel::TransferDataToWindow ()

bool	CBLASTSearchParamsPanel::TransferDataFromWindow ()

void	CBLASTSearchParamsPanel::OnRepeatTypeSelected (wxCommandEvent &event)

void	CBLASTSearchParamsPanel::OnWindowmaskerTaxIdSelected (wxCommandEvent &event)

void	CBLASTSearchParamsPanel::OnWMDownload (wxCommandEvent &event)

void	CBLASTSearchParamsPanel::OnStandaloneClick (wxCommandEvent &event)

wxString	CBLASTSearchParamsPanel::GetAdvParams () const

void	CBLASTSearchParamsPanel::SetAdvParams (wxString value)

wxString	CBLASTSearchParamsPanel::GetDbGeneticCode () const

void	CBLASTSearchParamsPanel::SetDbGeneticCode (wxString value)

double	CBLASTSearchParamsPanel::GetEValue () const

void	CBLASTSearchParamsPanel::SetEValue (double value)

bool	CBLASTSearchParamsPanel::GetFilterLowComplex () const

void	CBLASTSearchParamsPanel::SetFilterLowComplex (bool value)

wxString	CBLASTSearchParamsPanel::GetJobTitle () const

void	CBLASTSearchParamsPanel::SetJobTitle (wxString value)

wxString	CBLASTSearchParamsPanel::GetGeneticCode () const

void	CBLASTSearchParamsPanel::SetGeneticCode (wxString value)

long	CBLASTSearchParamsPanel::GetThreshold () const

void	CBLASTSearchParamsPanel::SetThreshold (long value)

long	CBLASTSearchParamsPanel::GetWordSize () const

void	CBLASTSearchParamsPanel::SetWordSize (long value)

wxBitmap	CBLASTSearchParamsPanel::GetBitmapResource (const wxString &name)

wxIcon	CBLASTSearchParamsPanel::GetIconResource (const wxString &name)

static bool	CBLASTSearchParamsPanel::ShowToolTips ()

void	CBLASTSearchParamsPanel::SetParams (CBLASTParams *params)

void	CBLASTSearchParamsPanel::x_InitGeneticCodesCombo ()

void	CBLASTSearchParamsPanel::x_HideShowInputs ()

void	CBLASTSearchParamsPanel::x_UpdateMaskCtrls ()

void	CBLASTSearchParamsPanel::x_InitTaxons ()

void	CBLASTSearchParamsPanel::x_ShowWM (bool show)

	CBlastSearchTask::CBlastSearchTask (IServiceLocator *srv_locator, CNetBLASTUIDataSource &ds, const string &tool_name)
	CBlastSearchTask. More...

virtual	CBlastSearchTask::~CBlastSearchTask ()

virtual void	CBlastSearchTask::Init_SubmitSearch (const CBLASTParams &params)
	setup the task for submitting and monitoring BLAST jobs, and for retrieving results More...

virtual void	CBlastSearchTask::Init_Monitoring (TDescriptors &descriptors)
	setup the task for monitoring BLAST jobs and for retrieving results More...

virtual void	CBlastSearchTask::Init_RetrieveRID (const vector< string > &RIDs)
	setup the task for retrieving results More...

virtual void	CBlastSearchTask::SetLoadingOptions (CSelectProjectOptions &options)
	define how the task results shall be handled More...

virtual string	CBlastSearchTask::GetStatusText () const
	overriding CAppTask::GetStatusText() More...

void	CBlastSearchTask::x_InitMonitoringStage (TDescriptors &descriptors)
	preapres App Job for monitoring stage of the task More...

void	CBlastSearchTask::x_ReportErrors (vector< string > &errors)

	CBLASTSeqToolJob::CBLASTSeqToolJob (const CBLASTParams &params)

static Boolean	CBLASTSeqToolJob::s_BlastInterrupt (SBlastProgress *prog)
	static callback for BLAST interruption this must match the API in CBl2Seq and BLAST More...

virtual void	CBLASTSeqToolJob::RequestCancel ()
	RequestCancel() is called to notify the Job that it shall exit Run() function ASAP. More...

virtual void	CBLASTSeqToolJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

void	CBLASTSeqToolJob::x_CreateProjectItems (vector< CRef< objects::CSeq_align_set > > &aligns)

	CBLASTToolManager::CBLASTToolManager ()
	CBLASTToolManager. More...

CRef< CNetBLASTUIDataSource >	CBLASTToolManager::GetBLASTDataSource ()

virtual void	CBLASTToolManager::x_SelectCompatibleInputObjects ()

virtual bool	CBLASTToolManager::x_IsNucInput () const
	defines whether Nucleotide or Protein options shall be selected by default More...

virtual void	CBLASTToolManager::x_CreateOptionsPanelIfNeeded ()

virtual bool	CBLASTToolManager::x_CreateParamsPanelIfNeeded ()

void	CBLASTToolManager::x_InitProjectParams ()

bool	CBLASTToolManager::x_ValidateParams ()
	validate parameters after Params page More...

	SCleanupAlignmentsParams::SCleanupAlignmentsParams ()

void	SCleanupAlignmentsParams::Init ()

	CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel ()

	CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel (wxWindow *parent, wxWindowID id=ID_CCLEANUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

bool	CCleanupAlignmentsParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CCLEANUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

	CCleanupAlignmentsParamsPanel::~CCleanupAlignmentsParamsPanel ()

void	CCleanupAlignmentsParamsPanel::Init ()

void	CCleanupAlignmentsParamsPanel::CreateControls ()

void	CCleanupAlignmentsParamsPanel::SetParams (SCleanupAlignmentsParams params, TConstScopedObjects objects)

bool	CCleanupAlignmentsParamsPanel::TransferDataToWindow ()

bool	CCleanupAlignmentsParamsPanel::TransferDataFromWindow ()

virtual void	CCleanupAlignmentsParamsPanel::SetRegistryPath (const string &path)
	CAlgoToolManagerParamsPanel. More...

virtual void	CCleanupAlignmentsParamsPanel::LoadSettings ()

virtual void	CCleanupAlignmentsParamsPanel::SaveSettings () const
	override in derived classes More...

void	CCleanupAlignmentsParamsPanel::OnComboboxSelected (wxCommandEvent &event)

wxBitmap	CCleanupAlignmentsParamsPanel::GetBitmapResource (const wxString &name)

wxIcon	CCleanupAlignmentsParamsPanel::GetIconResource (const wxString &name)

static bool	CCleanupAlignmentsParamsPanel::ShowToolTips ()

void	CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector ()
	Switch params panel according to current algo-selector. More...

	CCleanupAlignmentsToolManager::CCleanupAlignmentsToolManager ()

void	CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects ()
	select only Seq-aligns More...

bool	CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly () const

	CCleanupAlignmentsJob::CCleanupAlignmentsJob (const SCleanupAlignmentsParams &params)
	CCleanupAlignmentsJob. More...

virtual void	CCleanupAlignmentsJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CClustalOmegaTool::CClustalOmegaTool ()
	CClustalOmegaTool. More...

void	CClustalOmegaTool::x_SelectCompatibleInputObjects ()

	CClustalOmegaToolJob::CClustalOmegaToolJob (const CClustalOmegaToolParams &params)
	CClustalOmegaToolJob. More...

virtual wxString	CClustalOmegaToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)
	Returns the command line, that will be used to execute the third-party tool. More...

virtual TConstScopedObjects &	CClustalOmegaToolJob::x_GetObjects ()
	Returns the sequences that will be aligned. More...

	CClustalOmegaToolParams::CClustalOmegaToolParams ()

	CClustalOmegaToolParams::CClustalOmegaToolParams (const CClustalOmegaToolParams &data)

	CClustalOmegaToolParams::~CClustalOmegaToolParams ()

void	CClustalOmegaToolParams::operator= (const CClustalOmegaToolParams &data)

bool	CClustalOmegaToolParams::operator== (const CClustalOmegaToolParams &data) const

void	CClustalOmegaToolParams::Copy (const CClustalOmegaToolParams &data)

void	CClustalOmegaToolParams::Init ()

virtual void	CClustalOmegaToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CClustalOmegaToolParams::SaveSettings () const

virtual void	CClustalOmegaToolParams::LoadSettings ()

const TConstScopedObjects &	CClustalOmegaToolParams::GetObjects () const

TConstScopedObjects &	CClustalOmegaToolParams::SetObjects ()

wxString	CClustalOmegaToolParams::GetClustalOmegaPath () const

void	CClustalOmegaToolParams::SetClustalOmegaPath (wxString value)

wxString	CClustalOmegaToolParams::GetCommandLine () const

void	CClustalOmegaToolParams::SetCommandLine (wxString value)

bool	CClustalOmegaToolParams::GetGenerateTree () const

void	CClustalOmegaToolParams::SetGenerateTree (bool value)

wxString	CClustalOmegaToolParams::GetClustalOmegaExecutable () const

	CClustalwTool::CClustalwTool ()
	CClustalwTool. More...

void	CClustalwTool::x_SelectCompatibleInputObjects ()

	CClustalwToolJob::CClustalwToolJob (const CClustalwToolParams &params)
	CClustalwToolJob. More...

virtual wxString	CClustalwToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)
	Returns the command line, that will be used to execute the third-party tool. More...

virtual TConstScopedObjects &	CClustalwToolJob::x_GetObjects ()
	Returns the sequences that will be aligned. More...

	CClustalwToolParams::CClustalwToolParams ()

	CClustalwToolParams::CClustalwToolParams (const CClustalwToolParams &data)

	CClustalwToolParams::~CClustalwToolParams ()

void	CClustalwToolParams::operator= (const CClustalwToolParams &data)

bool	CClustalwToolParams::operator== (const CClustalwToolParams &data) const

void	CClustalwToolParams::Copy (const CClustalwToolParams &data)

void	CClustalwToolParams::Init ()

virtual void	CClustalwToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CClustalwToolParams::SaveSettings () const

virtual void	CClustalwToolParams::LoadSettings ()

const TConstScopedObjects &	CClustalwToolParams::GetObjects () const

TConstScopedObjects &	CClustalwToolParams::SetObjects ()

wxString	CClustalwToolParams::GetClustalWPath () const

void	CClustalwToolParams::SetClustalWPath (wxString value)

wxString	CClustalwToolParams::GetCommandLine () const

void	CClustalwToolParams::SetCommandLine (wxString value)

bool	CClustalwToolParams::GetGenerateTree () const

void	CClustalwToolParams::SetGenerateTree (bool value)

wxString	CClustalwToolParams::GetClustalWExecutable () const

	CCreateGeneModelToolManager::CCreateGeneModelToolManager ()

void	CCreateGeneModelToolManager::x_SelectCompatibleInputObjects ()

void	CCreateGeneModelToolManager::x_RemoveDuplicates ()

	SGeneCdsmRnaFeats::SGeneCdsmRnaFeats ()

	SGeneCdsmRnaFeats::~SGeneCdsmRnaFeats ()

CConstRef< objects::CSeq_id >	SGeneCdsmRnaFeats::GetID (objects::CScope *scope) const
	SGeneCdsmRnaFeats. More...

void	SGeneCdsmRnaFeats::CrossLinkTriple ()

static void	SGeneCdsmRnaFeats::s_CreateXRefLink (objects::CSeq_feat &from_feat, objects::CSeq_feat &to_feat)

static void	SGeneCdsmRnaFeats::s_CreateDBXref (const objects::CSeq_feat &from_feat, objects::CSeq_feat &to_feat, const string &dbname)

	CCreateGeneModelTask::CCreateGeneModelTask (const string &descr, CProjectService *service, CSelectProjectOptions &options, const SCreateGeneModelParams &params)

virtual	CCreateGeneModelTask::~CCreateGeneModelTask ()

static objects::CObject_id::TId	CCreateGeneModelTask::s_GetGeneID (const objects::CSeq_feat &feat)

static objects::CObject_id::TId	CCreateGeneModelTask::s_FindHighestFeatId (const objects::CSeq_entry_Handle seh)

static bool	CCreateGeneModelTask::s_FeaturesHaveIDs (const objects::CSeq_annot &annot)

static bool	CCreateGeneModelTask::s_FeaturesHaveXrefs (const objects::CSeq_annot &annot)

static void	CCreateGeneModelTask::s_AssignFeatureIds (objects::CSeq_annot &annot, objects::CObject_id::TId &max_id)

virtual ETaskState	CCreateGeneModelTask::x_Run ()
	override this function in derived classes More...

CRef< CCmdComposite >	CCreateGeneModelTask::x_GetCommand ()

void	CCreateGeneModelTask::x_StoreGeneratedFeats (const objects::CSeq_annot &annot, TGeneCDSmRNAList &gene_cds_rna) const

void	CCreateGeneModelTask::x_Group_By_GeneID (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh)

void	CCreateGeneModelTask::x_GroupGenes (const objects::CSeq_id_Handle &idh, CRef< objects::CSeq_feat > gene)

void	CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh, objects::CObject_id::TId max_id)

CRef< CCmdComposite >	CCreateGeneModelTask::x_AssignIDsAndUpdateGenes (objects::CSeq_annot &annot, const objects::CSeq_id_Handle &idh, objects::CSeq_entry_Handle seh)

void	CCreateGeneModelTask::x_GetUpdatedGeneCommand (objects::CSeq_entry_Handle seh, const objects::CSeq_id_Handle &idh, CCmdComposite *cmd)

bool	CCreateGeneModelTask::x_UpdateGeneOnSequence (TGeneCDSmRNAList &gene_cds_rna, CRef< objects::CSeq_feat > gene)

	CCrossAlignView::CCrossAlignView ()

virtual void	CCrossAlignView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual void	CCrossAlignView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

virtual const CObject *	CCrossAlignView::x_GetOrigObject () const

	CDotMatrixView::CDotMatrixView ()

virtual void	CDotMatrixView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual const CObject *	CDotMatrixView::x_GetOrigObject () const

void	CDotMatrixView::x_InitWidget ()

	CDotMatrixViewFactory::CDotMatrixViewFactory ()
	CDotMatrixViewFactory. More...

	CFindOverlapPanel::CFindOverlapPanel ()

	CFindOverlapPanel::CFindOverlapPanel (wxWindow *parent, wxWindowID id=ID_CFINDOVERLAPPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)

bool	CFindOverlapPanel::Create (wxWindow *parent, wxWindowID id=ID_CFINDOVERLAPPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)

	CFindOverlapPanel::~CFindOverlapPanel ()

void	CFindOverlapPanel::Init ()

void	CFindOverlapPanel::CreateControls ()

virtual bool	CFindOverlapPanel::TransferDataToWindow ()

virtual bool	CFindOverlapPanel::TransferDataFromWindow ()

CFindOverlapParams &	CFindOverlapPanel::GetData ()

const CFindOverlapParams &	CFindOverlapPanel::GetData () const

void	CFindOverlapPanel::SetData (const CFindOverlapParams &data)

wxBitmap	CFindOverlapPanel::GetBitmapResource (const wxString &name)

wxIcon	CFindOverlapPanel::GetIconResource (const wxString &name)

void	CFindOverlapPanel::SetObjects (TConstScopedObjects *objects)

static bool	CFindOverlapPanel::ShowToolTips ()

	CFindOverlapParams::CFindOverlapParams ()

	CFindOverlapParams::CFindOverlapParams (const CFindOverlapParams &data)

	CFindOverlapParams::~CFindOverlapParams ()

void	CFindOverlapParams::operator= (const CFindOverlapParams &data)

bool	CFindOverlapParams::operator== (const CFindOverlapParams &data) const

void	CFindOverlapParams::Copy (const CFindOverlapParams &data)

void	CFindOverlapParams::Init ()

virtual void	CFindOverlapParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CFindOverlapParams::SaveSettings () const
	IRegSettings. More...

virtual void	CFindOverlapParams::LoadSettings ()

const SConstScopedObject &	CFindOverlapParams::GetSeq1 () const

SConstScopedObject &	CFindOverlapParams::SetSeq1 ()

const SConstScopedObject &	CFindOverlapParams::GetSeq2 () const

SConstScopedObject &	CFindOverlapParams::SetSeq2 ()

wxString	CFindOverlapParams::GetBlastParams () const

void	CFindOverlapParams::SetBlastParams (wxString value)

int	CFindOverlapParams::GetFilterQuality () const

void	CFindOverlapParams::SetFilterQuality (int value)

wxString	CFindOverlapParams::GetMaxSlop () const

void	CFindOverlapParams::SetMaxSlop (wxString value)

	CFindOverlapTool::CFindOverlapTool ()
	CFindOverlapTool. More...

virtual void	CFindOverlapTool::x_SelectCompatibleInputObjects ()
	select only Seq-ids More...

	SGroupAlignmentsParams::SGroupAlignmentsParams ()

void	SGroupAlignmentsParams::Init ()

	CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel ()

	CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel (wxWindow *parent, wxWindowID id=ID_CGROUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

bool	CGroupAlignmentsParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CGROUPALIGNMENTSPARAMSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

	CGroupAlignmentsParamsPanel::~CGroupAlignmentsParamsPanel ()

void	CGroupAlignmentsParamsPanel::Init ()

void	CGroupAlignmentsParamsPanel::CreateControls ()

void	CGroupAlignmentsParamsPanel::SetParams (SGroupAlignmentsParams params, TConstScopedObjects objects)

bool	CGroupAlignmentsParamsPanel::TransferDataToWindow ()

bool	CGroupAlignmentsParamsPanel::TransferDataFromWindow ()

wxBitmap	CGroupAlignmentsParamsPanel::GetBitmapResource (const wxString &name)

wxIcon	CGroupAlignmentsParamsPanel::GetIconResource (const wxString &name)

static bool	CGroupAlignmentsParamsPanel::ShowToolTips ()

virtual void	CGroupAlignmentsParamsPanel::SetRegistryPath (const string &path)
	CAlgoToolManagerParamsPanel. More...

virtual void	CGroupAlignmentsParamsPanel::LoadSettings ()

virtual void	CGroupAlignmentsParamsPanel::SaveSettings () const
	override in derived classes More...

	CGroupAlignmentsToolManager::CGroupAlignmentsToolManager ()

void	CGroupAlignmentsToolManager::x_SelectCompatibleInputObjects ()
	select only Seq-aligns More...

	CGroupAlignmentsJob::CGroupAlignmentsJob (const SGroupAlignmentsParams &params)
	CGroupAlignmentsJob. More...

virtual void	CGroupAlignmentsJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CKalignTool::CKalignTool ()
	CKalignTool. More...

virtual void	CKalignTool::x_SelectCompatibleInputObjects ()

	CKalignToolJob::CKalignToolJob (const CKalignToolParams &params)
	CKalignToolJob. More...

virtual wxString	CKalignToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)
	Returns the command line, that will be used to execute the third-party tool. More...

virtual TConstScopedObjects &	CKalignToolJob::x_GetObjects ()
	Returns the sequences that will be aligned. More...

	CKalignToolParams::CKalignToolParams ()

	CKalignToolParams::CKalignToolParams (const CKalignToolParams &data)

	CKalignToolParams::~CKalignToolParams ()

void	CKalignToolParams::operator= (const CKalignToolParams &data)

bool	CKalignToolParams::operator== (const CKalignToolParams &data) const

void	CKalignToolParams::Copy (const CKalignToolParams &data)

void	CKalignToolParams::Init ()

virtual void	CKalignToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CKalignToolParams::SaveSettings () const

virtual void	CKalignToolParams::LoadSettings ()

const TConstScopedObjects &	CKalignToolParams::GetObjects () const

TConstScopedObjects &	CKalignToolParams::SetObjects ()

wxString	CKalignToolParams::GetCommandLine () const

void	CKalignToolParams::SetCommandLine (wxString value)

wxString	CKalignToolParams::GetKalignPath () const

void	CKalignToolParams::SetKalignPath (wxString value)

bool	CKalignToolParams::GetQuietFlag () const

void	CKalignToolParams::SetQuietFlag (bool value)

wxString	CKalignToolParams::GetKalignExecutable () const

	CMafftTool::CMafftTool ()
	CMafftTool. More...

virtual void	CMafftTool::x_SelectCompatibleInputObjects ()

	CMafftToolJob::CMafftToolJob (const CMafftToolParams &params)
	CMafftToolJob. More...

virtual wxString	CMafftToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)
	Returns the command line, that will be used to execute the third-party tool. More...

virtual TConstScopedObjects &	CMafftToolJob::x_GetObjects ()
	Returns the sequences that will be aligned. More...

virtual wxString	CMafftToolJob::x_GetWorkingDirectory () const
	Returns the directory where to execute the msa tool. More...

	CMafftToolParams::CMafftToolParams ()

	CMafftToolParams::CMafftToolParams (const CMafftToolParams &data)

	CMafftToolParams::~CMafftToolParams ()

void	CMafftToolParams::operator= (const CMafftToolParams &data)

bool	CMafftToolParams::operator== (const CMafftToolParams &data) const

void	CMafftToolParams::Copy (const CMafftToolParams &data)

void	CMafftToolParams::Init ()

virtual void	CMafftToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CMafftToolParams::SaveSettings () const

virtual void	CMafftToolParams::LoadSettings ()

const TConstScopedObjects &	CMafftToolParams::GetObjects () const

TConstScopedObjects &	CMafftToolParams::SetObjects ()

bool	CMafftToolParams::GetAutoFlag () const

void	CMafftToolParams::SetAutoFlag (bool value)

wxString	CMafftToolParams::GetCommandLine () const

void	CMafftToolParams::SetCommandLine (wxString value)

wxString	CMafftToolParams::GetMafftPath () const

void	CMafftToolParams::SetMafftPath (wxString value)

bool	CMafftToolParams::GetQuietFlag () const

void	CMafftToolParams::SetQuietFlag (bool value)

wxString	CMafftToolParams::GetMafftExecutable () const

	SMergeAlignmentsParams::SMergeAlignmentsParams ()
	SMergeAlignmentsParams. More...

void	SMergeAlignmentsParams::Init ()

	CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel ()
	CMergeAlignmentsParamsPanel. More...

	CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

bool	CMergeAlignmentsParamsPanel::Create (wxWindow *parent, wxWindowID id=ID_CBLASTSEARCHOPTIONSPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

	CMergeAlignmentsParamsPanel::~CMergeAlignmentsParamsPanel ()

void	CMergeAlignmentsParamsPanel::Init ()

void	CMergeAlignmentsParamsPanel::CreateControls ()

bool	CMergeAlignmentsParamsPanel::TransferDataToWindow ()

bool	CMergeAlignmentsParamsPanel::TransferDataFromWindow ()

wxBitmap	CMergeAlignmentsParamsPanel::GetBitmapResource (const wxString &name)

wxIcon	CMergeAlignmentsParamsPanel::GetIconResource (const wxString &name)

static bool	CMergeAlignmentsParamsPanel::ShowToolTips ()

void	CMergeAlignmentsParamsPanel::SetParams (SMergeAlignmentsParams params, TConstScopedObjects objects)

virtual void	CMergeAlignmentsParamsPanel::SetRegistryPath (const string &path)
	CAlgoToolManagerParamsPanel. More...

virtual void	CMergeAlignmentsParamsPanel::LoadSettings ()

virtual void	CMergeAlignmentsParamsPanel::SaveSettings () const
	override in derived classes More...

	CMergeAlignmentsToolManager::CMergeAlignmentsToolManager ()
	CMergeAlignmentsToolManager. More...

void	CMergeAlignmentsToolManager::x_SelectCompatibleInputObjects ()
	select only Seq-aligns More...

	CMergeAlignmentsJob::CMergeAlignmentsJob (const SMergeAlignmentsParams &params)
	CMergeAlignmentsJob. More...

virtual void	CMergeAlignmentsJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CMPCrossAlignView::CMPCrossAlignView ()

virtual void	CMPCrossAlignView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual void	CMPCrossAlignView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

const CObject *	CMPCrossAlignView::x_GetOrigObject () const

	CMSAToolJob::CMSAToolJob (const wxString &tool_name)
	CMSAToolJob. More...

virtual	CMSAToolJob::~CMSAToolJob ()

virtual bool	CMSAToolJob::BeforeRun ()
	Function will be called on the main thread before execution of Run Should not do any lengthy work returns true to continue job execution on worker thread false to quit execution with status - failed. More...

virtual void	CMSAToolJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

virtual void	CMSAToolJob::x_AddTreeProjectItem (const string &title, const string &comment)

virtual wxString	CMSAToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)=0
	Returns the command line, that will be used to execute the third-party tool. More...

virtual TConstScopedObjects &	CMSAToolJob::x_GetObjects ()=0
	Returns the sequences that will be aligned. More...

virtual wxString	CMSAToolJob::x_GetWorkingDirectory () const
	Returns the directory where to execute the msa tool. More...

	CMultiAlignView::DECLARE_EVENT_MAP ()

	CMultiAlignView::CMultiAlignView ()

void	CMultiAlignView::OnAlnWidgetSelChanged (CEvent *evt)

void	CMultiAlignView::OnOpenGraphicalView (CEvent *evt)

virtual void	CMultiAlignView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual const SwxMenuItemRec *	CMultiAlignView::GetMenuDef () const
	simpler way to provide a static menu using macros defined earlier in this file More...

virtual bool	CMultiAlignView::x_GetValidInputData (const CObject *obj)

virtual void	CMultiAlignView::x_RebuildObjectIndex ()

virtual void	CMultiAlignView::x_GetRowSeqLoc (CAlnVec::TNumrow row, CSelectionEvent::TRangeColl &loc) const

virtual bool	CMultiAlignView::x_GetSeqRangeSelection (CAlnMultiWidget::TRangeColl &seq_coll) const

virtual void	CMultiAlignView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

virtual const CObject *	CMultiAlignView::x_GetOrigObject () const

virtual bool	CMultiAlignView::x_MergeObjects (TConstScopedObjects &objects)

	CMultiAlignViewFactory::CMultiAlignViewFactory ()

	CSelRowHandle::CSelRowHandle (IAlnExplorer::TNumrow row)

IAlnExplorer::TNumrow	CSelRowHandle::GetNumrow () const

	CMuscleTool::CMuscleTool ()
	CMuscleTool. More...

virtual void	CMuscleTool::x_SelectCompatibleInputObjects ()

	CMuscleToolJob::CMuscleToolJob (const CMuscleToolParams &params)
	CMuscleToolJob. More...

virtual wxString	CMuscleToolJob::x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide)
	Returns the command line, that will be used to execute the third-party tool. More...

virtual TConstScopedObjects &	CMuscleToolJob::x_GetObjects ()
	Returns the sequences that will be aligned. More...

	CMuscleToolParams::CMuscleToolParams ()

	CMuscleToolParams::CMuscleToolParams (const CMuscleToolParams &data)

	CMuscleToolParams::~CMuscleToolParams ()

void	CMuscleToolParams::operator= (const CMuscleToolParams &data)

bool	CMuscleToolParams::operator== (const CMuscleToolParams &data) const

void	CMuscleToolParams::Copy (const CMuscleToolParams &data)

void	CMuscleToolParams::Init ()

virtual void	CMuscleToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CMuscleToolParams::SaveSettings () const

virtual void	CMuscleToolParams::LoadSettings ()

const TConstScopedObjects &	CMuscleToolParams::GetObjects () const

TConstScopedObjects &	CMuscleToolParams::SetObjects ()

wxString	CMuscleToolParams::GetCommandLine () const

void	CMuscleToolParams::SetCommandLine (wxString value)

bool	CMuscleToolParams::GetGenerateTree () const

void	CMuscleToolParams::SetGenerateTree (bool value)

wxString	CMuscleToolParams::GetMusclePath () const

void	CMuscleToolParams::SetMusclePath (wxString value)

int	CMuscleToolParams::GetScoringMethod () const

void	CMuscleToolParams::SetScoringMethod (int value)

wxString	CMuscleToolParams::GetMuscleExecutable () const

	CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ()

	CNeedlemanWunschToolParams::CNeedlemanWunschToolParams (const CNeedlemanWunschToolParams &data)

	CNeedlemanWunschToolParams::~CNeedlemanWunschToolParams ()

void	CNeedlemanWunschToolParams::operator= (const CNeedlemanWunschToolParams &data)

bool	CNeedlemanWunschToolParams::operator== (const CNeedlemanWunschToolParams &data) const

void	CNeedlemanWunschToolParams::Copy (const CNeedlemanWunschToolParams &data)

void	CNeedlemanWunschToolParams::Init ()

virtual void	CNeedlemanWunschToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CNeedlemanWunschToolParams::SaveSettings () const

virtual void	CNeedlemanWunschToolParams::LoadSettings ()

const TConstScopedObjects &	CNeedlemanWunschToolParams::GetObjects () const

TConstScopedObjects &	CNeedlemanWunschToolParams::SetObjects ()

int	CNeedlemanWunschToolParams::GetBandSize () const

void	CNeedlemanWunschToolParams::SetBandSize (int value)

int	CNeedlemanWunschToolParams::GetFirstSeqFreeEnds () const

void	CNeedlemanWunschToolParams::SetFirstSeqFreeEnds (int value)

int	CNeedlemanWunschToolParams::GetGapExtendCost () const

void	CNeedlemanWunschToolParams::SetGapExtendCost (int value)

int	CNeedlemanWunschToolParams::GetGapOpenCost () const

void	CNeedlemanWunschToolParams::SetGapOpenCost (int value)

int	CNeedlemanWunschToolParams::GetMatchCost () const

void	CNeedlemanWunschToolParams::SetMatchCost (int value)

int	CNeedlemanWunschToolParams::GetMismatchCost () const

void	CNeedlemanWunschToolParams::SetMismatchCost (int value)

int	CNeedlemanWunschToolParams::GetSecondSeqFreeEnds () const

void	CNeedlemanWunschToolParams::SetSecondSeqFreeEnds (int value)

	CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel ()

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

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

	CNetBlastDMSearchFormPanel::~CNetBlastDMSearchFormPanel ()

void	CNetBlastDMSearchFormPanel::Init ()

void	CNetBlastDMSearchFormPanel::CreateControls ()

bool	CNetBlastDMSearchFormPanel::TransferDataToWindow ()

void	CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated (wxCommandEvent &event)

void	CNetBlastDMSearchFormPanel::OnResetClick (wxCommandEvent &event)

void	CNetBlastDMSearchFormPanel::OnSubmittedCheckClick (wxCommandEvent &event)

bool	CNetBlastDMSearchFormPanel::GetCompleted () const

void	CNetBlastDMSearchFormPanel::SetCompleted (bool value)

bool	CNetBlastDMSearchFormPanel::GetSubmitted () const

void	CNetBlastDMSearchFormPanel::SetSubmitted (bool value)

bool	CNetBlastDMSearchFormPanel::GetFailed () const

void	CNetBlastDMSearchFormPanel::SetFailed (bool value)

bool	CNetBlastDMSearchFormPanel::GetRetrieved () const

void	CNetBlastDMSearchFormPanel::SetRetrieved (bool value)

bool	CNetBlastDMSearchFormPanel::GetExpired () const

void	CNetBlastDMSearchFormPanel::SetExpired (bool value)

wxString	CNetBlastDMSearchFormPanel::GetSearchValue () const

void	CNetBlastDMSearchFormPanel::SetSearchValue (wxString value)

wxBitmap	CNetBlastDMSearchFormPanel::GetBitmapResource (const wxString &name)

wxIcon	CNetBlastDMSearchFormPanel::GetIconResource (const wxString &name)

static bool	CNetBlastDMSearchFormPanel::ShowToolTips ()

void	CNetBlastDMSearchFormPanel::RestartSearch ()

	CNetBLAST_DMSearchTool::CNetBLAST_DMSearchTool ()
	IDMSearchTool. More...

void	CNetBLAST_DMSearchTool::GetDbNames (vector< string > &name)

virtual IDMSearchTool::TUIToolFlags	CNetBLAST_DMSearchTool::GetFlags (void)
	special flags More...

virtual CRef< CSearchJobBase >	CNetBLAST_DMSearchTool::x_CreateJob (IDMSearchQuery &query)
	implementing CSearchToolBase pure virtual function More...

CNetBLASTUIDataSource *	CNetBLAST_DMSearchTool::x_GetDataSource ()

	CNetBLAST_DMSearchQuery::CNetBLAST_DMSearchQuery (const TStates &states, const string &filter_str)
	CNetBLAST_DMSearchQuery. More...

virtual string	CNetBLAST_DMSearchQuery::ToString () const
	Prepare a string representation of a query (for logging and debugging) More...

	CNetBLAST_DMSearchForm::DECLARE_EVENT_MAP ()

	CNetBLAST_DMSearchForm::CNetBLAST_DMSearchForm (CNetBLAST_DMSearchTool &tool)
	CNetBLAST_DMSearchForm. More...

virtual	CNetBLAST_DMSearchForm::~CNetBLAST_DMSearchForm ()

void	CNetBLAST_DMSearchForm::SetDataSource (CNetBLASTUIDataSource *dataSource)

void	CNetBLAST_DMSearchForm::x_OnJobDescrChanged (CEvent *)

virtual void	CNetBLAST_DMSearchForm::x_LoadSettings (const CRegistryReadView &view)

virtual void	CNetBLAST_DMSearchForm::x_SaveSettings (CRegistryWriteView view) const

IDMSearchTool *	CNetBLAST_DMSearchForm::x_GetTool (void)

	CNetBLAST_DMSearchJob::CNetBLAST_DMSearchJob (CNetBLAST_DMSearchQuery &query, CNetBLASTUIDataSource &ds)
	CNetBLAST_DMSearchJob. More...

static string	CNetBlastJobDescriptor::GetStateLabel (EState state)

virtual	CNetBlastJobDescriptor::~CNetBlastJobDescriptor ()

EState	CNetBlastJobDescriptor::GetState () const

string	CNetBlastJobDescriptor::GetRID () const

string	CNetBlastJobDescriptor::GetJobTitle () const

string	CNetBlastJobDescriptor::GetDescription () const

string	CNetBlastJobDescriptor::GetErrors () const

time_t	CNetBlastJobDescriptor::GetSubmitTime () const

void	CNetBlastJobDescriptor::Init (const CBLASTParams &params, CNetBLASTUIDataSource &ds)

void	CNetBlastJobDescriptor::Init (const string &rid, CNetBLASTUIDataSource &ds)

void	CNetBlastJobDescriptor::Submit (objects::CBioseq_set &seq_set)

void	CNetBlastJobDescriptor::Check ()

CRef< objects::CSeq_align_set >	CNetBlastJobDescriptor::Retrieve ()

CRef< blast::CRemoteBlast >	CNetBlastJobDescriptor::GetRemoteBlast ()

void	CNetBlastJobDescriptor::Release ()
	release CRemoteBlast object to free associated resources More...

void	CNetBlastJobDescriptor::MarkDeleted (bool deleted)

bool	CNetBlastJobDescriptor::IsDeleted () const

objects::CUser_object *	CNetBlastJobDescriptor::ToUserObject () const

void	CNetBlastJobDescriptor::FromUserObject (const objects::CUser_object &user_obj)

	CNetBlastJobDescriptor::CNetBlastJobDescriptor ()
	CNetBlastJobDescriptor. More...

	CNetBlastJobDescriptor::CNetBlastJobDescriptor (CNetBLASTUIDataSource &ds)

	CNetBlastJobDescriptor::CNetBlastJobDescriptor (const CNetBlastJobDescriptor &)

CNetBlastJobDescriptor &	CNetBlastJobDescriptor::operator= (const CNetBlastJobDescriptor &)

void	CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded ()

void	CNetBlastJobDescriptor::x_NotifyDataSource ()

	CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel ()

	CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel (wxWindow *parent, wxWindowID id=ID_NETBLASTLOADOPTIONPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

bool	CNetBLASTLoadOptionPanel::Create (wxWindow *parent, wxWindowID id=ID_NETBLASTLOADOPTIONPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

	CNetBLASTLoadOptionPanel::~CNetBLASTLoadOptionPanel ()

void	CNetBLASTLoadOptionPanel::Init ()

void	CNetBLASTLoadOptionPanel::CreateControls ()

wxBitmap	CNetBLASTLoadOptionPanel::GetBitmapResource (const wxString &name)

wxIcon	CNetBLASTLoadOptionPanel::GetIconResource (const wxString &name)

static bool	CNetBLASTLoadOptionPanel::ShowToolTips ()

string	CNetBLASTLoadOptionPanel::GetInput () const

void	CNetBLASTLoadOptionPanel::SetInput (const string &input)

bool	CNetBLASTLoadOptionPanel::IsInputValid ()

void	CNetBLASTLoadOptionPanel::GetRIDs (vector< string > &rids)

	CNetBLASTUIDataSourceEvent::CNetBLASTUIDataSourceEvent ()

	CNetBLASTUIDataSource::CNetBLASTUIDataSource (CNetBLASTUIDataSourceType &type)

virtual	CNetBLASTUIDataSource::~CNetBLASTUIDataSource ()

void	CNetBLASTUIDataSource::x_SaveJobDescriptors ()

void	CNetBLASTUIDataSource::x_LoadJobDescriptors ()

void	CNetBLASTUIDataSource::x_OnJobDescrChanged (CNetBlastJobDescriptor &descr)
	callback - invoked by CNetBlastJobDescriptor More...

void	CNetBLASTUIDataSource::x_StartTask (CBlastSearchTask &task)

void	CNetBLASTUIDataSource::x_AutoStartMonitoring ()

	CNetBLASTUIDataSourceType::CNetBLASTUIDataSourceType ()
	CNetBLASTUIDataSourceType. More...

	CNetBLASTUILoadManager::CNetBLASTUILoadManager (CNetBLASTUIDataSource &data_source)
	CNetBLASTUILoadManager. More...

	CNGAlignJob::CNGAlignJob (const CNGAlignParams &params)
	CNGAlignJob. More...

virtual void	CNGAlignJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CNGAlignParams::CNGAlignParams ()

	CNGAlignParams::CNGAlignParams (const CNGAlignParams &data)

	CNGAlignParams::~CNGAlignParams ()

void	CNGAlignParams::operator= (const CNGAlignParams &data)

bool	CNGAlignParams::operator== (const CNGAlignParams &data) const

void	CNGAlignParams::Copy (const CNGAlignParams &data)

void	CNGAlignParams::Init ()

virtual void	CNGAlignParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CNGAlignParams::SaveSettings () const

virtual void	CNGAlignParams::LoadSettings ()

const SConstScopedObject &	CNGAlignParams::GetSubject () const

SConstScopedObject &	CNGAlignParams::SetSubject ()

const TConstScopedObjects &	CNGAlignParams::GetQueries () const

TConstScopedObjects &	CNGAlignParams::SetQueries ()

int	CNGAlignParams::GetFilterMode () const

void	CNGAlignParams::SetFilterMode (int value)

long	CNGAlignParams::GetWordSize () const

void	CNGAlignParams::SetWordSize (long value)

double	CNGAlignParams::GetEValue () const

void	CNGAlignParams::SetEValue (double value)

bool	CNGAlignParams::GetBestHit () const

void	CNGAlignParams::SetBestHit (bool value)

wxString	CNGAlignParams::GetJobTitle () const

void	CNGAlignParams::SetJobTitle (wxString value)

wxString	CNGAlignParams::GetAdvParams () const

void	CNGAlignParams::SetAdvParams (wxString value)

int	CNGAlignParams::GetWMTaxId () const

void	CNGAlignParams::SetWMTaxId (int value)

string	CNGAlignParams::GetWMDir () const

void	CNGAlignParams::SetWMDir (string value)

void	CNGAlignParams::LogDump ()

	CNGAlignTool::CNGAlignTool ()
	CNGAlignTool. More...

void	CNGAlignTool::x_CreateBALSTPanelIfNeeded ()

virtual void	CNGAlignTool::x_SelectCompatibleInputObjects ()

wxPanel *	CNGAlignTool::x_GetCurrentPage ()

bool	CNGAlignTool::x_IsFirstPage () const

bool	CNGAlignTool::x_IsLastPage () const

bool	CNGAlignTool::x_GoFirstPage ()

bool	CNGAlignTool::x_GoNextPage ()

bool	CNGAlignTool::x_GoPrevPage ()

bool	CNGAlignTool::x_GoLastPage ()

bool	CNGAlignTool::x_LoadPage ()

	CPhyTreeView::DECLARE_EVENT_MAP ()

	CPhyTreeView::CPhyTreeView ()

	CPhyTreeView::~CPhyTreeView ()

CRef< CPhyloTreeScheme >	CPhyTreeView::GetScheme ()

CPhyloTreeWidget *	CPhyTreeView::GetWidget () const

void	CPhyTreeView::OnBioTreeChanged ()

void	CPhyTreeView::OnExportTree (CEvent *evt)

void	CPhyTreeView::OnSomethingEdited (CEvent *evt)

void	CPhyTreeView::OnCreateSelectedSubtree (CEvent *evt)

void	CPhyTreeView::CommitTheChanges (CNcbiIstrstream &istr)

void	CPhyTreeView::AppliedEditToDataSource ()

void	CPhyTreeView::RebuildObjectIndex ()

virtual void	CPhyTreeView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual void	CPhyTreeView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

virtual const CObject *	CPhyTreeView::x_GetOrigObject () const

void	CPhyTreeView::x_QueryStatusChange (CEvent *evt)

	CPhyloTreeJob::CPhyloTreeJob (const objects::CBioTreeContainer *btc)

virtual void	CPhyloTreeJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CProSplignTool::CProSplignTool ()
	CProSplignTool. More...

virtual void	CProSplignTool::x_SelectCompatibleInputObjects ()

	CMolTypeValidator::CMolTypeValidator (MolType molType)

virtual CConstRef< CObject >	CMolTypeValidator::Validate (const objects::CSeq_id &id, objects::CScope &scope, wxString &errMessage)

	CSplignPanel::CSplignPanel ()

	CSplignPanel::CSplignPanel (wxWindow *parent, wxWindowID id=ID_CSPLIGNPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCLIP_CHILDREN\|wxTAB_TRAVERSAL, bool visibale=true)

bool	CSplignPanel::Create (wxWindow *parent, wxWindowID id=ID_CSPLIGNPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCLIP_CHILDREN\|wxTAB_TRAVERSAL, bool visibale=true)

	CSplignPanel::~CSplignPanel ()

void	CSplignPanel::Init ()

void	CSplignPanel::CreateControls ()

virtual bool	CSplignPanel::TransferDataFromWindow ()

SConstScopedObject	CSplignPanel::GetGenomicSeq () const

void	CSplignPanel::SetGenomicSeq (SConstScopedObject value)

TConstScopedObjects	CSplignPanel::GetCDNASeqs () const

void	CSplignPanel::SetCDNASeqs (TConstScopedObjects value)

CSplignParams &	CSplignPanel::GetData ()

const CSplignParams &	CSplignPanel::GetData () const

void	CSplignPanel::SetData (const CSplignParams &data)

wxBitmap	CSplignPanel::GetBitmapResource (const wxString &name)

wxIcon	CSplignPanel::GetIconResource (const wxString &name)

void	CSplignPanel::SetObjects (map< string, TConstScopedObjects > genomic, map< string, TConstScopedObjects > na)

static bool	CSplignPanel::ShowToolTips ()

	CSplignParams::CSplignParams ()

	CSplignParams::CSplignParams (const CSplignParams &data)

	CSplignParams::~CSplignParams ()

void	CSplignParams::operator= (const CSplignParams &data)

bool	CSplignParams::operator== (const CSplignParams &data) const

void	CSplignParams::Copy (const CSplignParams &data)

void	CSplignParams::Init ()

virtual void	CSplignParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CSplignParams::SaveSettings () const

virtual void	CSplignParams::LoadSettings ()

double	CSplignParams::GetCompPenalty () const

void	CSplignParams::SetCompPenalty (double value)

int	CSplignParams::GetDiscType () const

void	CSplignParams::SetDiscType (int value)

bool	CSplignParams::GetEndGapDetect () const

void	CSplignParams::SetEndGapDetect (bool value)

long	CSplignParams::GetMaxGenomicExtent () const

void	CSplignParams::SetMaxGenomicExtent (long value)

long	CSplignParams::GetMaxIntron () const

void	CSplignParams::SetMaxIntron (long value)

double	CSplignParams::GetMinCompIdentity () const

void	CSplignParams::SetMinCompIdentity (double value)

double	CSplignParams::GetMinExonIdentity () const

void	CSplignParams::SetMinExonIdentity (double value)

bool	CSplignParams::GetPolyADetect () const

void	CSplignParams::SetPolyADetect (bool value)

int	CSplignParams::GetCDNAStrand () const

void	CSplignParams::SetCDNAStrand (int value)

virtual void	CSplignParams::DebugDump (CDebugDumpContext ddc, unsigned int depth) const

	CSplignTool::CSplignTool ()
	CSplignTool. More...

virtual void	CSplignTool::x_SelectCompatibleInputObjects ()

	CCommonTaxTreeTool::CCommonTaxTreeTool ()
	CCommonTaxTreeTool. More...

void	CCommonTaxTreeTool::x_SelectCompatibleInputObjects ()

	CTaxTreeToolJob::CTaxTreeToolJob (const CTaxTreeToolParams &params)
	CTaxTreeToolJob. More...

virtual void	CTaxTreeToolJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CTaxTreeToolParams::CTaxTreeToolParams ()

	CTaxTreeToolParams::CTaxTreeToolParams (const CTaxTreeToolParams &data)

	CTaxTreeToolParams::~CTaxTreeToolParams ()

void	CTaxTreeToolParams::operator= (const CTaxTreeToolParams &data)

bool	CTaxTreeToolParams::operator== (const CTaxTreeToolParams &data) const

void	CTaxTreeToolParams::Copy (const CTaxTreeToolParams &data)

void	CTaxTreeToolParams::Init ()

virtual void	CTaxTreeToolParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CTaxTreeToolParams::SaveSettings () const

virtual void	CTaxTreeToolParams::LoadSettings ()

const TConstScopedObjects &	CTaxTreeToolParams::GetObjects () const

TConstScopedObjects &	CTaxTreeToolParams::SetObjects ()

	CTreeBuilderPanel::CTreeBuilderPanel ()

	CTreeBuilderPanel::CTreeBuilderPanel (wxWindow *parent, wxWindowID id=ID_CTreeBuilderPanel, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

bool	CTreeBuilderPanel::Create (wxWindow *parent, wxWindowID id=ID_CTreeBuilderPanel, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

	CTreeBuilderPanel::~CTreeBuilderPanel ()

void	CTreeBuilderPanel::Init ()

void	CTreeBuilderPanel::CreateControls ()

virtual bool	CTreeBuilderPanel::TransferDataToWindow ()

virtual bool	CTreeBuilderPanel::TransferDataFromWindow ()

CTreeBuilderParams &	CTreeBuilderPanel::GetData ()

const CTreeBuilderParams &	CTreeBuilderPanel::GetData () const

void	CTreeBuilderPanel::SetData (const CTreeBuilderParams &data)

wxBitmap	CTreeBuilderPanel::GetBitmapResource (const wxString &name)

wxIcon	CTreeBuilderPanel::GetIconResource (const wxString &name)

void	CTreeBuilderPanel::SetObjects (TConstScopedObjects *objects)

static bool	CTreeBuilderPanel::ShowToolTips ()

	CTreeBuilderParams::CTreeBuilderParams ()

	CTreeBuilderParams::CTreeBuilderParams (const CTreeBuilderParams &data)

	CTreeBuilderParams::~CTreeBuilderParams ()

void	CTreeBuilderParams::operator= (const CTreeBuilderParams &data)

bool	CTreeBuilderParams::operator== (const CTreeBuilderParams &data) const

void	CTreeBuilderParams::Copy (const CTreeBuilderParams &data)

void	CTreeBuilderParams::Init ()

virtual void	CTreeBuilderParams::SetRegistryPath (const string &path)
	IRegSettings. More...

virtual void	CTreeBuilderParams::SaveSettings () const
	IRegSettings. More...

virtual void	CTreeBuilderParams::LoadSettings ()

const SConstScopedObject &	CTreeBuilderParams::GetObject () const

SConstScopedObject &	CTreeBuilderParams::SetObject ()

wxString	CTreeBuilderParams::GetDistanceMethod () const

void	CTreeBuilderParams::SetDistanceMethod (wxString value)

wxString	CTreeBuilderParams::GetConstructMethod () const

void	CTreeBuilderParams::SetConstructMethod (wxString value)

wxString	CTreeBuilderParams::GetLeafLabels () const

void	CTreeBuilderParams::SetLeafLabels (wxString value)

	CTreeBuilderTool::CTreeBuilderTool ()
	CTreeBuilderTool. More...

virtual void	CTreeBuilderTool::x_SelectCompatibleInputObjects ()
	select only Seq-ids More...

	CDebugMacroToolJob::CDebugMacroToolJob (const CDebugMacroToolParams &params)
	CDebugMacroToolJob. More...

virtual void	CDebugMacroToolJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CTextAlignObjectLoader::CTextAlignObjectLoader (const CTextAlignParams &params)

	CTextAlignObjectLoader::CTextAlignObjectLoader (const CTextAlignParams &params, const vector< wxString > &filenames)

void	CTextAlignObjectLoader::Init ()

void	CTextAlignObjectLoader::LoadFromStream (CNcbiIstream &istr, TObjects &objects, string &errMsg)

	CAdvancedCleanupTool::CAdvancedCleanupTool ()
	CAdvancedCleanupTool. More...

virtual void	CAdvancedCleanupTool::x_SelectCompatibleInputObjects ()

	CCreateNeedlemanWunschToolManager::CCreateNeedlemanWunschToolManager ()

void	CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects ()
	select only Seq-aligns More...

	CCreateNeedlemanWunschJob::CCreateNeedlemanWunschJob (const CNeedlemanWunschToolParams &params)
	CCreateNeedlemanWunschJob. More...

bool	CCreateNeedlemanWunschJob::ProgressCallback (const string &status, float done)

virtual CConstIRef< IAppJobProgress >	CCreateNeedlemanWunschJob::GetProgress ()
	implement Run() in derived classes, make sure that exceptions are handled and m_StopRequested flag is respected. More...

virtual void	CCreateNeedlemanWunschJob::x_CreateProjectItems ()
	override this function in derived classes and populate m_Items. More...

	CMuscleToolPanel::CMuscleToolPanel ()

	CMuscleToolPanel::CMuscleToolPanel (wxWindow *parent, wxWindowID id=ID_CMUSCLEPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)

bool	CMuscleToolPanel::Create (wxWindow *parent, wxWindowID id=ID_CMUSCLEPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visible=true)

	CMuscleToolPanel::~CMuscleToolPanel ()

void	CMuscleToolPanel::Init ()

void	CMuscleToolPanel::CreateControls ()

virtual bool	CMuscleToolPanel::TransferDataFromWindow ()

void	CMuscleToolPanel::OnMusclePathClick (wxCommandEvent &event)

CMuscleToolParams &	CMuscleToolPanel::GetData ()

const CMuscleToolParams &	CMuscleToolPanel::GetData () const

void	CMuscleToolPanel::SetData (const CMuscleToolParams &data)

wxBitmap	CMuscleToolPanel::GetBitmapResource (const wxString &name)

wxIcon	CMuscleToolPanel::GetIconResource (const wxString &name)

void	CMuscleToolPanel::SetObjects (map< string, TConstScopedObjects > *objects)

static bool	CMuscleToolPanel::ShowToolTips ()

	CNGAlignPanel::CNGAlignPanel ()

	CNGAlignPanel::CNGAlignPanel (wxWindow *parent)

bool	CNGAlignPanel::Create (wxWindow *parent, wxWindowID id=ID_CNGALIGNPANEL)

	CNGAlignPanel::~CNGAlignPanel ()

void	CNGAlignPanel::Init ()

void	CNGAlignPanel::CreateControls ()

virtual bool	CNGAlignPanel::TransferDataFromWindow ()

const SConstScopedObject &	CNGAlignPanel::GetSubject () const

SConstScopedObject &	CNGAlignPanel::SetSubject ()

const TConstScopedObjects &	CNGAlignPanel::GetQueries () const

TConstScopedObjects &	CNGAlignPanel::SetQueries ()

wxBitmap	CNGAlignPanel::GetBitmapResource (const wxString &name)

wxIcon	CNGAlignPanel::GetIconResource (const wxString &name)

void	CNGAlignPanel::SetObjects (TConstScopedObjects *objects)

static bool	CNGAlignPanel::ShowToolTips ()

	CPslLoadManager::CPslLoadManager ()
	CPslLoadManager. More...

static string	CPslLoadManager::Id ()

static string	CPslLoadManager::Label ()

	CPslLoadManager::CPage::CPage (CPslLoadManager &manager)

virtual wxPanel *	CPslLoadManager::CPage::GetPanel ()

virtual bool	CPslLoadManager::CPage::CanLeavePage (bool)

CPslParamsPanel *	CPslLoadManager::x_GetParamsPanel ()

	CTaxTreeToolPanel::CTaxTreeToolPanel ()

	CTaxTreeToolPanel::CTaxTreeToolPanel (wxWindow *parent, wxWindowID id=ID_CTAXTREETOOLPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visibale=true)

bool	CTaxTreeToolPanel::Create (wxWindow *parent, wxWindowID id=ID_CTAXTREETOOLPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL, bool visibale=true)

	CTaxTreeToolPanel::~CTaxTreeToolPanel ()

void	CTaxTreeToolPanel::Init ()

void	CTaxTreeToolPanel::CreateControls ()

virtual bool	CTaxTreeToolPanel::TransferDataFromWindow ()

CTaxTreeToolParams &	CTaxTreeToolPanel::GetData ()

const CTaxTreeToolParams &	CTaxTreeToolPanel::GetData () const

void	CTaxTreeToolPanel::SetData (const CTaxTreeToolParams &data)

wxBitmap	CTaxTreeToolPanel::GetBitmapResource (const wxString &name)

wxIcon	CTaxTreeToolPanel::GetIconResource (const wxString &name)

void	CTaxTreeToolPanel::SetObjects (map< string, TConstScopedObjects > *objects)

static bool	CTaxTreeToolPanel::ShowToolTips ()

	CTextAlignLoaderManager::CTextAlignLoaderManager ()
	CTextAlignLoaderManager. More...

static string	CTextAlignLoaderManager::Id ()

static string	CTextAlignLoaderManager::Label ()

	CTextAlignLoaderManager::CPage::CPage (CTextAlignLoaderManager &manager)

virtual wxPanel *	CTextAlignLoaderManager::CPage::GetPanel ()

virtual bool	CTextAlignLoaderManager::CPage::CanLeavePage (bool)

CTextAlignParamsPanel *	CTextAlignLoaderManager::x_GetParamsPanel ()

Variables
CConstRef< CSeq_annot >	CAlignSpanView::m_OrigAnnot
	original data object passed to the view More...

CConstRef< CSeq_align >	CAlignSpanView::m_OrigAlign

CConstRef< CBioseq >	CAlignSpanView::m_OrigBioseq

vector< CConstRef< CSeq_align > >	CAlignSpanView::m_InputAligns

CRef< IAlnMultiDataSource >	CAlignSpanView::m_DataSource

CAnchoredAln	CAlignSpanView::m_AnchoredAln

wxPanel *	CAlignSpanView::m_Panel

wxStatusBar *	CAlignSpanView::m_StatusBar

CAlnSpanWidget *	CAlignSpanView::m_AlnWidget

unique_ptr< CAlnSpanVertModel >	CAlignSpanView::m_Model

CRef< CScope >	CAlignSpanView::m_Scope

CRef< CSeq_id >	CAlignSpanView::m_Seq_id

string	CAlignSpanView::m_RegPath

static CProjectViewTypeDescriptor	CAlignSpanView::m_TypeDescr

TAlignVector	CAnnotCompareView::m_Aligns

CAnnotCompareWidget *	CAnnotCompareView::m_AnnWidget

size_t	CBLAST_Dlg_Item::m_LabelPos

size_t	CBLAST_Dlg_Item::m_LabelLength

string	CBLAST_Dlg_Item::m_Path

bool	CBLAST_Dlg_Item::m_IsDatabase

bool	CBLAST_Dlg_Item::m_Visible

bool	CBLAST_Dlg_Item::m_Expanded

CBLAST_Dlg_Item *	CBLAST_Dlg_Item::m_Parent

TNameToItemMap *	CBLAST_Dlg_Item::m_ChildItems

wxTreeItemId	CBLAST_Dlg_Item::m_Id

wxTextCtrl *	CBLAST_DB_Dialog::m_SearchCtrl

wxStaticText *	CBLAST_DB_Dialog::m_StatusText

wxTreeCtrl *	CBLAST_DB_Dialog::m_TreeCtrl

wxButton *	CBLAST_DB_Dialog::m_OKBtn

const TDbMap *	CBLAST_DB_Dialog::m_DbMap

CRef< CBLAST_Dlg_Item >	CBLAST_DB_Dialog::m_Root

TItemDeque	CBLAST_DB_Dialog::m_CatItems

TItemDeque	CBLAST_DB_Dialog::m_DbItems

string	CBLAST_DB_Dialog::m_SelDatabase

CFastMutex	CNetBlastSubmittingJob::m_Mutex

string	CNetBlastSubmittingJob::m_Descr
	mutex to sync our internals More...

string	CNetBlastSubmittingJob::m_Status

TConstScopedObjects	CNetBlastSubmittingJob::m_SeqLocs

vector< CRef< CNetBlastJobDescriptor > >	CNetBlastSubmittingJob::m_Descriptors

vector< string >	CNetBlastSubmittingJob::m_Errors

CRef< CAppJobError >	CNetBlastSubmittingJob::m_Error

CFastMutex	CNetBlastMonitoringJob::m_Mutex

string	CNetBlastMonitoringJob::m_ToolName
	mutex to sync our internals More...

IServiceLocator *	CNetBlastMonitoringJob::m_SrvLocator

CRef< CNetBLASTUIDataSource >	CNetBlastMonitoringJob::m_NetBlastDS

string	CNetBlastMonitoringJob::m_Descr

string	CNetBlastMonitoringJob::m_Status

CSelectProjectOptions	CNetBlastMonitoringJob::m_LoadingOptions

int	CNetBlastMonitoringJob::m_WaitPeriodIndex

TDescriptors	CNetBlastMonitoringJob::m_Descriptors

vector< string >	CNetBlastMonitoringJob::m_Errors

CRef< CAppJobError >	CNetBlastMonitoringJob::m_Error

TDescriptors	CNetBlastLoadingJob::m_Descriptors

vector< string >	CNetBlastLoadingJob::m_Errors

CScope *	CNetBlastLoadingJob::m_Scope

wxRadioButton *	CBLASTSearchOptionsPanel::m_NucRadio

wxRadioButton *	CBLASTSearchOptionsPanel::m_ProtRadio

wxStaticText *	CBLASTSearchOptionsPanel::m_QuerySeqSetStatic

wxChoice *	CBLASTSearchOptionsPanel::m_QuerySeqSetCombo

CObjectListWidget *	CBLASTSearchOptionsPanel::m_QueryListCtrl

wxComboBox *	CBLASTSearchOptionsPanel::m_ProgramCombo

wxStaticBoxSizer *	CBLASTSearchOptionsPanel::m_LocalSizer

wxRadioButton *	CBLASTSearchOptionsPanel::m_SubjectTypeSeqsCtrl

wxRadioButton *	CBLASTSearchOptionsPanel::m_SubjectTypeNCBICtrl

wxRadioButton *	CBLASTSearchOptionsPanel::m_SubjectTypeLDBCtrl

wxStaticText *	CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic

wxChoice *	CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo

wxBoxSizer *	CBLASTSearchOptionsPanel::m_LocalSeqsSizer

CObjectListWidget *	CBLASTSearchOptionsPanel::m_SubjectListCtrl

wxFlexGridSizer *	CBLASTSearchOptionsPanel::m_NCBIDBSizer

wxBoxSizer *	CBLASTSearchOptionsPanel::m_DBSizer

wxComboBox *	CBLASTSearchOptionsPanel::m_DatabaseCombo

wxBitmapButton *	CBLASTSearchOptionsPanel::m_BrowseDBBtn

wxComboBox *	CBLASTSearchOptionsPanel::m_QueryCombo

wxBoxSizer *	CBLASTSearchOptionsPanel::m_LocalDBSizer

wxTextCtrl *	CBLASTSearchOptionsPanel::m_LocalDBCtrl

wxCheckBox *	CBLASTSearchOptionsPanel::m_LocalDBLoaderCtrl

CNetBLASTUIDataSource *	CBLASTSearchOptionsPanel::m_DataSource

string	CBLASTSearchOptionsPanel::m_ToolName

map< string, TConstScopedObjects > *	CBLASTSearchOptionsPanel::m_NucObjects

map< string, TConstScopedObjects > *	CBLASTSearchOptionsPanel::m_ProtObjects

CBLASTParams *	CBLASTSearchOptionsPanel::m_Params

wxTimer	CBLASTSearchOptionsPanel::m_Timer

int	CBLASTSearchOptionsPanel::m_DBLoadState

string	CBLASTSearchOptionsPanel::m_CurrentQuerySet

string	CBLASTSearchOptionsPanel::m_CurrentSubjectSet

blast::EProgram	CBLASTParams::SProgInfo::m_Program

string	CBLASTParams::SProgInfo::m_Label

bool	CBLASTParams::SProgInfo::m_NucInput

bool	CBLASTParams::SProgInfo::m_NucDB

bool	CBLASTParams::SProgInfo::m_NeedsThreshold

bool	CBLASTParams::SProgInfo::m_NeedsQueryGenCode

bool	CBLASTParams::SProgInfo::m_NeedsDbGenCode

bool	CBLASTParams::SProgInfo::m_UseDustFilter

int	CBLASTParams::SProgParams::m_Threshold

int	CBLASTParams::SProgParams::m_WordSize

double	CBLASTParams::SProgParams::m_eValue

bool	CBLASTParams::SProgParams::m_FilterLowComplex

int	CBLASTParams::SProgParams::m_QueryGeneticCode

int	CBLASTParams::SProgParams::m_DbGeneticCode

bool	CBLASTParams::SProgParams::m_MaskLowercase
	mask Lowercase features More...

bool	CBLASTParams::SProgParams::m_MaskRepeats
	mask Repeat features More...

string	CBLASTParams::SProgParams::m_RepeatLib

int	CBLASTParams::SProgParams::m_WM_TaxId
	winmask tax id More...

static TProgramAttrMap	CBLASTParams::sm_ProgramToAttr

bool	CBLASTParams::m_NucInput

TConstScopedObjects	CBLASTParams::m_SeqLocs

blast::EProgram	CBLASTParams::m_NucProgram

blast::EProgram	CBLASTParams::m_ProtProgram

string	CBLASTParams::m_NucDatabase

string	CBLASTParams::m_ProtDatabase

TMRUDatabases	CBLASTParams::m_NucMRUDatabases

TMRUDatabases	CBLASTParams::m_ProtMRUDatabases

string	CBLASTParams::m_EntrezQuery
	Params applying only to BLAST Search. More...

TMRUQueries	CBLASTParams::m_MRUQueries

TConstScopedObjects	CBLASTParams::m_SubjSeqLocs
	Params applying only to BLAST Sequences. More...

TProgramParamsMap	CBLASTParams::m_ProgToParams
	Common parameters. More...

string	CBLASTParams::m_AdvancedParams

string	CBLASTParams::m_JobTitle

bool	CBLASTParams::mf_FindComparts

bool	CBLASTParams::mf_Standalone

string	CBLASTParams::m_WM_Dir
	path to WM statistics databases More...

string	CBLASTParams::m_LocalNucDB

string	CBLASTParams::m_LocalProtDB

ESubjectType	CBLASTParams::m_SubjectType

bool	CBLASTParams::m_LocalDBLoader

wxFlexGridSizer *	CBLASTSearchParamsPanel::m_GeneralSizer

wxStaticText *	CBLASTSearchParamsPanel::m_ThreshLabel

wxTextCtrl *	CBLASTSearchParamsPanel::m_ThreshInput

wxStaticText *	CBLASTSearchParamsPanel::m_QueryGenCodeLabel

wxComboBox *	CBLASTSearchParamsPanel::m_QueryGenCodeCombo

wxStaticText *	CBLASTSearchParamsPanel::m_DbGenCodeLabel

wxComboBox *	CBLASTSearchParamsPanel::m_DbGenCodeCombo

wxChoice *	CBLASTSearchParamsPanel::m_RepeatType

wxCheckBox *	CBLASTSearchParamsPanel::m_LCRegionsCheck

wxCheckBox *	CBLASTSearchParamsPanel::m_RepeatsCheck

wxStaticBoxSizer *	CBLASTSearchParamsPanel::m_WMStaticBoxSizer

wxStaticText *	CBLASTSearchParamsPanel::m_WMStatic

wxChoice *	CBLASTSearchParamsPanel::m_WMTaxIds

wxButton *	CBLASTSearchParamsPanel::m_WMDownload

wxCheckBox *	CBLASTSearchParamsPanel::m_CompartCheck

wxCheckBox *	CBLASTSearchParamsPanel::m_chbStandalone

wxString	CBLASTSearchParamsPanel::m_AdvParams

wxString	CBLASTSearchParamsPanel::m_DbGeneticCode

double	CBLASTSearchParamsPanel::m_eValue

bool	CBLASTSearchParamsPanel::m_FilterLowComplex

wxString	CBLASTSearchParamsPanel::m_JobTitle

bool	CBLASTSearchParamsPanel::m_MaskLCRegions

bool	CBLASTSearchParamsPanel::m_MaskRepeats

wxString	CBLASTSearchParamsPanel::m_QueryGeneticCode

long	CBLASTSearchParamsPanel::m_Threshold

long	CBLASTSearchParamsPanel::m_WordSize

CBLASTParams *	CBLASTSearchParamsPanel::m_Params

bool	CBLASTSearchParamsPanel::m_Local

CTaxIdHelper::CAutoDelete	CBLASTSearchParamsPanel::m_AutoDelete

IServiceLocator *	CBlastSearchTask::m_SrvLocator

CRef< CNetBLASTUIDataSource >	CBlastSearchTask::m_NetBlastDS

string	CBlastSearchTask::m_ToolName
	name of the tool that launched the task; used in UI More...

ECommand	CBlastSearchTask::m_Command
	the command associated with the task More...

CSelectProjectOptions	CBlastSearchTask::m_LoadingOptions

string	CBlastSearchTask::m_ProjectFolderName

CRef< objects::CGBProjectHandle >	CBlastSearchTask::m_TargetProject

ECommand	CBlastSearchTask::m_Stage
	defines the current stage of the task More...

CRef< CNetBlastSubmittingJob >	CBlastSearchTask::m_SubmittingJob

CRef< CNetBlastMonitoringJob >	CBlastSearchTask::m_MonitoringJob

CRef< CNetBlastLoadingJob >	CBlastSearchTask::m_LoadingJob

CIRef< IAppTask >	CBlastSearchTask::m_CurrTask

CBLASTParams	CBLASTSeqToolJob::m_Params

TProcessHandle	CBLASTSeqToolJob::m_ProcHandle

CUIObject	CBLASTToolManager::m_Descriptor
	describes the Manager's UI properties More...

IServiceLocator *	CBLASTToolManager::m_SrvLocator

wxWindow *	CBLASTToolManager::m_ParentWindow

string	CBLASTToolManager::m_RegPath

string	CBLASTToolManager::m_LocalWinMaskDirPath

vector< TConstScopedObjects >	CBLASTToolManager::m_InputObjects

map< string, TConstScopedObjects >	CBLASTToolManager::m_NucObjects

map< string, TConstScopedObjects >	CBLASTToolManager::m_ProtObjects

bool	CBLASTToolManager::m_UseNucForMixInput

CBLASTParams	CBLASTToolManager::m_Params

EState	CBLASTToolManager::m_State

CBLASTSearchOptionsPanel *	CBLASTToolManager::m_OptionsPanel

CBLASTSearchParamsPanel *	CBLASTToolManager::m_ParamsPanel

SProjectSelectorParams	CBLASTToolManager::m_ProjectParams

string	SCleanupAlignmentsParams::m_RegPath

TConstScopedObjects	SCleanupAlignmentsParams::m_Alignments

EAlgorithm	SCleanupAlignmentsParams::m_Algo

int	SCleanupAlignmentsParams::m_HitFilter_MinLength

float	SCleanupAlignmentsParams::m_HitFilter_MinIdentity

bool	SCleanupAlignmentsParams::m_AlnMgr_PreserveRows

bool	SCleanupAlignmentsParams::m_AlnMgr_Transloc

bool	SCleanupAlignmentsParams::m_AlnMgr_Sort

bool	SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned

CObjectListWidget *	CCleanupAlignmentsParamsPanel::m_ObjectList

wxComboBox *	CCleanupAlignmentsParamsPanel::m_AlgoSelector

wxBoxSizer *	CCleanupAlignmentsParamsPanel::m_ParamsPanel

wxTextCtrl *	CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity

wxTextCtrl *	CCleanupAlignmentsParamsPanel::m_HitFilter_MinLength

wxCheckBox *	CCleanupAlignmentsParamsPanel::m_AlnMgr_Transloc

wxCheckBox *	CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort

wxCheckBox *	CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows

wxCheckBox *	CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned

SCleanupAlignmentsParams *	CCleanupAlignmentsParamsPanel::m_Params

TConstScopedObjects *	CCleanupAlignmentsParamsPanel::m_InputObjects

bool	CCleanupAlignmentsParamsPanel::m_InputListDirty

string	CCleanupAlignmentsParamsPanel::m_RegPath

TConstScopedObjects	CCleanupAlignmentsToolManager::m_Alignments

SCleanupAlignmentsParams	CCleanupAlignmentsToolManager::m_Params

CCleanupAlignmentsParamsPanel *	CCleanupAlignmentsToolManager::m_ParamsPanel

SCleanupAlignmentsParams	CCleanupAlignmentsJob::m_Params

TObjects	CClustalOmegaTool::m_Objects

CClustalOmegaToolParams	CClustalOmegaTool::m_Params

CClustalOmegaToolPanel *	CClustalOmegaTool::m_Panel

CClustalOmegaToolParams	CClustalOmegaToolJob::m_Params

wxString	CClustalOmegaToolParams::m_ClustalOmegaPath

wxString	CClustalOmegaToolParams::m_CommandLine

bool	CClustalOmegaToolParams::m_GenerateTree

string	CClustalOmegaToolParams::m_RegPath

TConstScopedObjects	CClustalOmegaToolParams::m_Objects

TObjects	CClustalwTool::m_Objects

CClustalwToolParams	CClustalwTool::m_Params

CClustalwToolPanel *	CClustalwTool::m_Panel

CClustalwToolParams	CClustalwToolJob::m_Params

wxString	CClustalwToolParams::m_ClustalWPath

wxString	CClustalwToolParams::m_CommandLine

bool	CClustalwToolParams::m_GenerateTree

string	CClustalwToolParams::m_RegPath

TConstScopedObjects	CClustalwToolParams::m_Objects

TConstScopedObjects	CCreateGeneModelToolManager::m_Alignments

SCreateGeneModelParams	CCreateGeneModelToolManager::m_Params

CCreateGeneModelParamsPanel *	CCreateGeneModelToolManager::m_ParamsPanel

CRef< objects::CSeq_feat >	SGeneCdsmRnaFeats::gene

CRef< objects::CSeq_feat >	SGeneCdsmRnaFeats::cds

CRef< objects::CSeq_feat >	SGeneCdsmRnaFeats::mRNA

static const string	CCreateGeneModelTask::sGeneDbName
	CCreateGeneModelTask. More...

CIRef< CProjectService >	CCreateGeneModelTask::m_Service

CSelectProjectOptions	CCreateGeneModelTask::m_Options

SCreateGeneModelParams	CCreateGeneModelTask::m_Params

TGeneModelMap	CCreateGeneModelTask::m_GeneModelMap

CSelectProjectOptions::TItems	CCreateGeneModelTask::m_Items

CRef< objects::CScope >	CCreateGeneModelTask::m_Scope

TAlignVector	CDotMatrixView::m_Aligns

CIRef< IHitMatrixDataSource >	CDotMatrixView::m_DataSource

CHitMatrixWidget *	CDotMatrixView::m_AlnWidget

static CProjectViewTypeDescriptor	CDotMatrixView::m_TypeDescr

CRef< COpenViewManager >	CDotMatrixViewFactory::m_ViewManager

CObjectListWidget *	CFindOverlapPanel::m_Seq1List

CObjectListWidget *	CFindOverlapPanel::m_Seq2List

CFindOverlapParams	CFindOverlapPanel::m_data

TConstScopedObjects *	CFindOverlapPanel::m_InputObjects

wxString	CFindOverlapParams::m_BlastParams

int	CFindOverlapParams::m_FilterQty

wxString	CFindOverlapParams::m_MaxSlop

string	CFindOverlapParams::m_RegPath

SConstScopedObject	CFindOverlapParams::m_Seq1

SConstScopedObject	CFindOverlapParams::m_Seq2

TConstScopedObjects	CFindOverlapTool::m_SeqIds

CFindOverlapParams	CFindOverlapTool::m_Params

CFindOverlapPanel *	CFindOverlapTool::m_Panel

string	SGroupAlignmentsParams::m_RegPath

TConstScopedObjects	SGroupAlignmentsParams::m_Alignments

bool	SGroupAlignmentsParams::m_GroupBySeqId

bool	SGroupAlignmentsParams::m_GroupByStrand

bool	SGroupAlignmentsParams::m_GroupByTaxId

bool	SGroupAlignmentsParams::m_GroupByLikeTaxId

bool	SGroupAlignmentsParams::m_GroupByRefSeq

bool	SGroupAlignmentsParams::m_GroupByPredictedRefSeq

bool	SGroupAlignmentsParams::m_GroupByEST

bool	SGroupAlignmentsParams::m_GroupByGenBank

bool	SGroupAlignmentsParams::m_GroupByWGS

bool	SGroupAlignmentsParams::m_GroupByHTGS

bool	SGroupAlignmentsParams::m_GroupByPatent

CObjectListWidget *	CGroupAlignmentsParamsPanel::m_ObjectList

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupBySeqId

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByStrand

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByTaxId

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByRefSeq

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByEST

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByGenBank

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByWGS

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByHTGS

wxCheckBox *	CGroupAlignmentsParamsPanel::m_GroupByPatent

SGroupAlignmentsParams *	CGroupAlignmentsParamsPanel::m_Params

TConstScopedObjects *	CGroupAlignmentsParamsPanel::m_InputObjects

bool	CGroupAlignmentsParamsPanel::m_InputListDirty

string	CGroupAlignmentsParamsPanel::m_RegPath

TConstScopedObjects	CGroupAlignmentsToolManager::m_Alignments

SGroupAlignmentsParams	CGroupAlignmentsToolManager::m_Params

CGroupAlignmentsParamsPanel *	CGroupAlignmentsToolManager::m_ParamsPanel

SGroupAlignmentsParams	CGroupAlignmentsJob::m_Params

TObjects	CKalignTool::m_Objects

CKalignToolParams	CKalignTool::m_Params

CKalignToolPanel *	CKalignTool::m_Panel

CKalignToolParams	CKalignToolJob::m_Params

wxString	CKalignToolParams::m_CommandLine

wxString	CKalignToolParams::m_KalignPath

bool	CKalignToolParams::m_QuietFlag

string	CKalignToolParams::m_RegPath

TConstScopedObjects	CKalignToolParams::m_Objects

TObjects	CMafftTool::m_Objects

CMafftToolParams	CMafftTool::m_Params

CMafftToolPanel *	CMafftTool::m_Panel

CMafftToolParams	CMafftToolJob::m_Params

bool	CMafftToolParams::m_AutoFlag

wxString	CMafftToolParams::m_CommandLine

wxString	CMafftToolParams::m_MafftPath

bool	CMafftToolParams::m_QuietFlag

string	CMafftToolParams::m_RegPath

TConstScopedObjects	CMafftToolParams::m_Objects

string	SMergeAlignmentsParams::m_RegPath

TConstScopedObjects	SMergeAlignmentsParams::m_Alignments

int	SMergeAlignmentsParams::m_Direction

int	SMergeAlignmentsParams::m_MergeAlgo

int	SMergeAlignmentsParams::m_MergeFlags

bool	SMergeAlignmentsParams::m_FillUnaligned

CObjectListWidget *	CMergeAlignmentsParamsPanel::m_ObjectListCtrl

wxCheckBox *	CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly

wxCheckBox *	CMergeAlignmentsParamsPanel::m_AssumeNegStrand

wxCheckBox *	CMergeAlignmentsParamsPanel::m_TruncateOverlap

wxCheckBox *	CMergeAlignmentsParamsPanel::m_SortInput

wxCheckBox *	CMergeAlignmentsParamsPanel::m_FillUnaligned

SMergeAlignmentsParams *	CMergeAlignmentsParamsPanel::m_Params

TConstScopedObjects *	CMergeAlignmentsParamsPanel::m_InputObjects

bool	CMergeAlignmentsParamsPanel::m_InputListDirty

string	CMergeAlignmentsParamsPanel::m_RegPath

TConstScopedObjects	CMergeAlignmentsToolManager::m_Alignments

SMergeAlignmentsParams	CMergeAlignmentsToolManager::m_Params

CMergeAlignmentsParamsPanel *	CMergeAlignmentsToolManager::m_ParamsPanel

SMergeAlignmentsParams	CMergeAlignmentsJob::m_Params

CConstRef< CSeq_annot >	CMPCrossAlignView::m_OrigAnnot
	original data object passed to the view More...

CConstRef< CSeq_align >	CMPCrossAlignView::m_OrigAlign

CIRef< ICrossAlnDataSource >	CMPCrossAlignView::m_DataSource

wxSplitterWindow *	CMPCrossAlignView::m_MainSplitter

TViews	CMPCrossAlignView::m_Views

static CProjectViewTypeDescriptor	CMPCrossAlignView::m_TypeDescr

wxString	CMSAToolJob::m_TmpIn

wxString	CMSAToolJob::m_TmpOut

wxString	CMSAToolJob::m_TmpTreeOut

long	CMSAToolJob::m_PId

TIdMap	CMSAToolJob::m_IdMap
	to make the alignment as robust as possible, we assign every sequence a unique identifer independeont of its existing identifiers this map allows us to convert back at the end More...

TSeqTypeMap	CMSAToolJob::m_SeqTypes

objects::CMappingRanges	CMSAToolJob::m_Ranges

wxString	CMSAToolJob::m_CmdLine

wxString	CMSAToolJob::m_ToolName

string	CMultiAlignView::m_RegPath

CRowStyleCatalog	CMultiAlignView::m_StyleCatalog

vector< string >	CMultiAlignView::m_ScoringMethods

string	CMultiAlignView::m_CurrentMethod

CAlnMultiDSBuilder	CMultiAlignView::m_Builder

bool	CMultiAlignView::m_Sparse

CConstRef< objects::CSeq_annot >	CMultiAlignView::m_OrigAnnot
	original data object passed to the view More...

CConstRef< objects::CSeq_align >	CMultiAlignView::m_OrigAlign

CIRef< IAlnMultiDataSource >	CMultiAlignView::m_DataSource

CAlnMultiWidget *	CMultiAlignView::m_AlnWidget

CObjectIndex	CMultiAlignView::m_ObjIndex

CRef< COpenViewManager >	CMultiAlignViewFactory::m_ViewManager

IAlnExplorer::TNumrow	CSelRowHandle::m_Numrow

TObjects	CMuscleTool::m_Objects

CMuscleToolParams	CMuscleTool::m_Params

CMuscleToolPanel *	CMuscleTool::m_Panel

CMuscleToolParams	CMuscleToolJob::m_Params

wxString	CMuscleToolParams::m_CommandLine

bool	CMuscleToolParams::m_GenerateTree

wxString	CMuscleToolParams::m_MusclePath

int	CMuscleToolParams::m_ScoringMethod

string	CMuscleToolParams::m_RegPath

TConstScopedObjects	CMuscleToolParams::m_Objects

int	CNeedlemanWunschToolParams::m_BandSize

int	CNeedlemanWunschToolParams::m_FirstSeqFreeEnds

int	CNeedlemanWunschToolParams::m_GapExtendCost

int	CNeedlemanWunschToolParams::m_GapOpenCost

int	CNeedlemanWunschToolParams::m_MatchCost

int	CNeedlemanWunschToolParams::m_MismatchCost

int	CNeedlemanWunschToolParams::m_SecondSeqFreeEnds

string	CNeedlemanWunschToolParams::m_RegPath

TConstScopedObjects	CNeedlemanWunschToolParams::m_Objects

wxTextCtrl *	CNetBlastDMSearchFormPanel::m_SearchCtrl

wxButton *	CNetBlastDMSearchFormPanel::m_ResetBtn

bool	CNetBlastDMSearchFormPanel::m_Completed

bool	CNetBlastDMSearchFormPanel::m_Submitted

bool	CNetBlastDMSearchFormPanel::m_Failed

bool	CNetBlastDMSearchFormPanel::m_Retrieved

bool	CNetBlastDMSearchFormPanel::m_Expired

wxString	CNetBlastDMSearchFormPanel::m_SearchValue

bool	CNetBlastDMSearchFormPanel::m_BlockEvents

IServiceLocator *	CNetBLAST_DMSearchTool::m_SrvLocator

TStates	CNetBLAST_DMSearchQuery::m_States
	select only Jobs with states from this set More...

string	CNetBLAST_DMSearchQuery::m_FilterStr
	select only Jobs that have attributes containg this string More...

CRef< CNetBLAST_DMSearchTool >	CNetBLAST_DMSearchForm::m_Tool

CNetBlastDMSearchFormPanel *	CNetBLAST_DMSearchForm::m_Panel

CRef< CNetBLASTUIDataSource >	CNetBLAST_DMSearchForm::m_NetBlastDS

CRef< CNetBLAST_DMSearchQuery >	CNetBLAST_DMSearchJob::m_Query

CRef< CNetBLASTUIDataSource >	CNetBLAST_DMSearchJob::m_NetBlastDS

CMutex	CNetBlastJobDescriptor::m_Mutex

CNetBLASTUIDataSource *	CNetBlastJobDescriptor::m_NetBlastDS

EState	CNetBlastJobDescriptor::m_State

string	CNetBlastJobDescriptor::m_RID
	Job attributes. More...

string	CNetBlastJobDescriptor::m_JobTitle

string	CNetBlastJobDescriptor::m_Description

string	CNetBlastJobDescriptor::m_Errors

time_t	CNetBlastJobDescriptor::m_SubmitTime

bool	CNetBlastJobDescriptor::m_Deleted

CRef< blast::CRemoteBlast >	CNetBlastJobDescriptor::m_RemoteBlast
	a proxy to Net BLAST that is used for updating Job state More...

CUIObject	CNetBLASTUIDataSource::m_Descr

CRef< CNetBLASTUIDataSourceType >	CNetBLASTUIDataSource::m_Type

IServiceLocator *	CNetBLASTUIDataSource::m_SrvLocator

string	CNetBLASTUIDataSource::m_RegPath

bool	CNetBLASTUIDataSource::m_Open

TJobDescrVec	CNetBLASTUIDataSource::m_JobDescrs

CFastMutex	CNetBLASTUIDataSource::m_JobDescrMutex

CUIObject	CNetBLASTUIDataSourceType::m_Descr

CRef< CNetBLASTUIDataSource >	CNetBLASTUILoadManager::m_DataSource

IServiceLocator *	CNetBLASTUILoadManager::m_SrvLocator

wxWindow *	CNetBLASTUILoadManager::m_ParentWindow

CUIObject	CNetBLASTUILoadManager::m_Descriptor

EState	CNetBLASTUILoadManager::m_State

string	CNetBLASTUILoadManager::m_RegPath

string	CNetBLASTUILoadManager::m_SavedInput

CNetBLASTLoadOptionPanel *	CNetBLASTUILoadManager::m_OptionPanel

CProjectSelectorPanel *	CNetBLASTUILoadManager::m_ProjectSelPanel

SProjectSelectorParams	CNetBLASTUILoadManager::m_ProjectParams

CNGAlignParams	CNGAlignJob::m_Params

bool	CNGAlignParams::m_BestHit

int	CNGAlignParams::m_FilterMode

long	CNGAlignParams::m_WordSize

double	CNGAlignParams::m_eValue

wxString	CNGAlignParams::m_JobTitle

wxString	CNGAlignParams::m_AdvParams

int	CNGAlignParams::m_WM_TaxId

string	CNGAlignParams::m_WM_Dir

string	CNGAlignParams::m_RegPath

SConstScopedObject	CNGAlignParams::m_Subject

TConstScopedObjects	CNGAlignParams::m_Queries

TConstScopedObjects	CNGAlignTool::m_SeqIds

TConstScopedObjects	CNGAlignTool::m_SeqLocs

CNGAlignParams	CNGAlignTool::m_Params

CNGAlignPanel *	CNGAlignTool::m_Panel

CNGAlignBLASTPanel *	CNGAlignTool::m_BLASTPanel

int	CNGAlignTool::m_CurrentPage

CConstRef< objects::CBioTreeContainer >	CPhyTreeView::m_BioTreeContainer

CRef< objects::CBioTreeContainer >	CPhyTreeView::m_Cont

CPhyloTree::TTreeIdx	CPhyTreeView::m_CurrentNode

CRef< CPhyloTreeDataSource >	CPhyTreeView::m_DataSource

CRef< CPhyloTreeScheme >	CPhyTreeView::m_Scheme

wxPanel *	CPhyTreeView::m_Panel

CObjectIndex	CPhyTreeView::m_ObjectIndex

bool	CPhyTreeView::m_EditUpdate

int	CPhyTreeView::m_InitialRotateLabels
	If rendering parms are stored in biotreecontainer, set them first time. More...

int	CPhyTreeView::m_InitialUseDistances

int	CPhyTreeView::m_InitialLayout

CRef< objects::CBioTreeContainer >	CPhyloTreeJob::m_Btc

TObjects	CProSplignTool::m_ProteinObjects

TObjects	CProSplignTool::m_NAObjects

CProSplignParams	CProSplignTool::m_Params

CProSplignPanel *	CProSplignTool::m_Panel

MolType	CMolTypeValidator::m_MolType

CObjectListWidgetSel *	CSplignPanel::m_GenomicList

CObjectListWidgetSel *	CSplignPanel::m_cDNAList

SConstScopedObject	CSplignPanel::m_GenomicSeq

TConstScopedObjects	CSplignPanel::m_cDNASeqs

CSplignParams	CSplignPanel::m_data

string	CSplignPanel::m_RegPath

CMolTypeValidator	CSplignPanel::m_GenomicListAccValidator

CMolTypeValidator	CSplignPanel::m_CDNAListAccValidator

double	CSplignParams::m_CompPenalty

int	CSplignParams::m_DiscType

bool	CSplignParams::m_EndGapDetect

long	CSplignParams::m_MaxGenomicExtent

long	CSplignParams::m_MaxIntron

double	CSplignParams::m_MinCompIdentity

double	CSplignParams::m_MinExonIdentity

bool	CSplignParams::m_PolyADetect

int	CSplignParams::m_cDNA_strand

string	CSplignParams::m_RegPath

TObjects	CSplignTool::m_GenomicObjects

TObjects	CSplignTool::m_NAObjects

CSplignParams	CSplignTool::m_Params

CSplignPanel *	CSplignTool::m_Panel

TObjects	CCommonTaxTreeTool::m_Objects

CTaxTreeToolParams	CCommonTaxTreeTool::m_Params

CTaxTreeToolPanel *	CCommonTaxTreeTool::m_Panel

CTaxTreeToolParams	CTaxTreeToolJob::m_Params

string	CTaxTreeToolParams::m_RegPath

TConstScopedObjects	CTaxTreeToolParams::m_Objects

CObjectListWidget *	CTreeBuilderPanel::m_Seq1List

CTreeBuilderParams	CTreeBuilderPanel::m_data

TConstScopedObjects *	CTreeBuilderPanel::m_InputObjects

wxChoice *	CTreeBuilderPanel::m_pDistance

wxChoice *	CTreeBuilderPanel::m_pConstruct

wxChoice *	CTreeBuilderPanel::m_pLabels

wxString	CTreeBuilderParams::m_DistanceMethod

wxString	CTreeBuilderParams::m_ConstructMethod

wxString	CTreeBuilderParams::m_LeafLabels

string	CTreeBuilderParams::m_RegPath

SConstScopedObject	CTreeBuilderParams::m_Object

TConstScopedObjects	CTreeBuilderTool::m_SeqIds

CTreeBuilderParams	CTreeBuilderTool::m_Params

CTreeBuilderPanel *	CTreeBuilderTool::m_Panel

CDebugMacroToolParams	CDebugMacroToolJob::m_Params

CTextAlignParams	CTextAlignObjectLoader::m_Params

vector< wxString >	CTextAlignObjectLoader::m_FileNames

TObjects	CTextAlignObjectLoader::m_Objects

CRef< objects::CScope >	CTextAlignObjectLoader::m_Scope

TConstScopedObjects	CAdvancedCleanupTool::m_Alignments

CAdvancedCleanupParams	CAdvancedCleanupTool::m_Params

CAdvancedCleanupParamsPanel *	CAdvancedCleanupTool::m_Panel

TConstScopedObjects	CCreateNeedlemanWunschToolManager::m_Objects

CNeedlemanWunschToolParams	CCreateNeedlemanWunschToolManager::m_Params

CAlignNeedlemanWunschPanel *	CCreateNeedlemanWunschToolManager::m_Panel

CNeedlemanWunschToolParams	CCreateNeedlemanWunschJob::m_Params

float	CCreateNeedlemanWunschJob::m_Done

CObjectListWidgetSel *	CMuscleToolPanel::m_LocationSel

CMuscleToolParams	CMuscleToolPanel::m_data

TConstScopedObjects *	CMuscleToolPanel::m_InputObjects

CObjectListWidget *	CNGAlignPanel::m_QueryListCtrl

CObjectListWidget *	CNGAlignPanel::m_SubjectListCtrl

SConstScopedObject	CNGAlignPanel::m_Subject

TConstScopedObjects	CNGAlignPanel::m_Queries

CPslLoadManager &	CPslLoadManager::CPage::m_Manager

CUIObject	CPslLoadManager::m_Descr

IServiceLocator *	CPslLoadManager::m_SrvLocator

wxWindow *	CPslLoadManager::m_ParentWindow

EState	CPslLoadManager::m_State

string	CPslLoadManager::m_RegPath

CPslParamsPanel *	CPslLoadManager::m_ParamsPanel

CPslLoadParams	CPslLoadManager::m_Params

vector< wxString >	CPslLoadManager::m_FileNames

CPage	CPslLoadManager::m_OptionsPage

CObjectListWidgetSel *	CTaxTreeToolPanel::m_SeqIds

CTaxTreeToolParams	CTaxTreeToolPanel::m_data

TConstScopedObjects *	CTaxTreeToolPanel::m_InputObjects

CTextAlignLoaderManager &	CTextAlignLoaderManager::CPage::m_Manager

CUIObject	CTextAlignLoaderManager::m_Descr

IServiceLocator *	CTextAlignLoaderManager::m_SrvLocator

wxWindow *	CTextAlignLoaderManager::m_ParentWindow

EState	CTextAlignLoaderManager::m_State

string	CTextAlignLoaderManager::m_RegPath

CTextAlignParamsPanel *	CTextAlignLoaderManager::m_ParamsPanel

CTextAlignParams	CTextAlignLoaderManager::m_Params

vector< wxString >	CTextAlignLoaderManager::m_FileNames

CPage	CTextAlignLoaderManager::m_OptionsPage

Friends
class	CAlignSpanView::CAlignSpanViewFactory

class	CAnnotCompareView::CAnnotCompareViewFactory

class	CClustalOmegaToolParams::CClustalOmegaToolPanel

class	CClustalwToolParams::CClustalwToolPanel

class	CCrossAlignView::CCrossAlignViewFactory

class	CDotMatrixView::CDotMatrixViewFactory

class	CFindOverlapParams::CFindOverlapPanel

class	CKalignToolParams::CKalignToolPanel

class	CMafftToolParams::CMafftToolPanel

class	CMPCrossAlignView::CMPCrossAlignViewFactory

class	CMultiAlignView::CMultiAlignViewFactory

class	CMuscleToolParams::CMuscleToolPanel

class	CNeedlemanWunschToolParams::CAlignNeedlemanWunschPanel

class	CNetBlastJobDescriptor::CNetBLASTUIDataSource

class	CNetBLASTUIDataSource::CNetBlastJobDescriptor

class	CNetBLASTUIDataSource::CNetBlastDSEvtHandler

class	CNGAlignParams::CNGAlignPanel

class	CNGAlignParams::CNGAlignBLASTPanel

class	CPhyTreeView::CPhyTreeViewFactory

class	CSplignParams::CSplignPanel

class	CTaxTreeToolParams::CTaxTreeToolPanel

class	CTreeBuilderParams::CTreeBuilderPanel

class	CTreeBuilderParams::CTreeBuilderTool

IWMClient interface implementation
virtual wxWindow *	CAlignSpanView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CAlignSpanView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CAlignSpanView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CAlignSpanView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

IProjectView implementation
virtual void	CAlignSpanView::OnProjectChanged (CProjectViewEvent &evt)

ISelectionClient Implementation
virtual void	CAlignSpanView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

virtual void	CAlignSpanView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

CProjectViewBase overridables
virtual void	CAlignSpanView::GetVisibleRanges (CVisibleRange &vrange) const
	populate a visible range event for broadcasting More...

CProjectView callback overridables
virtual void	CAlignSpanView::OnWidgetRangeChanged ()

virtual void	CAlignSpanView::OnWidgetSelChanged ()

IRegSettings interface implementation
virtual void	CAlignSpanView::SetRegistryPath (const string &reg_path)

virtual void	CAlignSpanView::LoadSettings ()

virtual void	CAlignSpanView::SaveSettings () const

CProjectViewBase internal overridables
virtual void	CAlignSpanView::x_CreateMenuBarMenu ()
	initializes m_MenuBarMenu; override in derived classes More...

virtual const CObject *	CAlignSpanView::x_GetOrigObject () const

CProjectView internal overridables
virtual objects::CScope *	CAlignSpanView::x_PreAttachToProject (TConstScopedObjects &objects)

virtual void	CAlignSpanView::x_PostAttachToProject ()

virtual void	CAlignSpanView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

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

IProjectViewFactory interface implementation
virtual IView *	CAlignSpanViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CAlignSpanViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CAlignSpanViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual const CProjectViewTypeDescriptor &	CAlignSpanViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual int	CAlignSpanViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

IWMClient interface implementation
virtual wxWindow *	CAnnotCompareView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CAnnotCompareView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CAnnotCompareView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CAnnotCompareView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

IProjectView implementation
virtual void	CAnnotCompareView::OnProjectChanged (CProjectViewEvent &evt)

ISelectionClient Implementation
void	CAnnotCompareView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

void	CAnnotCompareView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

CProjectViewBase overridables
virtual void	CAnnotCompareView::GetVisibleRanges (CVisibleRange &vrange) const
	populate a visible range event for broadcasting More...

CProjectView internal overridables
virtual objects::CScope *	CAnnotCompareView::x_PreAttachToProject (TConstScopedObjects &objects)

virtual void	CAnnotCompareView::x_PostAttachToProject ()

virtual void	CAnnotCompareView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

IExtension interface implementation
virtual string	CAnnotCompareViewFactory::GetExtensionIdentifier () const
	CAnnotCompareViewFactory. More...

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

IProjectViewFactory interface implementation
virtual IView *	CAnnotCompareViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CAnnotCompareViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CAnnotCompareViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual const CProjectViewTypeDescriptor &	CAnnotCompareViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual int	CAnnotCompareViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

IAppJob implementation
virtual EJobState	CNetBlastSubmittingJob::Run ()
	Function that does all the useful work, called by the Engine. More...

virtual CConstIRef< IAppJobProgress >	CNetBlastSubmittingJob::GetProgress ()
	return progress object, the function shall be synchronized internally. More...

virtual CRef< CObject >	CNetBlastSubmittingJob::GetResult ()
	Returns the Job Result. More...

virtual CConstIRef< IAppJobError >	CNetBlastSubmittingJob::GetError ()
	Returns IAppJobError object describing internal error that caused the Job to fail. More...

virtual string	CNetBlastSubmittingJob::GetDescr () const
	Returns a human readable description of the Job (optional) More...

IAppJob implementation
virtual EJobState	CNetBlastMonitoringJob::Run ()
	Function that does all the useful work, called by the Engine. More...

virtual CConstIRef< IAppJobProgress >	CNetBlastMonitoringJob::GetProgress ()
	return progress object, the function shall be synchronized internally. More...

virtual CRef< CObject >	CNetBlastMonitoringJob::GetResult ()
	Returns the Job Result. More...

virtual CConstIRef< IAppJobError >	CNetBlastMonitoringJob::GetError ()
	Returns IAppJobError object describing internal error that caused the Job to fail. More...

virtual string	CNetBlastMonitoringJob::GetDescr () const
	Returns a human readable description of the Job (optional) More...

IWaitPeriod implementation
virtual CTimeSpan	CNetBlastMonitoringJob::GetWaitPeriod ()
	returns a period of time after which the task shall be executed again More...

CAlgoToolManagerParamsPanel implementation
virtual void	CBLASTSearchOptionsPanel::LoadSettings ()

virtual void	CBLASTSearchOptionsPanel::SaveSettings () const
	override in derived classes More...

void	CBLASTSearchOptionsPanel::RestoreDefaults ()
	override in derived classes More...

CTaxIdHelper::ICallback interface implementation
virtual void	CBLASTSearchParamsPanel::TaxonsLoaded (bool local)

CAlgoToolManagerParamsPanel implementation
virtual void	CBLASTSearchParamsPanel::LoadSettings ()

virtual void	CBLASTSearchParamsPanel::SaveSettings () const
	override in derived classes More...

void	CBLASTSearchParamsPanel::RestoreDefaults ()
	override in derived classes More...

CCompositeAppTask overridables
virtual CIRef< IAppTask >	CBlastSearchTask::x_GetCurrentSubTask ()
	returns a references to the current subtask More...

virtual CIRef< IAppTask >	CBlastSearchTask::x_NextSubTask ()
	prepares the next subtask (makes it current), this function is used for iterating subtasks. More...

virtual ETaskState	CBlastSearchTask::x_RunCurrentSubTask ()
	runs the current subtask; one may override this function in order to perform special pre-execution or post-execution actions More...

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

virtual void	CBLASTToolManager::SetParentWindow (wxWindow *parent)

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

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

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

virtual wxPanel *	CBLASTToolManager::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

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

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

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

virtual bool	CBLASTToolManager::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 *	CBLASTToolManager::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...

virtual void	CBLASTToolManager::RestoreDefaults ()
	Restores the default options for the current panel. More...

IUIAlgoToolManager interface implementation
virtual string	CBLASTToolManager::GetCategory ()
	returns the name for the ToolCategory to which the tool belongs. More...

virtual string	CBLASTToolManager::SetInputObjects (const vector< TConstScopedObjects > &input)
	sets input objects that can be used as arguments for the tool. More...

virtual bool	CBLASTToolManager::CanQuickLaunch () const

virtual IAppTask *	CBLASTToolManager::QuickLaunch ()

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

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

virtual void	CBLASTToolManager::LoadSettings ()

virtual void	CBLASTToolManager::SaveSettings () const

IRegSettings interface implementation
virtual void	SCleanupAlignmentsParams::SetRegistryPath (const string &reg_path)

virtual void	SCleanupAlignmentsParams::LoadSettings ()

virtual void	SCleanupAlignmentsParams::SaveSettings () const

CAlgoToolManagerParamsPanel implementation
void	CCleanupAlignmentsParamsPanel::RestoreDefaults ()
	override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CCleanupAlignmentsToolManager::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CCleanupAlignmentsToolManager::CleanUI ()
	override this function in a derived class and clean extra members More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CCleanupAlignmentsToolManager::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CCleanupAlignmentsToolManager::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CCleanupAlignmentsToolManager::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CCleanupAlignmentsToolManager::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CClustalOmegaTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CClustalOmegaTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CClustalOmegaTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CClustalOmegaTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CClustalOmegaTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CClustalOmegaTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CClustalOmegaTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CClustalOmegaTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CClustalwTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CClustalwTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CClustalwTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CClustalwTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CClustalwTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CClustalwTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CClustalwTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CClustalwTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CCreateGeneModelToolManager::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CCreateGeneModelToolManager::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual IAppTask *	CCreateGeneModelToolManager::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...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CCreateGeneModelToolManager::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CCreateGeneModelToolManager::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CCreateGeneModelToolManager::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CCreateGeneModelToolManager::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CCreateGeneModelToolManager::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

IWMClient interface implementation
virtual wxWindow *	CCrossAlignView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CCrossAlignView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CCrossAlignView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CCrossAlignView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

IProjectView implementation
virtual void	CCrossAlignView::OnProjectChanged (CProjectViewEvent &evt)

ISelectionClient Implementation
void	CCrossAlignView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

void	CCrossAlignView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

CProjectViewBase overridables
virtual void	CCrossAlignView::GetVisibleRanges (CVisibleRange &vrange) const
	populate a visible range event for broadcasting More...

IVisibleRangeClient interface implementation
virtual void	CCrossAlignView::OnVisibleRangeChanged (const CVisibleRange &vrange, IVisibleRangeClient *source)

CProjectView internal overridables
CConstRef< CSeq_annot >	CCrossAlignView::m_OrigAnnot
	original data object passed to the view More...

CConstRef< CSeq_align >	CCrossAlignView::m_OrigAlign

CIRef< ICrossAlnDataSource >	CCrossAlignView::m_DataSource

CCrossAlnWidget *	CCrossAlignView::m_AlnWidget

virtual objects::CScope *	CCrossAlignView::x_PreAttachToProject (TConstScopedObjects &objects)

virtual void	CCrossAlignView::x_PostAttachToProject ()

IExtension interface implementation
virtual string	CCrossAlignViewFactory::GetExtensionIdentifier () const
	CCrossAlignViewFactory. More...

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

IProjectViewFactory interface implementation
virtual IView *	CCrossAlignViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CCrossAlignViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CCrossAlignViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual void	CCrossAlignViewFactory::RegisterCommands (CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register commands used by view More...

virtual const CProjectViewTypeDescriptor &	CCrossAlignViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual int	CCrossAlignViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

IWMClient interface implementation
virtual wxWindow *	CDotMatrixView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CDotMatrixView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CDotMatrixView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CDotMatrixView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

IProjectView implementation
virtual void	CDotMatrixView::OnProjectChanged (CProjectViewEvent &evt)

ISelectionClient Implementation
void	CDotMatrixView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

void	CDotMatrixView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

CProjectViewBase overridables
virtual void	CDotMatrixView::GetVisibleRanges (CVisibleRange &vrange) const
	populate a visible range event for broadcasting More...

IVisibleRangeClient interface implementation
virtual void	CDotMatrixView::OnVisibleRangeChanged (const CVisibleRange &vrange, IVisibleRangeClient *source)

CProjectView internal overridables
virtual objects::CScope *	CDotMatrixView::x_PreAttachToProject (TConstScopedObjects &objects)

virtual void	CDotMatrixView::x_PostAttachToProject ()

virtual void	CDotMatrixView::x_OnSetSelection (CSelectionEvent &evt)
	override in derived classes in order to handle selection broadcast More...

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

IProjectViewFactory interface implementation
virtual IView *	CDotMatrixViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CDotMatrixViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CDotMatrixViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual void	CDotMatrixViewFactory::RegisterCommands (CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register commands used by view More...

virtual const CProjectViewTypeDescriptor &	CDotMatrixViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual IOpenViewManager *	CDotMatrixViewFactory::GetOpenViewManager ()

virtual int	CDotMatrixViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

virtual vector< int >	CDotMatrixViewFactory::CombineInputObjects (const TConstScopedObjects &objects)

IRegSettings interface implementation
virtual void	CFindOverlapPanel::LoadSettings ()

virtual void	CFindOverlapPanel::SaveSettings () const
	override in derived classes More...

CAlgoToolManagerParamsPanel implementation
void	CFindOverlapPanel::RestoreDefaults ()
	override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CFindOverlapTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CFindOverlapTool::CleanUI ()
	override this function in a derived class and clean extra members More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CFindOverlapTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CFindOverlapTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CFindOverlapTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CFindOverlapTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CFindOverlapTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

IRegSettings interface implementation
virtual void	SGroupAlignmentsParams::SetRegistryPath (const string &reg_path)

virtual void	SGroupAlignmentsParams::LoadSettings ()

virtual void	SGroupAlignmentsParams::SaveSettings () const

CAlgoToolManagerParamsPanel implementation
void	CGroupAlignmentsParamsPanel::RestoreDefaults ()
	override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CGroupAlignmentsToolManager::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CGroupAlignmentsToolManager::CleanUI ()
	override this function in a derived class and clean extra members More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CGroupAlignmentsToolManager::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CGroupAlignmentsToolManager::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual CDataLoadingAppJob *	CGroupAlignmentsToolManager::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

virtual void	CGroupAlignmentsToolManager::x_InitProjectParams ()
	init m_ProjectParams, in particular can select target project based on the tool input More...

virtual bool	CGroupAlignmentsToolManager::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CKalignTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CKalignTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CKalignTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CKalignTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CKalignTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CKalignTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CKalignTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CKalignTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

virtual bool	CKalignTool::CanQuickLaunch () const

virtual IAppTask *	CKalignTool::QuickLaunch ()

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CMafftTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CMafftTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CMafftTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CMafftTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CMafftTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CMafftTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CMafftTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CMafftTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

virtual bool	CMafftTool::CanQuickLaunch () const

virtual IAppTask *	CMafftTool::QuickLaunch ()

IRegSettings interface implementation
virtual void	SMergeAlignmentsParams::SetRegistryPath (const string &reg_path)

virtual void	SMergeAlignmentsParams::LoadSettings ()

virtual void	SMergeAlignmentsParams::SaveSettings () const

CAlgoToolManagerParamsPanel implementation
void	CMergeAlignmentsParamsPanel::RestoreDefaults ()
	override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CMergeAlignmentsToolManager::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CMergeAlignmentsToolManager::CleanUI ()
	override this function in a derived class and clean extra members More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CMergeAlignmentsToolManager::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CMergeAlignmentsToolManager::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CMergeAlignmentsToolManager::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CMergeAlignmentsToolManager::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

virtual void	CMergeAlignmentsToolManager::x_InitProjectParams ()
	init m_ProjectParams, in particular can select target project based on the tool input More...

IVisibleRangeService interface implementation
virtual void	CMPCrossAlignView::AttachClient (IVisibleRangeClient *)

virtual void	CMPCrossAlignView::DetachClient (IVisibleRangeClient *)

virtual void	CMPCrossAlignView::BroadcastVisibleRange (const CVisibleRange &vrange, IVisibleRangeClient *source)

IWMClient interface implementation
virtual wxWindow *	CMPCrossAlignView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CMPCrossAlignView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CMPCrossAlignView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CMPCrossAlignView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

virtual void	CMPCrossAlignView::SetWorkbench (IWorkbench *workbench)
	IView implementation. More...

IProjectView implementation
virtual void	CMPCrossAlignView::DestroyView ()
	disconnects view from the project and associated data More...

virtual bool	CMPCrossAlignView::InitView (TConstScopedObjects &objects, const objects::CUser_object *params)
	initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project More...

virtual void	CMPCrossAlignView::OnProjectChanged ()

ISelectionClient Implementation
virtual void	CMPCrossAlignView::SetSelection (CSelectionEvent &evt)
	handles selection broadcast received from Selection Service this function acts as a shell, it controlls state and catches exceptions. More...

virtual void	CMPCrossAlignView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

virtual void	CMPCrossAlignView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

virtual void	CMPCrossAlignView::GetMainObject (TConstScopedObjects &objs) const
	Adds the main data objects represented by the client to "objects". More...

CProjectViewBase overridables
virtual void	CMPCrossAlignView::GetVisibleRanges (CVisibleRange &vrange) const
	populate a visible range event for broadcasting More...

IVisibleRangeClient interface implementation
virtual void	CMPCrossAlignView::OnVisibleRangeChanged (const CVisibleRange &vrange, IVisibleRangeClient *source)

IExtension interface implementation
virtual string	CMPCrossAlignViewFactory::GetExtensionIdentifier () const
	CMPCrossAlignViewFactory. More...

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

IProjectViewFactory interface implementation
virtual IView *	CMPCrossAlignViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CMPCrossAlignViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CMPCrossAlignViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual void	CMPCrossAlignViewFactory::RegisterCommands (CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register commands used by view More...

virtual const CProjectViewTypeDescriptor &	CMPCrossAlignViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual int	CMPCrossAlignViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

virtual bool	CMPCrossAlignViewFactory::IsCompatibleWith (const CObject &object, objects::CScope &scope)

IWMClient interface implementation
virtual wxWindow *	CMultiAlignView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CMultiAlignView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CMultiAlignView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CMultiAlignView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

IProjectView implementation
virtual bool	CMultiAlignView::InitView (TConstScopedObjects &objects, const objects::CUser_object *params)
	initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project More...

virtual void	CMultiAlignView::OnProjectChanged ()

virtual void	CMultiAlignView::OnProjectChanged (CProjectViewEvent &evt)

ISelectionClient implementation
void	CMultiAlignView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

void	CMultiAlignView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

IRegSettings interface implementation
virtual void	CMultiAlignView::SetRegistryPath (const string &reg_path)

virtual void	CMultiAlignView::LoadSettings ()

virtual void	CMultiAlignView::SaveSettings () const

CUIDataSource::IListener implementation
virtual void	CMultiAlignView::OnDSChanged (CDataChangeNotifier::CUpdate &update)

IExtension interface implementation
virtual string	CMultiAlignViewFactory::GetExtensionIdentifier () const
	CMultiAlignViewFactory. More...

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

IProjectViewFactory interface implementation
virtual IView *	CMultiAlignViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CMultiAlignViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CMultiAlignViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual void	CMultiAlignViewFactory::RegisterCommands (CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register commands used by view More...

virtual const CProjectViewTypeDescriptor &	CMultiAlignViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual IOpenViewManager *	CMultiAlignViewFactory::GetOpenViewManager ()

virtual bool	CMultiAlignViewFactory::IsCompatibleWith (const CObject &object, objects::CScope &scope)

virtual int	CMultiAlignViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CMuscleTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CMuscleTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CMuscleTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CMuscleTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CMuscleTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CMuscleTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CMuscleTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CMuscleTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

virtual bool	CMuscleTool::CanQuickLaunch () const

virtual IAppTask *	CMuscleTool::QuickLaunch ()

IUITool implementation
virtual IUITool *	CNetBLAST_DMSearchTool::Clone () const

virtual string	CNetBLAST_DMSearchTool::GetName () const
	returns unique name of the method that is used in UI to identify it More...

virtual string	CNetBLAST_DMSearchTool::GetDescription () const
	returns a detailed description of the method that is used in UI More...

IDMSearchTool implementation
virtual CIRef< IDMSearchForm >	CNetBLAST_DMSearchTool::CreateSearchForm ()
	factory method for creating a form representing the tool More...

virtual bool	CNetBLAST_DMSearchTool::IsCompatible (IDataMiningContext *context)
	retuns true if the tool is compatible with the provided Search Context More...

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

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

IDMSearchForm implementation
virtual void	CNetBLAST_DMSearchForm::Create ()

virtual void	CNetBLAST_DMSearchForm::Init ()

virtual void	CNetBLAST_DMSearchForm::Update ()

virtual CIRef< IDMSearchQuery >	CNetBLAST_DMSearchForm::ConstructQuery ()

virtual wxSizer *	CNetBLAST_DMSearchForm::GetWidget (wxWindow *parent)
	return a widget associated with the form; the form controls the lifetime of the widget (do not delete the widget) More...

virtual void	CNetBLAST_DMSearchForm::UpdateContexts ()
	updates m_ContextCombo More...

CSearchJobBase overridables
virtual bool	CNetBLAST_DMSearchJob::x_ValidateParams ()
	returns true if Job params are correct, implement in derived classes More...

virtual EJobState	CNetBLAST_DMSearchJob::x_DoSearch ()
	performs searching, assuming that params are correct; Implement in derived classes More...

virtual CObjectListTableModel *	CNetBLAST_DMSearchJob::x_GetNewOLTModel () const
	factory method creating new column handler for CObjectListWidget More...

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

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

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

virtual void	CNetBLASTUIDataSource::SaveSettings () const

virtual void	CNetBLASTUIDataSource::LoadSettings ()

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

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

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

virtual bool	CNetBLASTUIDataSource::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	CNetBLASTUIDataSource::Close ()

virtual void	CNetBLASTUIDataSource::EditProperties ()

virtual IUIToolManager *	CNetBLASTUIDataSource::GetLoadManager ()

virtual int	CNetBLASTUIDataSource::GetDefaultCommand ()

virtual wxEvtHandler *	CNetBLASTUIDataSource::CreateEvtHandler ()

IObjectCmdContributor implementation
virtual IObjectCmdContributor::TContribution	CNetBLASTUIDataSource::GetMenu (TConstScopedObjects &objects)
	returns a menu with commands applicable to the objects and optional command handler for the commands caller assumes ownership of the returned objects More...

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

Interface for accessing Net BLAST services and objects
CRef< CNetBlastJobDescriptor >	CNetBLASTUIDataSource::CreateJobDescriptor (const CBLASTParams &params)

CRef< CNetBlastJobDescriptor >	CNetBLASTUIDataSource::CreateJobDescriptor (const string &rid)

void	CNetBLASTUIDataSource::GetJobDescriptors (TJobDescrVec &descriptors)
	returns Job Descriptors not marked as Deleted More...

CRef< CNetBlastJobDescriptor >	CNetBLASTUIDataSource::FindJobDescriptor (const string &rid)

void	CNetBLASTUIDataSource::StartRetrievingTask (TJobDescrVec &descriptors)

void	CNetBLASTUIDataSource::StartMonitoringTask (TJobDescrVec &descriptors)

void	CNetBLASTUIDataSource::DeleteJobDescriptors (TJobDescrVec &descriptors)

void	CNetBLASTUIDataSource::OnExplore ()

void	CNetBLASTUIDataSource::OnLoadRIDs ()

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

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

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

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

virtual void	CNetBLASTUILoadManager::SetParentWindow (wxWindow *parent)

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

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

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

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

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

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

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

virtual bool	CNetBLASTUILoadManager::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 *	CNetBLASTUILoadManager::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	CNetBLASTUILoadManager::SetRegistryPath (const string &path)

virtual void	CNetBLASTUILoadManager::LoadSettings ()

virtual void	CNetBLASTUILoadManager::SaveSettings () const

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CNGAlignTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CNGAlignTool::CleanUI ()
	override this function in a derived class and clean extra members More...

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

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CNGAlignTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CNGAlignTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CNGAlignTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CNGAlignTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CNGAlignTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

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

virtual bool	CNGAlignTool::IsMultiScopeInputAccepted () const

IWMClient interface implementation
virtual wxWindow *	CPhyTreeView::GetWindow ()
	returns a pointer to the wxWindow representing the client More...

IView interface implementation
virtual const CViewTypeDescriptor &	CPhyTreeView::GetTypeDescriptor () const
	return an object providing meta information about thei view type More...

virtual void	CPhyTreeView::CreateViewWindow (wxWindow *parent)
	create Window corresponding to the view More...

virtual void	CPhyTreeView::DestroyViewWindow ()
	destroy Window corresponding to the view More...

IProjectView implementation
virtual bool	CPhyTreeView::InitView (TConstScopedObjects &objects, const objects::CUser_object *params)
	initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project More...

virtual void	CPhyTreeView::OnProjectChanged (CProjectViewEvent &evt)

ISelectionClient Implementation
void	CPhyTreeView::GetSelection (CSelectionEvent &evt) const
	get selection for broadcasting More...

void	CPhyTreeView::GetSelection (TConstScopedObjects &objs) const
	shall return data objects representing selected things, return one data object for every selected thing. More...

CProjectViewBase overridables
virtual void	CPhyTreeView::GetVisibleRanges (CVisibleRange &vrange) const
	populate a visible range event for broadcasting More...

IRegSettings interface implementation
virtual void	CPhyTreeView::SetRegistryPath (const string &reg_path)

virtual void	CPhyTreeView::LoadSettings ()

virtual void	CPhyTreeView::SaveSettings () const

IExtension interface implementation
virtual string	CPhyTreeViewFactory::GetExtensionIdentifier () const
	CPhyTreeViewFactory. More...

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

IProjectViewFactory interface implementation
virtual IView *	CPhyTreeViewFactory::CreateInstance () const
	creates a view instance More...

virtual IView *	CPhyTreeViewFactory::CreateInstanceByFingerprint (const TFingerprint &fingerprint) const
	if fingerprint is recognized - creates and returns a new instance More...

virtual void	CPhyTreeViewFactory::RegisterIconAliases (wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register images used by view More...

virtual void	CPhyTreeViewFactory::RegisterCommands (CUICommandRegistry &cmd_reg, wxFileArtProvider &provider)
	called by the framework to give Factory a chance to register commands used by view More...

virtual const CProjectViewTypeDescriptor &	CPhyTreeViewFactory::GetProjectViewTypeDescriptor () const
	returns a Descriptor for the View Type supported by the Factory More...

virtual int	CPhyTreeViewFactory::TestInputObjects (TConstScopedObjects &objects)
	tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith() More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CProSplignTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CProSplignTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CProSplignTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CProSplignTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CProSplignTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CProSplignTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CProSplignTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CProSplignTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

IRegSettings interface implementation
virtual void	CSplignPanel::SetRegistryPath (const string &path)
	CAlgoToolManagerParamsPanel. More...

virtual void	CSplignPanel::LoadSettings ()

virtual void	CSplignPanel::SaveSettings () const
	override in derived classes More...

CAlgoToolManagerParamsPanel implementation
void	CSplignPanel::RestoreDefaults ()
	override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CSplignTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CSplignTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CSplignTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CSplignTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CSplignTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CSplignTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CSplignTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CSplignTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

virtual bool	CSplignTool::CanQuickLaunch () const

virtual IAppTask *	CSplignTool::QuickLaunch ()

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CCommonTaxTreeTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CCommonTaxTreeTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CCommonTaxTreeTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CCommonTaxTreeTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CCommonTaxTreeTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CCommonTaxTreeTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CCommonTaxTreeTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

CAlgoToolManagerParamsPanel implementation
void	CTreeBuilderPanel::RestoreDefaults ()
	override in derived classes More...

IRegSettings interface implementation
virtual void	CTreeBuilderPanel::LoadSettings ()

virtual void	CTreeBuilderPanel::SaveSettings () const
	override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CTreeBuilderTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CTreeBuilderTool::CleanUI ()
	override this function in a derived class and clean extra members More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CTreeBuilderTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CTreeBuilderTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CTreeBuilderTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CTreeBuilderTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CTreeBuilderTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

IObjectLoader implementation
virtual TObjects &	CTextAlignObjectLoader::GetObjects ()

virtual string	CTextAlignObjectLoader::GetDescription () const

IExecuteUnit implementation
virtual bool	CTextAlignObjectLoader::PreExecute ()

virtual bool	CTextAlignObjectLoader::Execute (ICanceled &canceled)

virtual bool	CTextAlignObjectLoader::PostExecute ()

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CAdvancedCleanupTool::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CAdvancedCleanupTool::CleanUI ()
	override this function in a derived class and clean extra members More...

virtual wxPanel *	CAdvancedCleanupTool::GetMaxPanel ()
	Return the panel that occupies max size on display, to calculate dialog window size. More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CAdvancedCleanupTool::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CAdvancedCleanupTool::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CAdvancedCleanupTool::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual bool	CAdvancedCleanupTool::x_ValidateParams ()
	validates user input in Parameters panel, report errors if any More...

virtual CDataLoadingAppJob *	CAdvancedCleanupTool::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

overriding IUIToolManager functions implemented in CAlgoToolManagerBase
virtual void	CCreateNeedlemanWunschToolManager::InitUI ()
	override this function in a derived class and initialize extra members More...

virtual void	CCreateNeedlemanWunschToolManager::CleanUI ()
	override this function in a derived class and clean extra members More...

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

overriding CAlgoToolManagerBase virtual functions
virtual CAlgoToolManagerParamsPanel *	CCreateNeedlemanWunschToolManager::x_GetParamsPanel ()
	returns a pointer to the parameters panel, override in derived classes More...

virtual IRegSettings *	CCreateNeedlemanWunschToolManager::x_GetParamsAsRegSetting ()
	return a pointer to Parameters object as IRegSettings interface More...

virtual bool	CCreateNeedlemanWunschToolManager::x_CreateParamsPanelIfNeeded ()
	returns / creates Parameters panel, override in derived classes see cpp file for example More...

virtual CDataLoadingAppJob *	CCreateNeedlemanWunschToolManager::x_CreateLoadingJob ()
	factory method for creating the job that executes the tool algorithm override in derived classes More...

CAlgoToolManagerParamsPanel implementation
void	CMuscleToolPanel::RestoreDefaults ()
	override in derived classes More...

IRegSettings interface implementation
virtual void	CMuscleToolPanel::SetRegistryPath (const string &path)
	CAlgoToolManagerParamsPanel. More...

virtual void	CMuscleToolPanel::LoadSettings ()

virtual void	CMuscleToolPanel::SaveSettings () const
	override in derived classes More...

CAlgoToolManagerParamsPanel implementation
virtual void	CNGAlignPanel::RestoreDefaults ()
	override in derived classes More...

IRegSettings interface implementation
virtual void	CNGAlignPanel::LoadSettings ()

virtual void	CNGAlignPanel::SaveSettings () const
	override in derived classes More...

IFileLoadPanelClient interface implementation
virtual string	CPslLoadManager::GetLabel () const

virtual wxString	CPslLoadManager::GetFormatWildcard () const
	return file wildcard for the format (example - ".txt;.tab" ) More...

virtual string	CPslLoadManager::GetFileLoaderId () const

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

virtual void	CPslLoadManager::SetParentWindow (wxWindow *parent)

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

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

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

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

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

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

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

virtual bool	CPslLoadManager::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 *	CPslLoadManager::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...

virtual IExecuteUnit *	CPslLoadManager::GetExecuteUnit ()

virtual IWizardPage *	CPslLoadManager::GetFirstPage ()
	Returns first options page (if any) of the tool to be shown in wizard dialog. More...

virtual wxString	CPslLoadManager::GetFormatWildcard ()

virtual bool	CPslLoadManager::ValidateFilenames (const vector< wxString > &filenames)
	checks given filenames and returns true if the manager can handle them, otherwise - shows an error message More...

virtual void	CPslLoadManager::SetFilenames (const vector< wxString > &filenames)
	initilize the manager with the given filenames More...

virtual void	CPslLoadManager::GetFilenames (vector< wxString > &filenames) const
	get actual filenames that will be opened More...

virtual bool	CPslLoadManager::IsInitialState ()
	return true if the current state of the loader UI is the first valid state (first step in a wizard-like sequence) More...

virtual bool	CPslLoadManager::RecognizeFormat (const wxString &filename)
	return true if the given file format is supported by this manager More...

virtual bool	CPslLoadManager::RecognizeFormat (CFormatGuess::EFormat fmt)
	return true if the given file format is supported by this manager More...

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

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

virtual void	CPslLoadManager::LoadSettings ()

virtual void	CPslLoadManager::SaveSettings () const

CAlgoToolManagerParamsPanel implementation
void	CTaxTreeToolPanel::RestoreDefaults ()
	override in derived classes More...

IRegSettings interface implementation
virtual void	CTaxTreeToolPanel::SetRegistryPath (const string &path)
	CAlgoToolManagerParamsPanel. More...

virtual void	CTaxTreeToolPanel::LoadSettings ()

virtual void	CTaxTreeToolPanel::SaveSettings () const
	override in derived classes More...

IFileLoadPanelClient interface implementation
virtual string	CTextAlignLoaderManager::GetLabel () const

virtual wxString	CTextAlignLoaderManager::GetFormatWildcard () const
	return file wildcard for the format (example - ".txt;.tab" ) More...

virtual string	CTextAlignLoaderManager::GetFileLoaderId () const

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

virtual void	CTextAlignLoaderManager::SetParentWindow (wxWindow *parent)

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

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

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

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

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

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

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

virtual bool	CTextAlignLoaderManager::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 *	CTextAlignLoaderManager::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...

virtual IExecuteUnit *	CTextAlignLoaderManager::GetExecuteUnit ()

virtual IWizardPage *	CTextAlignLoaderManager::GetFirstPage ()
	Returns first options page (if any) of the tool to be shown in wizard dialog. More...

virtual IWizardPage *	CTextAlignLoaderManager::GetOptionsPage ()
	Returns page for tool options (long wizard path via "Options" button) More...

virtual void	CTextAlignLoaderManager::SetPrevPage (IWizardPage *prevPage)
	Sets a wizard page which should show before the first page of the tool. More...

virtual wxString	CTextAlignLoaderManager::GetFormatWildcard ()

virtual bool	CTextAlignLoaderManager::ValidateFilenames (const vector< wxString > &filenames)
	checks given filenames and returns true if the manager can handle them, otherwise - shows an error message More...

virtual void	CTextAlignLoaderManager::SetFilenames (const vector< wxString > &filenames)
	initilize the manager with the given filenames More...

virtual void	CTextAlignLoaderManager::GetFilenames (vector< wxString > &filenames) const
	get actual filenames that will be opened More...

virtual bool	CTextAlignLoaderManager::IsInitialState ()
	return true if the current state of the loader UI is the first valid state (first step in a wizard-like sequence) More...

virtual bool	CTextAlignLoaderManager::RecognizeFormat (const wxString &filename)
	return true if the given file format is supported by this manager More...

virtual bool	CTextAlignLoaderManager::RecognizeFormat (CFormatGuess::EFormat fmt)
	return true if the given file format is supported by this manager More...

virtual bool	CTextAlignLoaderManager::CanGuessFormat () const
	returns true if loader's format can be guessed More...

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

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

virtual void	CTextAlignLoaderManager::LoadSettings ()

virtual void	CTextAlignLoaderManager::SaveSettings () const

Detailed Description

Macro Definition Documentation

◆ NET_BLAST_DM_TOOL_NAME

#define NET_BLAST_DM_TOOL_NAME "NCBI Net BLAST"

Definition at line 81 of file net_blast_ui_data_source.hpp.

◆ NET_BLAST_LOADER_LABEL

#define NET_BLAST_LOADER_LABEL "RIDs from NCBI Net BLAST"

Definition at line 60 of file net_blast_ui_load_manager.hpp.

Typedef Documentation

◆ TAlignVector [1/2]

typedef vector< CConstRef<objects::CSeq_align> > CAnnotCompareView::TAlignVector

Definition at line 57 of file annot_compare_view.hpp.

◆ TAlignVector [2/2]

typedef vector< CConstRef<objects::CSeq_align> > CDotMatrixView::TAlignVector

Definition at line 58 of file dot_matrix_view.hpp.

◆ TAnnotVector

typedef vector< CConstRef<objects::CSeq_annot> > CAnnotCompareView::TAnnotVector

Definition at line 56 of file annot_compare_view.hpp.

◆ TDbMap

typedef CBLASTDatabases::TDbMap CBLAST_DB_Dialog::TDbMap

Definition at line 183 of file blast_db_dialog.hpp.

◆ TDescriptors [1/4]

typedef vector< CRef<CNetBlastJobDescriptor> > CNetBlastSubmittingJob::TDescriptors

Definition at line 69 of file blast_jobs.hpp.

◆ TDescriptors [2/4]

typedef vector< CRef<CNetBlastJobDescriptor> > CNetBlastMonitoringJob::TDescriptors

Definition at line 116 of file blast_jobs.hpp.

◆ TDescriptors [3/4]

typedef vector< CRef<CNetBlastJobDescriptor> > CNetBlastLoadingJob::TDescriptors

Definition at line 173 of file blast_jobs.hpp.

◆ TDescriptors [4/4]

typedef vector< CRef<CNetBlastJobDescriptor> > CBlastSearchTask::TDescriptors

Definition at line 60 of file blast_search_task.hpp.

◆ TGeneCDSmRNAList

typedef list<SGeneCdsmRnaFeats> CCreateGeneModelTask::TGeneCDSmRNAList

a loader might be tied with a specific project item.

if so, we need to know such that they will go together and get added to the same project.

Definition at line 130 of file create_gene_model_tool_manager.hpp.

◆ TGeneModelMap

typedef map<objects::CSeq_id_Handle, TGeneCDSmRNAList> CCreateGeneModelTask::TGeneModelMap

Definition at line 131 of file create_gene_model_tool_manager.hpp.

◆ TIdMap

typedef map<string, TLocPair> CMSAToolJob::TIdMap

Definition at line 65 of file msa_tool_job.hpp.

◆ TItemDeque

typedef deque<CBLAST_Dlg_Item*> CBLAST_DB_Dialog::TItemDeque

protected

Definition at line 204 of file blast_db_dialog.hpp.

◆ TItemRef

typedef CRef<objects::CProjectItem> CCreateGeneModelTask::TItemRef

Definition at line 125 of file create_gene_model_tool_manager.hpp.

◆ TJobDescrVec

typedef vector< CRef<CNetBlastJobDescriptor> > CNetBLASTUIDataSource::TJobDescrVec

Definition at line 110 of file net_blast_ui_data_source.hpp.

◆ TLoaderRef

typedef CRef<objects::CLoaderDescriptor> CCreateGeneModelTask::TLoaderRef

Definition at line 124 of file create_gene_model_tool_manager.hpp.

◆ TLocPair

typedef pair< CConstRef<objects::CSeq_loc>, CRef<objects::CScope> > CMSAToolJob::TLocPair

Definition at line 64 of file msa_tool_job.hpp.

◆ TMRUDatabases

typedef CMRUList<string> CBLASTParams::TMRUDatabases

Definition at line 63 of file blast_search_params.hpp.

◆ TMRUQueries

typedef CMRUList<string> CBLASTParams::TMRUQueries

Definition at line 64 of file blast_search_params.hpp.

typedef set<CNetBlastJobDescriptor::EState> CNetBLAST_DMSearchQuery::TStates

Definition at line 113 of file net_blast_dm_search_tool.hpp.

◆ TTaxIdLabelMap

typedef map<int, string> CNetBLASTUIDataSource::TTaxIdLabelMap

Definition at line 111 of file net_blast_ui_data_source.hpp.

◆ TUserFields

typedef list< CConstRef<objects::CUser_field> > CNetBLASTUIDataSource::TUserFields

protected

Definition at line 181 of file net_blast_ui_data_source.hpp.

◆ TViews

typedef vector< CIRef<IProjectView> > CMPCrossAlignView::TViews

private

Definition at line 114 of file mp_cross_align_view.hpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Enumerator
ID_CMUSCLEPANEL
ID_PANEL
ID_CHOICE2
ID_CHECKBOX12
ID_TEXTCTRL11
ID_TEXTCTRL12
ID_BITMAPBUTTON1

Definition at line 130 of file muscle_tool_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CNGALIGNPANEL
ID_QUERY_LIST
ID_SUBJ_LIST

Definition at line 125 of file ngalign_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CTAXTREETOOLPANEL
ID_PANEL3

Definition at line 128 of file taxtree_tool_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CBLAST_DB_DIALOG
ID_SEARCH
ID_RESET_BTN
wxID_STATUS
ID_TREECTRL

Definition at line 173 of file blast_db_dialog.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CBLASTSEARCHOPTIONSPANEL
ID_NUC_RADIO
ID_PROT_RADIO
ID_QUERY_SEQ_SET
ID_LIST
ID_PROGRAM_COMBO
ID_RADIOBUTTON
ID_RADIOBUTTON2
ID_RADIOBUTTON1
ID_SUBJECT_SEQ_SET
ID_SUBJ_LIST
ID_DB_COMBO
ID_SELECT_NCBI_DB
ID_ENTREZ_COMBO
ID_TEXTCTRL
ID_SELECT_LOCAL_DB_BTN
ID_CHECKBOX

Definition at line 165 of file blast_search_options_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_DBS_LOADING_TEXT
ID_DBS_LOADING_PROGRESS
ID_DBS_FAILED
ID_DBS_TRY_AGAIN

Definition at line 186 of file blast_search_options_panel.hpp.

◆ anonymous enum

anonymous enum

protected

Enumerator
ID_CBLASTSEARCHPARAMSPANEL
ID_WORDSIZE
ID_E_VALUE
ID_THRESHOLD
ID_GEN_CODE
ID_COMBOBOX
ID_LOW_COMPLEXITY
ID_STATIC_REPEAT_TYPE
ID_REPEAT_TYPE
ID_MASK_LOWERCASE
ID_MASK_REPEATS
ID_WMTI_CHOICE
ID_BUTTON
ID_ADV_TEXT
ID_COMPARTMENTS
ID_TITLE_TEXT
ID_STANDALONE

Definition at line 197 of file blast_search_params_panel.hpp.

◆ anonymous enum

anonymous enum

protected

Enumerator
ID_LOADING_TEXT
ID_LOADING_PROGRESS

Definition at line 218 of file blast_search_params_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CCLEANUPALIGNMENTSPARAMSPANEL
ID_LISTCTRL2
ID_COMBOBOX
ID_TEXTCTRL1
ID_TEXTCTRL
ID_CHECKBOX1
ID_CHECKBOX2
ID_CHECKBOX
ID_CHECKBOX5

Definition at line 181 of file cleanup_alignments_params_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CFINDOVERLAPPANEL
ID_LISTCTRL3
ID_LISTCTRL4
ID_TEXTCTRL2
ID_TEXTCTRL4
ID_TEXTCTRL5

Definition at line 124 of file find_overlap_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CGROUPALIGNMENTSPARAMSPANEL
ID_LISTCTRL
ID_CHECKBOX_SEQID
ID_CHECKBOX_STRAND
ID_CHECKBOX_TAXID
ID_CHECKBOX_SIMILAR_TAXID
ID_CHECKBOX_REFSEQ
ID_CHECKBOX_EST
ID_CHECKBOX_REFSEQ_PREDICTED
ID_CHECKBOX_GENBANK
ID_CHECKBOX_WGS
ID_CHECKBOX_HTGS
ID_CHECKBOX_PATENT

Definition at line 165 of file group_alignments_params_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CBLASTSEARCHOPTIONSPANEL
ID_LISTCTRL1
ID_CHECKBOX6
ID_CHECKBOX7
ID_CHECKBOX8
ID_CHECKBOX9
ID_CHECKBOX10

Definition at line 149 of file merge_alignments_params_panel.hpp.

◆ anonymous enum

anonymous enum

protected

Enumerator
ID_CNETBLASTDMSEARCHFORM
ID_FILTER_INPUT
ID_SUBMITTED_CHECK
ID_COMPLETED_CHECK
ID_FAILED_CHECK
ID_RETRIEVED_CHECK
ID_EXPIRED_CHECK

Definition at line 139 of file net_blast_dm_search_form_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_NETBLASTLOADOPTIONPANEL
ID_TEXTCTRL1

Definition at line 94 of file net_blast_load_option_panel.hpp.

◆ anonymous enum

anonymous enum

private

Enumerator
kQueryPanelID
kPhylpWidgetID

Definition at line 132 of file phy_tree_view.hpp.

◆ anonymous enum

anonymous enum

private

Enumerator
ID_CSPLIGNPANEL
ID_PANEL1
ID_PANEL2
ID_CHOICE3
ID_CHOICE4
ID_CHECKBOX3
ID_CHECKBOX4
ID_TEXTCTRL7
ID_TEXTCTRL6
ID_TEXTCTRL8
ID_TEXTCTRL9
ID_TEXTCTRL13

Definition at line 159 of file splign_panel.hpp.

◆ anonymous enum

anonymous enum

Enumerator
ID_CTreeBuilderPanel
ID_LISTCTRL3
ID_LISTCTRL4
ID_TEXTCTRL2
ID_TEXTCTRL3
ID_TEXTCTRL4
ID_TEXTCTRL5

Definition at line 126 of file tree_builder_panel.hpp.

◆ EAlgorithm

enum SCleanupAlignmentsParams::EAlgorithm

which algorithm are we using?

Enumerator
eHitFilter
eAlignmentManager

Definition at line 106 of file cleanup_alignments_params_panel.hpp.

◆ ECommand

enum CBlastSearchTask::ECommand

protected

Enumerator
eInvalid
eSubmit
eMonitor	submit request, monitor and retrieve results
eRetrieve	monitor and retrieve resutlts
eFinished	only retrieve resutlts

Definition at line 84 of file blast_search_task.hpp.

◆ EEventId

enum CNetBLASTUIDataSourceEvent::EEventId

Enumerator
eJobDescrChanged

Definition at line 86 of file net_blast_ui_data_source.hpp.

◆ EFreeEndType

enum CNeedlemanWunschToolParams::EFreeEndType

Enumerator
eNone
eLeft
eRight
eBoth

Definition at line 55 of file needlemanwunsch_tool_params.hpp.

◆ ENetBlastCommands

enum ENetBlastCommands

commands introduced by Net BLAST data source

Enumerator
eCmdRetriveBlastJobs
eCmdMonitorBlastJobs
eCmdDeleteBlastJobs
eCmdExploreNetBLAST
eCmdLoadRIDs
eCmdBlastWinMask

Definition at line 71 of file net_blast_ui_data_source.hpp.

◆ EState [1/5]

enum CBLASTToolManager::EState

protected

Enumerator
eInvalid
eOptions
eParams
eCompleted

Definition at line 113 of file blast_tool_manager.hpp.

◆ EState [2/5]

enum CNetBlastJobDescriptor::EState

Enumerator
eInvalidState
eInitial
eSubmitted
eCompleted
eFailed
eRetrieved
eExpired

Definition at line 69 of file net_blast_job_descr.hpp.

◆ EState [3/5]

enum CNetBLASTUILoadManager::EState

protected

Enumerator
eInvalid
eSelectRID
eSelectProject
eCompleted

Definition at line 95 of file net_blast_ui_load_manager.hpp.

◆ EState [4/5]

enum CPslLoadManager::EState

protected

Enumerator
eInvalid
eParams
eCompleted

Definition at line 124 of file psl_load_manager.hpp.

◆ EState [5/5]

enum CTextAlignLoaderManager::EState

protected

Enumerator
eInvalid
eParams
eCompleted

Definition at line 126 of file text_align_load_manager.hpp.

◆ ESubjectType

enum CBLASTParams::ESubjectType

Enumerator
eSequences
eNCBIDB
eLocalDB

Definition at line 66 of file blast_search_params.hpp.

◆ MolType

enum CMolTypeValidator::MolType

Enumerator
kGenomic
kCDNA
kProtein
kNucleotide

Definition at line 77 of file splign_panel.hpp.

Function Documentation

◆ AddChild()

void CBLAST_Dlg_Item::AddChild ( CBLAST_Dlg_Item & item )

Definition at line 116 of file blast_db_dialog.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), CBLAST_Dlg_Item::GetLabel(), map_checker< Container >::insert(), CBLAST_Dlg_Item::m_ChildItems, CBLAST_Dlg_Item::m_Parent, and NULL.

Referenced by CBLAST_DB_Dialog::x_CreateItems().

◆ AppliedEditToDataSource()

void CPhyTreeView::AppliedEditToDataSource ( )

inline

Definition at line 115 of file phy_tree_view.hpp.

References CPhyTreeView::m_EditUpdate.

Referenced by CChangePhyloPropertyCmd::Execute(), CChangePhyloExpandCollapseCmd::Execute(), CChangePhyloSelectionSetCmd::PerformEdit(), CChangePhyloPropertyCmd::Unexecute(), and CChangePhyloExpandCollapseCmd::Unexecute().

◆ AttachClient()

virtual void CMPCrossAlignView::AttachClient ( IVisibleRangeClient * )

inlinevirtual

Implements IVisibleRangeService.

Definition at line 61 of file mp_cross_align_view.hpp.

◆ AutoCreateDefaultDataSource()

bool CNetBLASTUIDataSourceType::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 649 of file net_blast_ui_data_source.cpp.

◆ BeforeRun()

bool CMSAToolJob::BeforeRun ( )

protectedvirtual

Function will be called on the main thread before execution of Run Should not do any lengthy work returns true to continue job execution on worker thread false to quit execution with status - failed.

Reimplemented from IAppJob.

Definition at line 158 of file msa_tool_job.cpp.

References env, eUnknown, GUI_AsyncExec(), Info(), ITERATE, LOG_POST, CMSAToolJob::m_CmdLine, CMSAToolJob::m_IdMap, CMSAToolJob::m_PId, CMSAToolJob::m_Ranges, CMSAToolJob::m_SeqTypes, CMSAToolJob::m_TmpIn, CMSAToolJob::m_TmpOut, CMSAToolJob::m_ToolName, NCBI_THROW, s_DumpSequences_wRange(), wxT, CMSAToolJob::x_GetCommandLine(), CMSAToolJob::x_GetObjects(), and CMSAToolJob::x_GetWorkingDirectory().

◆ BroadcastVisibleRange()

void CMPCrossAlignView::BroadcastVisibleRange	(	const CVisibleRange &	vrange,
		IVisibleRangeClient *	source
	)

References CBLASTDatabases::GetInstance(), and CBLASTDatabases::Loaded().

◆ CanGuessFormat()

virtual bool CTextAlignLoaderManager::CanGuessFormat ( ) const

inlinevirtual

returns true if loader's format can be guessed

Reimplemented from IFileFormatLoaderManager.

Definition at line 105 of file text_align_load_manager.hpp.

◆ CanLeavePage() [1/2]

virtual bool CPslLoadManager::CPage::CanLeavePage ( bool )

inlinevirtual

Implements IWizardPage.

Definition at line 136 of file psl_load_manager.hpp.

◆ CanLeavePage() [2/2]

virtual bool CTextAlignLoaderManager::CPage::CanLeavePage ( bool )

inlinevirtual

Implements IWizardPage.

Definition at line 138 of file text_align_load_manager.hpp.

◆ CAnnotCompareView()

CAnnotCompareView::CAnnotCompareView ( )

Definition at line 71 of file annot_compare_view.cpp.

◆ CanQuickLaunch() [1/5]

bool CBLASTToolManager::CanQuickLaunch ( ) const

virtual

Implements IUIAlgoToolManager.

Definition at line 354 of file blast_tool_manager.cpp.

References CBLASTParams::eNCBIDB, CBLASTParams::GetSubjectType(), and CBLASTToolManager::m_Params.

◆ CanQuickLaunch() [2/5]

virtual bool CKalignTool::CanQuickLaunch ( ) const

inlineprotectedvirtual

Reimplemented from CAlgoToolManagerBase.

Definition at line 78 of file kalign_tool.hpp.

◆ CanQuickLaunch() [3/5]

virtual bool CMafftTool::CanQuickLaunch ( ) const

inlineprotectedvirtual

Reimplemented from CAlgoToolManagerBase.

Definition at line 78 of file mafft_tool.hpp.

◆ CanQuickLaunch() [4/5]

virtual bool CMuscleTool::CanQuickLaunch ( ) const

inlineprotectedvirtual

Reimplemented from CAlgoToolManagerBase.

Definition at line 78 of file muscle_tool.hpp.

◆ CanQuickLaunch() [5/5]

virtual bool CSplignTool::CanQuickLaunch ( ) const

inlineprotectedvirtual

Reimplemented from CAlgoToolManagerBase.

Definition at line 78 of file splign_tool.hpp.

◆ CBLAST_DB_Dialog() [1/2]

CBLAST_DB_Dialog::CBLAST_DB_Dialog ( )

Definition at line 149 of file blast_db_dialog.cpp.

References Init().

◆ CBLAST_DB_Dialog() [2/2]

CBLAST_DB_Dialog::CBLAST_DB_Dialog	(	wxWindow *	parent,
		wxWindowID	id = `ID_CBLAST_DB_DIALOG`,
		const wxString &	caption = `wxEmptyString`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL`
	)

Definition at line 155 of file blast_db_dialog.cpp.

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

◆ CBLAST_Dlg_Item() [1/2]

CBLAST_Dlg_Item::CBLAST_Dlg_Item ( )

Definition at line 65 of file blast_db_dialog.cpp.

◆ CBLAST_Dlg_Item() [2/2]

CBLAST_Dlg_Item::CBLAST_Dlg_Item	(	const string &	label,
		const string &	path,
		bool	is_database = `false`
	)

Definition at line 75 of file blast_db_dialog.cpp.

References _ASSERT, label, CBLAST_Dlg_Item::m_LabelLength, and CBLAST_Dlg_Item::m_LabelPos.

◆ CBLASTParams()

CBLASTParams::CBLASTParams ( )

Definition at line 248 of file blast_search_params.cpp.

References eBlastn, eBlastp, eBlastx, eDiscMegablast, eMegablast, map_checker< Container >::empty(), eTblastn, eTblastx, i, info, map_checker< Container >::insert(), CBLASTParams::m_ProgToParams, n, s_DefaultParams(), sc_ProgPairs, and CBLASTParams::sm_ProgramToAttr.

◆ CBLASTSearchOptionsPanel() [1/2]

CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel ( )

Definition at line 102 of file blast_search_options_panel.cpp.

References Init().

◆ CBLASTSearchOptionsPanel() [2/2]

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

Definition at line 114 of file blast_search_options_panel.cpp.

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

◆ CBLASTSearchParamsPanel() [1/2]

CBLASTSearchParamsPanel::CBLASTSearchParamsPanel ( )

Definition at line 83 of file blast_search_params_panel.cpp.

References Init().

◆ CBLASTSearchParamsPanel() [2/2]

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

Definition at line 90 of file blast_search_params_panel.cpp.

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

◆ CBlastSearchTask()

CBlastSearchTask::CBlastSearchTask	(	IServiceLocator *	srv_locator,
		CNetBLASTUIDataSource &	ds,
		const string &	tool_name
	)

CBlastSearchTask.

Definition at line 46 of file blast_search_task.cpp.

◆ CBLASTSeqToolJob()

CBLASTSeqToolJob::CBLASTSeqToolJob ( const CBLASTParams & params )

Definition at line 132 of file blast_seq_tool_job.cpp.

References CAppJob::m_Descr.

◆ CBLASTToolManager()

CBLASTToolManager::CBLASTToolManager ( )

CBLASTToolManager.

Definition at line 61 of file blast_tool_manager.cpp.

References CBLASTToolManager::m_Descriptor, and CUIObject::SetLogEvent().

◆ CCleanupAlignmentsJob()

CCleanupAlignmentsJob::CCleanupAlignmentsJob ( const SCleanupAlignmentsParams & params )

CCleanupAlignmentsJob.

Definition at line 203 of file cleanup_alignments_tool_manager.cpp.

References CAppJob::m_Descr.

◆ CCleanupAlignmentsParamsPanel() [1/2]

CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel ( )

Definition at line 94 of file cleanup_alignments_params_panel.cpp.

References Init().

◆ CCleanupAlignmentsParamsPanel() [2/2]

CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CCLEANUPALIGNMENTSPARAMSPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 102 of file cleanup_alignments_params_panel.cpp.

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

◆ CCleanupAlignmentsToolManager()

CCleanupAlignmentsToolManager::CCleanupAlignmentsToolManager ( )

Definition at line 58 of file cleanup_alignments_tool_manager.cpp.

◆ CClustalOmegaTool()

CClustalOmegaTool::CClustalOmegaTool ( )

CClustalOmegaTool.

Definition at line 47 of file clustal_omega_tool.cpp.

◆ CClustalOmegaToolJob()

CClustalOmegaToolJob::CClustalOmegaToolJob ( const CClustalOmegaToolParams & params )

CClustalOmegaToolJob.

Definition at line 44 of file clustal_omega_tool_job.cpp.

References CAppJob::m_Descr.

◆ CClustalOmegaToolParams() [1/2]

CClustalOmegaToolParams::CClustalOmegaToolParams ( )

Definition at line 45 of file clustal_omega_tool_params.cpp.

References CClustalOmegaToolParams::Init().

◆ CClustalOmegaToolParams() [2/2]

CClustalOmegaToolParams::CClustalOmegaToolParams ( const CClustalOmegaToolParams & data )

Definition at line 50 of file clustal_omega_tool_params.cpp.

References CClustalOmegaToolParams::Copy(), data, and CClustalOmegaToolParams::Init().

◆ CClustalwTool()

CClustalwTool::CClustalwTool ( )

CClustalwTool.

Definition at line 47 of file clustalw_tool.cpp.

◆ CClustalwToolJob()

CClustalwToolJob::CClustalwToolJob ( const CClustalwToolParams & params )

CClustalwToolJob.

Definition at line 44 of file clustalw_tool_job.cpp.

References CAppJob::m_Descr.

◆ CClustalwToolParams() [1/2]

CClustalwToolParams::CClustalwToolParams ( )

Definition at line 41 of file clustalw_tool_params.cpp.

References CClustalwToolParams::Init().

◆ CClustalwToolParams() [2/2]

CClustalwToolParams::CClustalwToolParams ( const CClustalwToolParams & data )

Definition at line 45 of file clustalw_tool_params.cpp.

References CClustalwToolParams::Copy(), data, and CClustalwToolParams::Init().

◆ CCommonTaxTreeTool()

CCommonTaxTreeTool::CCommonTaxTreeTool ( )

CCommonTaxTreeTool.

Definition at line 47 of file taxtree_tool.cpp.

◆ CCreateGeneModelTask()

CCreateGeneModelTask::CCreateGeneModelTask	(	const string &	descr,
		CProjectService *	service,
		CSelectProjectOptions &	options,
		const SCreateGeneModelParams &	params
	)

inline

Definition at line 133 of file create_gene_model_tool_manager.hpp.

◆ CCreateGeneModelToolManager()

CCreateGeneModelToolManager::CCreateGeneModelToolManager ( )

Definition at line 62 of file create_gene_model_tool_manager.cpp.

◆ CCreateNeedlemanWunschJob()

CCreateNeedlemanWunschJob::CCreateNeedlemanWunschJob ( const CNeedlemanWunschToolParams & params )

CCreateNeedlemanWunschJob.

Definition at line 160 of file create_needleman_wunsch_tool_manager.cpp.

References CAppJob::m_Descr.

◆ CCreateNeedlemanWunschToolManager()

CCreateNeedlemanWunschToolManager::CCreateNeedlemanWunschToolManager ( )

Definition at line 68 of file create_needleman_wunsch_tool_manager.cpp.

◆ CCrossAlignView()

CCrossAlignView::CCrossAlignView ( )

Definition at line 71 of file cross_align_view.cpp.

◆ CDebugMacroToolJob()

CDebugMacroToolJob::CDebugMacroToolJob ( const CDebugMacroToolParams & params )

CDebugMacroToolJob.

Definition at line 51 of file debug_macro_tool_job.cpp.

References CAppJob::m_Descr.

◆ CDotMatrixView()

CDotMatrixView::CDotMatrixView ( )

Definition at line 81 of file dot_matrix_view.cpp.

◆ CDotMatrixViewFactory()

CDotMatrixViewFactory::CDotMatrixViewFactory ( )

CDotMatrixViewFactory.

Definition at line 372 of file dot_matrix_view.cpp.

◆ CFindOverlapPanel() [1/2]

CFindOverlapPanel::CFindOverlapPanel ( )

Definition at line 61 of file find_overlap_panel.cpp.

References Init().

◆ CFindOverlapPanel() [2/2]

CFindOverlapPanel::CFindOverlapPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CFINDOVERLAPPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`,
		bool	visible = `true`
	)

Definition at line 66 of file find_overlap_panel.cpp.

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

◆ CFindOverlapParams() [1/2]

CFindOverlapParams::CFindOverlapParams ( )

Definition at line 40 of file find_overlap_params.cpp.

References CFindOverlapParams::Init().

◆ CFindOverlapParams() [2/2]

CFindOverlapParams::CFindOverlapParams ( const CFindOverlapParams & data )

Definition at line 44 of file find_overlap_params.cpp.

References CFindOverlapParams::Copy(), data, and CFindOverlapParams::Init().

◆ CFindOverlapTool()

CFindOverlapTool::CFindOverlapTool ( )

CFindOverlapTool.

Definition at line 71 of file find_overlap_tool.cpp.

◆ CGroupAlignmentsJob()

CGroupAlignmentsJob::CGroupAlignmentsJob ( const SGroupAlignmentsParams & params )

CGroupAlignmentsJob.

Definition at line 169 of file group_alignments_tool_manager.cpp.

References CAppJob::m_Descr, and CAppJob::m_Mutex.

◆ CGroupAlignmentsParamsPanel() [1/2]

CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel ( )

Definition at line 143 of file group_alignments_params_panel.cpp.

References CGroupAlignmentsParamsPanel::Init().

◆ CGroupAlignmentsParamsPanel() [2/2]

CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CGROUPALIGNMENTSPARAMSPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 148 of file group_alignments_params_panel.cpp.

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

◆ CGroupAlignmentsToolManager()

CGroupAlignmentsToolManager::CGroupAlignmentsToolManager ( )

Definition at line 51 of file group_alignments_tool_manager.cpp.

◆ Check()

void CNetBlastJobDescriptor::Check ( )

Definition at line 303 of file net_blast_job_descr.cpp.

References done, CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eSubmitted, eUnknown, CNetBlastJobDescriptor::m_Errors, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_State, NCBI_THROW, CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded(), and CNetBlastJobDescriptor::x_NotifyDataSource().

Referenced by CNetBlastLoadingJob::x_CreateProjectItems().

◆ CKalignTool()

CKalignTool::CKalignTool ( )

CKalignTool.

Definition at line 46 of file kalign_tool.cpp.

◆ CKalignToolJob()

CKalignToolJob::CKalignToolJob ( const CKalignToolParams & params )

CKalignToolJob.

Definition at line 42 of file kalign_tool_job.cpp.

References CAppJob::m_Descr.

◆ CKalignToolParams() [1/2]

CKalignToolParams::CKalignToolParams ( )

Definition at line 41 of file kalign_tool_params.cpp.

References CKalignToolParams::Init().

◆ CKalignToolParams() [2/2]

CKalignToolParams::CKalignToolParams ( const CKalignToolParams & data )

Definition at line 46 of file kalign_tool_params.cpp.

References CKalignToolParams::Copy(), data, and CKalignToolParams::Init().

◆ CleanUI() [1/21]

void CBLASTToolManager::CleanUI ( )

IUITool * CNetBLAST_DMSearchTool::Clone ( void ) const

virtual

Implements CSearchToolBase.

Definition at line 149 of file net_blast_dm_search_tool.cpp.

References CNetBLAST_DMSearchTool::CNetBLAST_DMSearchTool().

◆ Close()

bool CNetBLASTUIDataSource::Close ( void )

virtual

Implements IUIDataSource.

Definition at line 256 of file net_blast_ui_data_source.cpp.

References CStopWatch::AsSmartString(), ERR_POST, CStopWatch::eStart, CExtensionRegistry::GetInstance(), Info(), kAppExpCmdExtPoint, kCmdExtPoint, CNetBLASTUIDataSource::m_JobDescrs, CNetBLASTUIDataSource::m_Open, CStopWatch::Restart(), CStopWatch::Stop(), and CNetBLASTUIDataSource::x_SaveJobDescriptors().

◆ CMafftTool()

CMafftTool::CMafftTool ( )

CMafftTool.

Definition at line 46 of file mafft_tool.cpp.

◆ CMafftToolJob()

CMafftToolJob::CMafftToolJob ( const CMafftToolParams & params )

CMafftToolJob.

Definition at line 42 of file mafft_tool_job.cpp.

References CAppJob::m_Descr.

◆ CMafftToolParams() [1/2]

CMafftToolParams::CMafftToolParams ( )

Definition at line 41 of file mafft_tool_params.cpp.

References CMafftToolParams::Init().

◆ CMafftToolParams() [2/2]

CMafftToolParams::CMafftToolParams ( const CMafftToolParams & data )

Definition at line 46 of file mafft_tool_params.cpp.

References CMafftToolParams::Copy(), data, and CMafftToolParams::Init().

◆ CMergeAlignmentsJob()

CMergeAlignmentsJob::CMergeAlignmentsJob ( const SMergeAlignmentsParams & params )

CMergeAlignmentsJob.

Definition at line 179 of file merge_alignments_tool_manager.cpp.

References CAppJob::m_Descr.

◆ CMergeAlignmentsParamsPanel() [1/2]

CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel ( )

CMergeAlignmentsParamsPanel.

Definition at line 118 of file merge_alignments_params_panel.cpp.

References Init().

◆ CMergeAlignmentsParamsPanel() [2/2]

CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CBLASTSEARCHOPTIONSPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 124 of file merge_alignments_params_panel.cpp.

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

◆ CMergeAlignmentsToolManager()

CMergeAlignmentsToolManager::CMergeAlignmentsToolManager ( )

CMergeAlignmentsToolManager.

Definition at line 63 of file merge_alignments_tool_manager.cpp.

◆ CMolTypeValidator()

CMolTypeValidator::CMolTypeValidator ( MolType molType )

inline

Definition at line 85 of file splign_panel.hpp.

◆ CMPCrossAlignView()

CMPCrossAlignView::CMPCrossAlignView ( )

Definition at line 73 of file mp_cross_align_view.cpp.

◆ CMSAToolJob()

CMSAToolJob::CMSAToolJob ( const wxString & tool_name )

CMSAToolJob.

Definition at line 151 of file msa_tool_job.cpp.

◆ CMultiAlignView()

CMultiAlignView::CMultiAlignView ( )

◆ CMultiAlignViewFactory()

CMultiAlignViewFactory::CMultiAlignViewFactory ( )

Definition at line 1215 of file multi_align_view.cpp.

References CMultiAlignViewFactory::m_ViewManager.

◆ CMuscleTool()

CMuscleTool::CMuscleTool ( )

CMuscleTool.

Definition at line 46 of file muscle_tool.cpp.

◆ CMuscleToolJob()

CMuscleToolJob::CMuscleToolJob ( const CMuscleToolParams & params )

CMuscleToolJob.

Definition at line 50 of file muscle_tool_job.cpp.

References CAppJob::m_Descr.

◆ CMuscleToolPanel() [1/2]

CMuscleToolPanel::CMuscleToolPanel ( )

Definition at line 70 of file muscle_tool_panel.cpp.

References Init().

◆ CMuscleToolPanel() [2/2]

CMuscleToolPanel::CMuscleToolPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CMUSCLEPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`,
		bool	visible = `true`
	)

Definition at line 75 of file muscle_tool_panel.cpp.

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

◆ CMuscleToolParams() [1/2]

CMuscleToolParams::CMuscleToolParams ( )

Definition at line 41 of file muscle_tool_params.cpp.

References CMuscleToolParams::Init().

◆ CMuscleToolParams() [2/2]

CMuscleToolParams::CMuscleToolParams ( const CMuscleToolParams & data )

Definition at line 46 of file muscle_tool_params.cpp.

References CMuscleToolParams::Copy(), data, and CMuscleToolParams::Init().

◆ CNeedlemanWunschToolParams() [1/2]

CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ( )

Definition at line 40 of file needlemanwunsch_tool_params.cpp.

References CNeedlemanWunschToolParams::Init().

◆ CNeedlemanWunschToolParams() [2/2]

CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ( const CNeedlemanWunschToolParams & data )

Definition at line 44 of file needlemanwunsch_tool_params.cpp.

References CNeedlemanWunschToolParams::Copy(), data, and CNeedlemanWunschToolParams::Init().

◆ CNetBLAST_DMSearchForm()

CNetBLAST_DMSearchForm::CNetBLAST_DMSearchForm ( CNetBLAST_DMSearchTool & tool )

CNetBLAST_DMSearchForm.

Definition at line 245 of file net_blast_dm_search_tool.cpp.

◆ CNetBLAST_DMSearchJob()

CNetBLAST_DMSearchJob::CNetBLAST_DMSearchJob	(	CNetBLAST_DMSearchQuery &	query,
		CNetBLASTUIDataSource &	ds
	)

CNetBLAST_DMSearchJob.

Definition at line 372 of file net_blast_dm_search_tool.cpp.

◆ CNetBLAST_DMSearchQuery()

CNetBLAST_DMSearchQuery::CNetBLAST_DMSearchQuery	(	const TStates &	states,
		const string &	filter_str
	)

CNetBLAST_DMSearchQuery.

Definition at line 358 of file net_blast_dm_search_tool.cpp.

◆ CNetBLAST_DMSearchTool()

CNetBLAST_DMSearchTool::CNetBLAST_DMSearchTool ( )

IDMSearchTool.

Definition at line 143 of file net_blast_dm_search_tool.cpp.

Referenced by CNetBLAST_DMSearchTool::Clone().

◆ CNetBlastDMSearchFormPanel() [1/2]

CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel ( )

Definition at line 75 of file net_blast_dm_search_form_panel.cpp.

References Init().

◆ CNetBlastDMSearchFormPanel() [2/2]

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

Definition at line 81 of file net_blast_dm_search_form_panel.cpp.

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

◆ CNetBlastJobDescriptor() [1/3]

CNetBlastJobDescriptor::CNetBlastJobDescriptor ( )

protected

CNetBlastJobDescriptor.

Definition at line 107 of file net_blast_job_descr.cpp.

References CLabel::HasHandler(), CNetBlastJobDescriptor::m_SubmitTime, and CLabel::RegisterLabelHandler().

Referenced by CNetBlastJobDescriptor::CNetBlastJobDescriptor().

◆ CNetBlastJobDescriptor() [2/3]

CNetBlastJobDescriptor::CNetBlastJobDescriptor ( CNetBLASTUIDataSource & ds )

protected

Definition at line 121 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::CNetBlastJobDescriptor(), CLabel::HasHandler(), CNetBlastJobDescriptor::m_SubmitTime, and CLabel::RegisterLabelHandler().

◆ CNetBlastJobDescriptor() [3/3]

CNetBlastJobDescriptor::CNetBlastJobDescriptor ( const CNetBlastJobDescriptor & )

protected

◆ CNetBlastLoadingJob()

CNetBlastLoadingJob::CNetBlastLoadingJob	(	CNetBLASTUIDataSource &	ds,
		const vector< string > *	RIDs = `NULL`,
		CScope *	scope = `NULL`
	)

CNetBlastLoadingJob.

Definition at line 482 of file blast_jobs.cpp.

References CAppJob::m_Descr, CAppJob::m_Mutex, and CNetBlastLoadingJob::SetRIDs().

◆ CNetBLASTLoadOptionPanel() [1/2]

CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel ( )

Definition at line 57 of file net_blast_load_option_panel.cpp.

References Init().

◆ CNetBLASTLoadOptionPanel() [2/2]

CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_NETBLASTLOADOPTIONPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 63 of file net_blast_load_option_panel.cpp.

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

◆ CNetBlastMonitoringJob()

CNetBlastMonitoringJob::CNetBlastMonitoringJob	(	CNetBLASTUIDataSource &	ds,
		IServiceLocator *	srv_locator,
		const string &	tool_name,
		TDescriptors &	descriptors
	)

CNetBlastSubmittingJob.

Definition at line 263 of file blast_jobs.cpp.

References CNetBlastMonitoringJob::m_Descr, CNetBlastMonitoringJob::m_Mutex, CNetBlastMonitoringJob::m_SrvLocator, and CNetBlastMonitoringJob::m_ToolName.

◆ CNetBlastSubmittingJob()

CNetBlastSubmittingJob::CNetBlastSubmittingJob	(	string	tool_name,
		const CBLASTParams &	params,
		CNetBLASTUIDataSource &	ds
	)

CNetBlastSubmittingJob.

Definition at line 68 of file blast_jobs.cpp.

References _ASSERT, CNetBLASTUIDataSource::CreateJobDescriptor(), CBLASTParams::GetSeqLocs(), i, CNetBlastSubmittingJob::m_Descr, CNetBlastSubmittingJob::m_Descriptors, and CNetBlastSubmittingJob::m_SeqLocs.

◆ CNetBLASTUIDataSource()

CNetBLASTUIDataSource::CNetBLASTUIDataSource ( CNetBLASTUIDataSourceType & type )

Definition at line 144 of file net_blast_ui_data_source.cpp.

◆ CNetBLASTUIDataSourceEvent()

CNetBLASTUIDataSourceEvent::CNetBLASTUIDataSourceEvent ( )

inline

Definition at line 90 of file net_blast_ui_data_source.hpp.

◆ CNetBLASTUIDataSourceType()

CNetBLASTUIDataSourceType::CNetBLASTUIDataSourceType ( )

CNetBLASTUIDataSourceType.

Definition at line 629 of file net_blast_ui_data_source.cpp.

◆ CNetBLASTUILoadManager()

CNetBLASTUILoadManager::CNetBLASTUILoadManager ( CNetBLASTUIDataSource & data_source )

CNetBLASTUILoadManager.

Definition at line 52 of file net_blast_ui_load_manager.cpp.

References CNetBLASTUILoadManager::m_Descriptor, and CUIObject::SetLogEvent().

◆ CNGAlignJob()

CNGAlignJob::CNGAlignJob ( const CNGAlignParams & params )

CNGAlignJob.

Definition at line 71 of file ngalign_job.cpp.

References CAppJob::m_Descr.

◆ CNGAlignPanel() [1/2]

CNGAlignPanel::CNGAlignPanel ( )

Definition at line 67 of file ngalign_panel.cpp.

References Init().

◆ CNGAlignPanel() [2/2]

CNGAlignPanel::CNGAlignPanel ( wxWindow * parent )

Definition at line 72 of file ngalign_panel.cpp.

References CNGAlignPanel::Create(), and CNGAlignPanel::Init().

◆ CNGAlignParams() [1/2]

CNGAlignParams::CNGAlignParams ( )

Definition at line 44 of file ngalign_params.cpp.

References CNGAlignParams::Init().

◆ CNGAlignParams() [2/2]

CNGAlignParams::CNGAlignParams ( const CNGAlignParams & data )

Definition at line 49 of file ngalign_params.cpp.

References CNGAlignParams::Copy(), data, and CNGAlignParams::Init().

◆ CNGAlignTool()

CNGAlignTool::CNGAlignTool ( )

CNGAlignTool.

Definition at line 56 of file ngalign_tool.cpp.

◆ CombineInputObjects()

vector< int > CDotMatrixViewFactory::CombineInputObjects ( const TConstScopedObjects & objects )

virtual

Reimplemented from IProjectViewFactory.

Definition at line 447 of file dot_matrix_view.cpp.

◆ CommitTheChanges()

void CPhyTreeView::CommitTheChanges ( CNcbiIstrstream & istr )

Definition at line 1798 of file phy_tree_view.cpp.

References CConstRef< C, Locker >::GetPointer(), CBioTreeContainer_Base::GetTreetype(), CBioTreeContainer_Base::IsSetTreetype(), CPhyTreeView::m_BioTreeContainer, MSerial_AsnText, CBioTreeContainer_Base::Reset(), and CBioTreeContainer_Base::SetTreetype().

Referenced by CChangePhyloTreeCommand::Execute(), and CChangePhyloTreeCommand::Unexecute().

◆ ConstructQuery()

CIRef< IDMSearchQuery > CNetBLAST_DMSearchForm::ConstructQuery ( )

virtual

Reimplemented from CSearchFormBase.

Definition at line 325 of file net_blast_dm_search_tool.cpp.

References CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eRetrieved, CNetBlastJobDescriptor::eSubmitted, CNetBlastDMSearchFormPanel::GetCompleted(), CNetBlastDMSearchFormPanel::GetExpired(), CNetBlastDMSearchFormPanel::GetFailed(), CNetBlastDMSearchFormPanel::GetRetrieved(), CNetBlastDMSearchFormPanel::GetSearchValue(), CNetBlastDMSearchFormPanel::GetSubmitted(), set< Key, Compare >::insert(), CNetBLAST_DMSearchForm::m_Panel, CRef< C, Locker >::Reset(), and ToStdString().

◆ Copy() [1/11]

void CClustalOmegaToolParams::Copy ( const CClustalOmegaToolParams & data )

Definition at line 75 of file clustal_omega_tool_params.cpp.

References data, CClustalOmegaToolParams::m_ClustalOmegaPath, CClustalOmegaToolParams::m_CommandLine, CClustalOmegaToolParams::m_GenerateTree, and CClustalOmegaToolParams::m_Objects.

Referenced by CClustalOmegaToolParams::CClustalOmegaToolParams(), and CClustalOmegaToolParams::operator=().

◆ Copy() [2/11]

void CClustalwToolParams::Copy ( const CClustalwToolParams & data )

Definition at line 66 of file clustalw_tool_params.cpp.

References data, CClustalwToolParams::m_ClustalWPath, CClustalwToolParams::m_CommandLine, CClustalwToolParams::m_GenerateTree, and CClustalwToolParams::m_Objects.

Referenced by CClustalwToolParams::CClustalwToolParams(), and CClustalwToolParams::operator=().

◆ Copy() [3/11]

void CFindOverlapParams::Copy ( const CFindOverlapParams & data )

Definition at line 65 of file find_overlap_params.cpp.

References data, CFindOverlapParams::m_BlastParams, CFindOverlapParams::m_FilterQty, CFindOverlapParams::m_MaxSlop, CFindOverlapParams::m_Seq1, and CFindOverlapParams::m_Seq2.

Referenced by CFindOverlapParams::CFindOverlapParams(), and CFindOverlapParams::operator=().

◆ Copy() [4/11]

void CKalignToolParams::Copy ( const CKalignToolParams & data )

Definition at line 71 of file kalign_tool_params.cpp.

References data, CKalignToolParams::m_CommandLine, CKalignToolParams::m_KalignPath, CKalignToolParams::m_Objects, and CKalignToolParams::m_QuietFlag.

Referenced by CKalignToolParams::CKalignToolParams(), and CKalignToolParams::operator=().

◆ Copy() [5/11]

void CMafftToolParams::Copy ( const CMafftToolParams & data )

Definition at line 72 of file mafft_tool_params.cpp.

References data, CMafftToolParams::m_AutoFlag, CMafftToolParams::m_CommandLine, CMafftToolParams::m_MafftPath, CMafftToolParams::m_Objects, and CMafftToolParams::m_QuietFlag.

Referenced by CMafftToolParams::CMafftToolParams(), and CMafftToolParams::operator=().

◆ Copy() [6/11]

void CMuscleToolParams::Copy ( const CMuscleToolParams & data )

Definition at line 72 of file muscle_tool_params.cpp.

References data, CMuscleToolParams::m_CommandLine, CMuscleToolParams::m_GenerateTree, CMuscleToolParams::m_MusclePath, CMuscleToolParams::m_Objects, and CMuscleToolParams::m_ScoringMethod.

Referenced by CMuscleToolParams::CMuscleToolParams(), and CMuscleToolParams::operator=().

◆ Copy() [7/11]

void CNeedlemanWunschToolParams::Copy ( const CNeedlemanWunschToolParams & data )

Definition at line 69 of file needlemanwunsch_tool_params.cpp.

References data, CNeedlemanWunschToolParams::m_BandSize, CNeedlemanWunschToolParams::m_FirstSeqFreeEnds, CNeedlemanWunschToolParams::m_GapExtendCost, CNeedlemanWunschToolParams::m_GapOpenCost, CNeedlemanWunschToolParams::m_MatchCost, CNeedlemanWunschToolParams::m_MismatchCost, CNeedlemanWunschToolParams::m_Objects, and CNeedlemanWunschToolParams::m_SecondSeqFreeEnds.

Referenced by CNeedlemanWunschToolParams::CNeedlemanWunschToolParams(), and CNeedlemanWunschToolParams::operator=().

◆ Copy() [8/11]

void CNGAlignParams::Copy ( const CNGAlignParams & data )

Definition at line 79 of file ngalign_params.cpp.

References data, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_JobTitle, CNGAlignParams::m_Queries, CNGAlignParams::m_Subject, CNGAlignParams::m_WM_Dir, CNGAlignParams::m_WM_TaxId, and CNGAlignParams::m_WordSize.

Referenced by CNGAlignParams::CNGAlignParams(), and CNGAlignParams::operator=().

◆ Copy() [9/11]

void CSplignParams::Copy ( const CSplignParams & data )

Definition at line 71 of file splign_params.cpp.

References data, CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, and CSplignParams::m_PolyADetect.

Referenced by CSplignParams::CSplignParams(), and CSplignParams::operator=().

◆ Copy() [10/11]

void CTaxTreeToolParams::Copy ( const CTaxTreeToolParams & data )

Definition at line 62 of file taxtree_tool_params.cpp.

References data, and CTaxTreeToolParams::m_Objects.

Referenced by CTaxTreeToolParams::CTaxTreeToolParams(), and CTaxTreeToolParams::operator=().

◆ Copy() [11/11]

void CTreeBuilderParams::Copy ( const CTreeBuilderParams & data )

Definition at line 65 of file tree_builder_params.cpp.

References data, CTreeBuilderParams::m_ConstructMethod, CTreeBuilderParams::m_DistanceMethod, CTreeBuilderParams::m_LeafLabels, and CTreeBuilderParams::m_Object.

Referenced by CTreeBuilderParams::CTreeBuilderParams(), and CTreeBuilderParams::operator=().

◆ CPage() [1/2]

CPslLoadManager::CPage::CPage ( CPslLoadManager & manager )

inline

Definition at line 134 of file psl_load_manager.hpp.

◆ CPage() [2/2]

CTextAlignLoaderManager::CPage::CPage ( CTextAlignLoaderManager & manager )

inline

Definition at line 136 of file text_align_load_manager.hpp.

◆ CPhyloTreeJob()

CPhyloTreeJob::CPhyloTreeJob ( const objects::CBioTreeContainer * btc )

Definition at line 1897 of file phy_tree_view.cpp.

References CPhyloTreeJob::m_Btc, CAppJob::m_Descr, CAppJob::m_Mutex, and CRef< C, Locker >::Reset().

◆ CPhyTreeView()

CPhyTreeView::CPhyTreeView ( )

Definition at line 720 of file phy_tree_view.cpp.

References CAttribMenu::AddFloatReadOnly(), CAttribMenu::AddSubMenuUnique(), CAttribMenuInstance::GetInstance(), m_CreateProperyUndoCommand, m_CreateUndoCommand, m_DataSourceInitTimer, m_ExecOnBioTreeChanged, m_ExecutePropertyCommand, and m_ExecuteUndoCommand.

◆ CProSplignTool()

CProSplignTool::CProSplignTool ( )

CProSplignTool.

Definition at line 96 of file prosplign_tool.cpp.

◆ CPslLoadManager()

CPslLoadManager::CPslLoadManager ( )

CPslLoadManager.

Definition at line 52 of file psl_load_manager.cpp.

References CFileExtensions::GetLabel(), CUIObject::Init(), CFileExtensions::kPSL, CPslLoadManager::m_Descr, CUIObject::SetLogEvent(), and ToStdString().

◆ Create() [1/15]

void CNetBLAST_DMSearchForm::Create ( void )

virtual

Reimplemented from IDMSearchForm.

Definition at line 259 of file net_blast_dm_search_tool.cpp.

◆ Create() [2/15]

bool CBLAST_DB_Dialog::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CBLAST_DB_DIALOG`,
		const wxString &	caption = `wxEmptyString`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL`
	)

Definition at line 162 of file blast_db_dialog.cpp.

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

Referenced by CBLAST_DB_Dialog::CBLAST_DB_Dialog().

◆ Create() [3/15]

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

Definition at line 123 of file blast_search_options_panel.cpp.

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

Referenced by CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel(), CBLASTToolManager::GetMaxPanel(), and CBLASTToolManager::x_CreateOptionsPanelIfNeeded().

◆ Create() [4/15]

bool CMergeAlignmentsParamsPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CBLASTSEARCHOPTIONSPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 131 of file merge_alignments_params_panel.cpp.

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

Referenced by CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel(), and CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ Create() [5/15]

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

Definition at line 103 of file blast_search_params_panel.cpp.

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

Referenced by CBLASTSearchParamsPanel::CBLASTSearchParamsPanel().

◆ Create() [6/15]

bool CCleanupAlignmentsParamsPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CCLEANUPALIGNMENTSPARAMSPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 108 of file cleanup_alignments_params_panel.cpp.

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

Referenced by CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel(), and CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ Create() [7/15]

bool CFindOverlapPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CFINDOVERLAPPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`,
		bool	visible = `true`
	)

Definition at line 73 of file find_overlap_panel.cpp.

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

Referenced by CFindOverlapPanel::CFindOverlapPanel().

◆ Create() [8/15]

bool CGroupAlignmentsParamsPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CGROUPALIGNMENTSPARAMSPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 154 of file group_alignments_params_panel.cpp.

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

Referenced by CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel(), and CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ Create() [9/15]

bool CMuscleToolPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CMUSCLEPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`,
		bool	visible = `true`
	)

Definition at line 81 of file muscle_tool_panel.cpp.

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

Referenced by CMuscleToolPanel::CMuscleToolPanel(), and CMuscleTool::GetMaxPanel().

◆ Create() [10/15]

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

Definition at line 88 of file net_blast_dm_search_form_panel.cpp.

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

Referenced by CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel().

◆ Create() [11/15]

bool CNGAlignPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CNGALIGNPANEL`
	)

Definition at line 78 of file ngalign_panel.cpp.

References CNGAlignPanel::CreateControls(), and SYMBOL_CNGALIGNPANEL_STYLE.

Referenced by CNGAlignPanel::CNGAlignPanel().

◆ Create() [12/15]

bool CSplignPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CSPLIGNPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxCLIP_CHILDREN\|wxTAB_TRAVERSAL`,
		bool	visibale = `true`
	)

Definition at line 167 of file splign_panel.cpp.

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

Referenced by CSplignPanel::CSplignPanel(), CProSplignTool::GetMaxPanel(), and CSplignTool::GetMaxPanel().

◆ Create() [13/15]

bool CTaxTreeToolPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CTAXTREETOOLPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`,
		bool	visibale = `true`
	)

Definition at line 70 of file taxtree_tool_panel.cpp.

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

Referenced by CTaxTreeToolPanel::CTaxTreeToolPanel(), and CCommonTaxTreeTool::GetMaxPanel().

◆ Create() [14/15]

bool CTreeBuilderPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_CTreeBuilderPanel`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 85 of file tree_builder_panel.cpp.

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

Referenced by CTreeBuilderPanel::CTreeBuilderPanel(), and CTreeBuilderTool::x_CreateParamsPanelIfNeeded().

◆ Create() [15/15]

bool CNetBLASTLoadOptionPanel::Create	(	wxWindow *	parent,
		wxWindowID	id = `ID_NETBLASTLOADOPTIONPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 70 of file net_blast_load_option_panel.cpp.

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

Referenced by CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel().

◆ CreateControls() [1/14]

void CBLAST_DB_Dialog::CreateControls ( )

Definition at line 198 of file blast_db_dialog.cpp.

References _, CBLAST_DB_Dialog::ID_RESET_BTN, CBLAST_DB_Dialog::ID_SEARCH, CBLAST_DB_Dialog::ID_TREECTRL, CBLAST_DB_Dialog::m_OKBtn, CBLAST_DB_Dialog::m_SearchCtrl, CBLAST_DB_Dialog::m_StatusText, CBLAST_DB_Dialog::m_TreeCtrl, CBLAST_DB_Dialog::wxID_STATUS, and wxTR_GBENCH_LINES.

Referenced by CBLAST_DB_Dialog::Create().

◆ CreateControls() [2/14]

void CBLASTSearchOptionsPanel::CreateControls ( )

Definition at line 205 of file blast_search_options_panel.cpp.

Referenced by CBLASTSearchOptionsPanel::Create().

◆ CreateControls() [3/14]

void CBLASTSearchParamsPanel::CreateControls ( )

Definition at line 151 of file blast_search_params_panel.cpp.

Referenced by CBLASTSearchParamsPanel::Create().

◆ CreateControls() [4/14]

void CCleanupAlignmentsParamsPanel::CreateControls ( )

Definition at line 144 of file cleanup_alignments_params_panel.cpp.

Referenced by CCleanupAlignmentsParamsPanel::Create().

◆ CreateControls() [5/14]

void CFindOverlapPanel::CreateControls ( )

Definition at line 105 of file find_overlap_panel.cpp.

References _, CFindOverlapPanel::GetData(), CFindOverlapPanel::ID_LISTCTRL3, CFindOverlapPanel::ID_LISTCTRL4, CFindOverlapPanel::ID_TEXTCTRL2, CFindOverlapPanel::ID_TEXTCTRL4, CFindOverlapPanel::ID_TEXTCTRL5, CFindOverlapPanel::m_Seq1List, CFindOverlapPanel::m_Seq2List, and wxID_ANY.

Referenced by CFindOverlapPanel::Create().

◆ CreateControls() [6/14]

void CGroupAlignmentsParamsPanel::CreateControls ( )

Definition at line 196 of file group_alignments_params_panel.cpp.

Referenced by CGroupAlignmentsParamsPanel::Create().

◆ CreateControls() [7/14]

void CMergeAlignmentsParamsPanel::CreateControls ( )

Definition at line 169 of file merge_alignments_params_panel.cpp.

Referenced by CMergeAlignmentsParamsPanel::Create().

◆ CreateControls() [8/14]

void CNetBlastDMSearchFormPanel::CreateControls ( )

Definition at line 121 of file net_blast_dm_search_form_panel.cpp.

Referenced by CNetBlastDMSearchFormPanel::Create().

◆ CreateControls() [9/14]

void CNetBLASTLoadOptionPanel::CreateControls ( )

Definition at line 132 of file net_blast_load_option_panel.cpp.

References _, _ASSERT, entries, CNetBLASTLoadOptionPanel::ID_TEXTCTRL1, and wxID_ANY.

Referenced by CNetBLASTLoadOptionPanel::Create().

◆ CreateControls() [10/14]

◆ CreateControls() [11/14]

void CTreeBuilderPanel::CreateControls ( )

◆ CreateControls() [12/14]

void CMuscleToolPanel::CreateControls ( )

◆ CreateControls() [13/14]

void CNGAlignPanel::CreateControls ( )

Definition at line 109 of file ngalign_panel.cpp.

References _, CNGAlignPanel::ID_QUERY_LIST, CNGAlignPanel::ID_SUBJ_LIST, CNGAlignPanel::m_QueryListCtrl, CNGAlignPanel::m_SubjectListCtrl, and wxID_ANY.

Referenced by CNGAlignPanel::Create().

CRef< CNetBlastJobDescriptor > CNetBLASTUIDataSource::CreateJobDescriptor ( const CBLASTParams & params )

Definition at line 397 of file net_blast_ui_data_source.cpp.

void CPhyTreeView::CreateViewWindow ( wxWindow * parent )

virtual

create Window corresponding to the view

Implements CProjectViewBase.

Definition at line 793 of file phy_tree_view.cpp.

References _ASSERT, CEventHandler::AddListener(), CGlWidgetBase::Create(), CQueryParsePanel::Create(), CEventHandler::ePool_Child, CEventHandler::ePool_Parent, CRef< C, Locker >::GetPointerOrNull(), CPhyTreeView::kPhylpWidgetID, CPhyTreeView::kQueryPanelID, CPhyTreeView::m_DataSource, CPhyTreeView::m_Panel, and CPhyloTreeWidget::SetQueryPanel().

◆ CrossLinkTriple()

void SGeneCdsmRnaFeats::CrossLinkTriple ( )

Definition at line 227 of file create_gene_model_tool_manager.cpp.

References SGeneCdsmRnaFeats::cds, dbname(), SGeneCdsmRnaFeats::gene, SGeneCdsmRnaFeats::mRNA, SGeneCdsmRnaFeats::s_CreateDBXref(), SGeneCdsmRnaFeats::s_CreateXRefLink(), and CCreateGeneModelTask::sGeneDbName.

Referenced by CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats(), and CCreateGeneModelTask::x_UpdateGeneOnSequence().

◆ CSelRowHandle()

CSelRowHandle::CSelRowHandle ( IAlnExplorer::TNumrow row )

inline

Definition at line 190 of file multi_align_view.hpp.

◆ CSplignPanel() [1/2]

CSplignPanel::CSplignPanel ( )

Definition at line 152 of file splign_panel.cpp.

References CSplignPanel::Init().

◆ CSplignPanel() [2/2]

CSplignPanel::CSplignPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CSPLIGNPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxCLIP_CHILDREN\|wxTAB_TRAVERSAL`,
		bool	visibale = `true`
	)

Definition at line 159 of file splign_panel.cpp.

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

◆ CSplignParams() [1/2]

CSplignParams::CSplignParams ( )

Definition at line 40 of file splign_params.cpp.

References CSplignParams::Init().

◆ CSplignParams() [2/2]

CSplignParams::CSplignParams ( const CSplignParams & data )

Definition at line 44 of file splign_params.cpp.

References CSplignParams::Copy(), data, and CSplignParams::Init().

◆ CSplignTool()

CSplignTool::CSplignTool ( )

CSplignTool.

Definition at line 62 of file splign_tool.cpp.

◆ CTaxTreeToolJob()

CTaxTreeToolJob::CTaxTreeToolJob ( const CTaxTreeToolParams & params )

CTaxTreeToolJob.

Definition at line 60 of file taxtree_tool_job.cpp.

References CAppJob::m_Descr.

◆ CTaxTreeToolPanel() [1/2]

CTaxTreeToolPanel::CTaxTreeToolPanel ( )

Definition at line 59 of file taxtree_tool_panel.cpp.

References Init().

◆ CTaxTreeToolPanel() [2/2]

CTaxTreeToolPanel::CTaxTreeToolPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CTAXTREETOOLPANEL`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`,
		bool	visibale = `true`
	)

Definition at line 64 of file taxtree_tool_panel.cpp.

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

◆ CTaxTreeToolParams() [1/2]

CTaxTreeToolParams::CTaxTreeToolParams ( )

Definition at line 40 of file taxtree_tool_params.cpp.

References CTaxTreeToolParams::Init().

◆ CTaxTreeToolParams() [2/2]

CTaxTreeToolParams::CTaxTreeToolParams ( const CTaxTreeToolParams & data )

Definition at line 44 of file taxtree_tool_params.cpp.

References CTaxTreeToolParams::Copy(), data, and CTaxTreeToolParams::Init().

◆ CTextAlignLoaderManager()

CTextAlignLoaderManager::CTextAlignLoaderManager ( )

CTextAlignLoaderManager.

Definition at line 51 of file text_align_load_manager.cpp.

References CFileExtensions::GetLabel(), CUIObject::Init(), CFileExtensions::kTextAlign, CTextAlignLoaderManager::m_Descr, CUIObject::SetLogEvent(), and ToStdString().

◆ CTextAlignObjectLoader() [1/2]

CTextAlignObjectLoader::CTextAlignObjectLoader ( const CTextAlignParams & params )

Definition at line 62 of file text_align_object_loader.cpp.

◆ CTextAlignObjectLoader() [2/2]

CTextAlignObjectLoader::CTextAlignObjectLoader	(	const CTextAlignParams &	params,
		const vector< wxString > &	filenames
	)

Definition at line 67 of file text_align_object_loader.cpp.

◆ CTreeBuilderPanel() [1/2]

CTreeBuilderPanel::CTreeBuilderPanel ( )

Definition at line 73 of file tree_builder_panel.cpp.

References Init().

◆ CTreeBuilderPanel() [2/2]

CTreeBuilderPanel::CTreeBuilderPanel	(	wxWindow *	parent,
		wxWindowID	id = `ID_CTreeBuilderPanel`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxTAB_TRAVERSAL`
	)

Definition at line 78 of file tree_builder_panel.cpp.

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

◆ CTreeBuilderParams() [1/2]

CTreeBuilderParams::CTreeBuilderParams ( )

Definition at line 40 of file tree_builder_params.cpp.

References CTreeBuilderParams::Init().

◆ CTreeBuilderParams() [2/2]

CTreeBuilderParams::CTreeBuilderParams ( const CTreeBuilderParams & data )

Definition at line 44 of file tree_builder_params.cpp.

References CTreeBuilderParams::Copy(), data, and CTreeBuilderParams::Init().

◆ CTreeBuilderTool()

CTreeBuilderTool::CTreeBuilderTool ( )

CTreeBuilderTool.

Definition at line 86 of file tree_builder_tool.cpp.

◆ DebugDump()

void CSplignParams::DebugDump	(	CDebugDumpContext	ddc,
		unsigned int	depth
	)		const

virtual

Implements CDebugDumpable.

Definition at line 148 of file splign_params.cpp.

References CDebugDumpContext::Log(), CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, CSplignParams::m_PolyADetect, and CDebugDumpContext::SetFrame().

◆ DECLARE_EVENT_MAP() [1/3]

CMultiAlignView::DECLARE_EVENT_MAP ( )

private

◆ DECLARE_EVENT_MAP() [2/3]

CNetBLAST_DMSearchForm::DECLARE_EVENT_MAP ( )

private

◆ DECLARE_EVENT_MAP() [3/3]

CPhyTreeView::DECLARE_EVENT_MAP ( )

void CPhyTreeView::DestroyViewWindow ( )

virtual

destroy Window corresponding to the view

Implements CProjectViewBase.

Definition at line 824 of file phy_tree_view.cpp.

References CPhyTreeView::m_Panel, and NULL.

Referenced by CPhyTreeView::~CPhyTreeView().

◆ DetachClient()

virtual void CMPCrossAlignView::DetachClient ( IVisibleRangeClient * )

inlinevirtual

Implements IVisibleRangeService.

Definition at line 62 of file mp_cross_align_view.hpp.

◆ DoTransition() [1/5]

bool CBLASTToolManager::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 221 of file blast_tool_manager.cpp.

◆ DoTransition() [2/5]

bool CNetBLASTUILoadManager::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 152 of file net_blast_ui_load_manager.cpp.

References _ASSERT, IUIToolManager::eBack, CNetBLASTUILoadManager::eCompleted, IUIToolManager::eNext, CNetBLASTUILoadManager::eSelectProject, CNetBLASTUILoadManager::eSelectRID, CNetBLASTLoadOptionPanel::IsInputValid(), CNetBLASTUILoadManager::m_OptionPanel, CNetBLASTUILoadManager::m_ProjectSelPanel, CNetBLASTUILoadManager::m_State, and CProjectSelectorPanel::TransferDataFromWindow().

◆ DoTransition() [3/5]

bool CNGAlignTool::DoTransition ( EAction action )

protectedvirtual

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.

Reimplemented from CAlgoToolManagerBase.

Definition at line 99 of file ngalign_tool.cpp.

References _ASSERT, CAlgoToolManagerBase::eCompleted, CAlgoToolManagerBase::eInvalid, IUIToolManager::eNext, CAlgoToolManagerBase::eParams, CAlgoToolManagerBase::eSelectProject, CNGAlignTool::m_Panel, CAlgoToolManagerBase::m_ProjectSelPanel, CAlgoToolManagerBase::m_State, next(), CNGAlignPanel::SaveSettings(), CProjectSelectorPanel::TransferDataFromWindow(), CProjectSelectorPanel::TransferDataToWindow(), CAlgoToolManagerBase::x_CreateProjectPanelIfNeeded(), CNGAlignTool::x_GetCurrentPage(), CNGAlignTool::x_GoFirstPage(), CNGAlignTool::x_GoLastPage(), CNGAlignTool::x_GoNextPage(), CNGAlignTool::x_GoPrevPage(), CNGAlignTool::x_IsFirstPage(), and CNGAlignTool::x_IsLastPage().

◆ DoTransition() [4/5]

bool CPslLoadManager::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 156 of file psl_load_manager.cpp.

References _ASSERT, IUIToolManager::eBack, CPslLoadManager::eCompleted, IUIToolManager::eNext, CPslLoadManager::eParams, CPslParamsPanel::GetData(), CPslLoadManager::m_Params, CPslLoadManager::m_ParamsPanel, CPslLoadManager::m_State, and CPslParamsPanel::TransferDataFromWindow().

◆ DoTransition() [5/5]

bool CTextAlignLoaderManager::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 153 of file text_align_load_manager.cpp.

References _ASSERT, IUIToolManager::eBack, CTextAlignLoaderManager::eCompleted, IUIToolManager::eNext, CTextAlignLoaderManager::eParams, CTextAlignParamsPanel::GetData(), CTextAlignLoaderManager::m_Params, CTextAlignLoaderManager::m_ParamsPanel, CTextAlignLoaderManager::m_State, and CTextAlignParamsPanel::TransferDataFromWindow().

◆ EditProperties()

void CNetBLASTUIDataSource::EditProperties ( )

virtual

Definition at line 283 of file net_blast_ui_data_source.cpp.

◆ Execute()

bool CTextAlignObjectLoader::Execute ( ICanceled & canceled )

virtual

Implements IExecuteUnit.

Definition at line 87 of file text_align_object_loader.cpp.

References file, CException::GetMsg(), CTextAlignObjectLoader::Init(), ICanceled::IsCanceled(), ITERATE, kEmptyStr, CTextAlignObjectLoader::LoadFromStream(), CTextAlignObjectLoader::m_FileNames, CTextAlignObjectLoader::m_Objects, ToStdString(), CException::what(), and CReportLoaderErrors::x_UpdateHTMLResults().

◆ Expand()

void CBLAST_Dlg_Item::Expand ( bool expand )

inline

Definition at line 92 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_Expanded.

Referenced by CBLAST_DB_Dialog::x_UpdateCollapsedState().

◆ FindCompartments()

void CBLASTParams::FindCompartments ( bool req )

inline

Definition at line 163 of file blast_search_params.hpp.

Referenced by CBLASTSearchParamsPanel::TransferDataFromWindow().

◆ FindJobDescriptor()

CRef< CNetBlastJobDescriptor > CNetBLASTUIDataSource::FindJobDescriptor ( const string & rid )

Definition at line 433 of file net_blast_ui_data_source.cpp.

References i, CNetBLASTUIDataSource::m_JobDescrMutex, CNetBLASTUIDataSource::m_JobDescrs, and result.

Referenced by CNetBlastLoadingJob::SetRIDs().

◆ FromUserObject() [1/2]

void CBLASTParams::FromUserObject ( const objects::CUser_object & user_obj )

Definition at line 551 of file blast_search_params.cpp.

References CBLASTParams::eLocalDB, CBLASTParams::eNCBIDB, CBLASTParams::eSequences, CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::C_Data::GetObject(), CBLASTParams::GetProgramByLabel(), CBLASTParams::GetProgramLabel(), CUser_field_Base::C_Data::GetStr(), kAdvParamsTag, kEntrezQueryTag, kJobTitleTag, kLocalDBLoader, kLocalNucDB, kLocalProtDB, kNucDBTag, kNucMRUDBsTag, kNucProgTag, kProtDBTag, kProtMRUDBsTag, kProtProgTag, kSubjectType, CBLASTParams::m_AdvancedParams, CBLASTParams::m_EntrezQuery, CBLASTParams::m_JobTitle, CBLASTParams::m_LocalDBLoader, CBLASTParams::m_LocalNucDB, CBLASTParams::m_LocalProtDB, CBLASTParams::m_NucDatabase, CBLASTParams::m_NucMRUDatabases, CBLASTParams::m_NucProgram, CBLASTParams::m_ProgToParams, CBLASTParams::m_ProtDatabase, CBLASTParams::m_ProtMRUDatabases, CBLASTParams::m_ProtProgram, CBLASTParams::m_SubjectType, NON_CONST_ITERATE, CMRUList< T >::SetItems(), val, and CBLASTParams::x_FromUserObject().

Referenced by CBLASTToolManager::LoadSettings().

◆ FromUserObject() [2/2]

void CNetBlastJobDescriptor::FromUserObject ( const objects::CUser_object & user_obj )

Definition at line 412 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::eInvalidState, CTime::GetTimeT(), kDescrTag, kErrorsTag, kRIDTag, kStateTag, kSubmitTimeTag, kTitleTag, CNetBlastJobDescriptor::m_Description, CNetBlastJobDescriptor::m_Errors, CNetBlastJobDescriptor::m_JobTitle, CNetBlastJobDescriptor::m_RID, CNetBlastJobDescriptor::m_State, and CNetBlastJobDescriptor::m_SubmitTime.

◆ GetAdvancedParams() [1/2]

string & CBLASTParams::GetAdvancedParams ( )

Definition at line 466 of file blast_search_params.cpp.

References CBLASTParams::m_AdvancedParams.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ GetAdvancedParams() [2/2]

string CBLASTParams::GetAdvancedParams ( ) const

Definition at line 472 of file blast_search_params.cpp.

References CBLASTParams::m_AdvancedParams.

wxBitmap CBLAST_DB_Dialog::GetBitmapResource ( const wxString & name )

Definition at line 252 of file blast_db_dialog.cpp.

◆ GetBitmapResource() [2/14]

wxBitmap CBLASTSearchOptionsPanel::GetBitmapResource ( const wxString & name )

Definition at line 374 of file blast_search_options_panel.cpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls().

◆ GetBitmapResource() [3/14]

wxBitmap CBLASTSearchParamsPanel::GetBitmapResource ( const wxString & name )

Definition at line 348 of file blast_search_params_panel.cpp.

◆ GetBitmapResource() [4/14]

wxBitmap CCleanupAlignmentsParamsPanel::GetBitmapResource ( const wxString & name )

Definition at line 244 of file cleanup_alignments_params_panel.cpp.

◆ GetBitmapResource() [5/14]

wxBitmap CFindOverlapPanel::GetBitmapResource ( const wxString & name )

Definition at line 168 of file find_overlap_panel.cpp.

◆ GetBitmapResource() [6/14]

wxBitmap CGroupAlignmentsParamsPanel::GetBitmapResource ( const wxString & name )

Definition at line 265 of file group_alignments_params_panel.cpp.

◆ GetBitmapResource() [7/14]

wxBitmap CMergeAlignmentsParamsPanel::GetBitmapResource ( const wxString & name )

Definition at line 216 of file merge_alignments_params_panel.cpp.

◆ GetBitmapResource() [8/14]

wxBitmap CNetBlastDMSearchFormPanel::GetBitmapResource ( const wxString & name )

Definition at line 178 of file net_blast_dm_search_form_panel.cpp.

◆ GetBitmapResource() [9/14]

wxBitmap CNetBLASTLoadOptionPanel::GetBitmapResource ( const wxString & name )

Definition at line 211 of file net_blast_load_option_panel.cpp.

◆ GetBitmapResource() [10/14]

wxBitmap CSplignPanel::GetBitmapResource ( const wxString & name )

Definition at line 306 of file splign_panel.cpp.

◆ GetBitmapResource() [11/14]

wxBitmap CTreeBuilderPanel::GetBitmapResource ( const wxString & name )

Definition at line 183 of file tree_builder_panel.cpp.

◆ GetBitmapResource() [12/14]

wxBitmap CMuscleToolPanel::GetBitmapResource ( const wxString & name )

Definition at line 193 of file muscle_tool_panel.cpp.

Referenced by CMuscleToolPanel::CreateControls().

◆ GetBitmapResource() [13/14]

wxBitmap CNGAlignPanel::GetBitmapResource ( const wxString & name )

Definition at line 138 of file ngalign_panel.cpp.

◆ GetBitmapResource() [14/14]

wxBitmap CTaxTreeToolPanel::GetBitmapResource ( const wxString & name )

Definition at line 127 of file taxtree_tool_panel.cpp.

◆ GetBLASTDataSource()

CRef< CNetBLASTUIDataSource > CBLASTToolManager::GetBLASTDataSource ( )

protected

Definition at line 170 of file blast_tool_manager.cpp.

References IServiceLocator::GetServiceByType(), and CBLASTToolManager::m_SrvLocator.

Referenced by CBLASTToolManager::GetTask(), CBLASTToolManager::QuickLaunch(), and CBLASTToolManager::x_CreateOptionsPanelIfNeeded().

◆ GetBlastParams()

wxString CFindOverlapParams::GetBlastParams ( ) const

inline

Definition at line 83 of file find_overlap_params.hpp.

References CFindOverlapParams::m_BlastParams.

Referenced by CFindOverlapJob::x_CreateProjectItems(), and CFindOverlapJob::x_PrepareAligner().

◆ GetCategory()

string CBLASTToolManager::GetCategory ( )

virtual

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

Tools are shown in in UI groupped by Categories.

Implements IUIAlgoToolManager.

Definition at line 326 of file blast_tool_manager.cpp.

◆ GetCDNASeqs()

TConstScopedObjects CSplignPanel::GetCDNASeqs ( ) const

inline

Definition at line 135 of file splign_panel.hpp.

References CSplignPanel::m_cDNASeqs.

Referenced by CSplignTool::x_CreateLoadingJob().

◆ GetCDNAStrand()

int CSplignParams::GetCDNAStrand ( ) const

inline

Definition at line 101 of file splign_params.hpp.

References CSplignParams::m_cDNA_strand.

Referenced by CSplignJob::x_CreateProjectItems().

◆ GetChildByLabel()

CBLAST_Dlg_Item * CBLAST_Dlg_Item::GetChildByLabel ( const string & label )

Definition at line 103 of file blast_db_dialog.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), label, CBLAST_Dlg_Item::m_ChildItems, and NULL.

Referenced by CBLAST_DB_Dialog::x_CreateItems().

◆ GetChildItems()

TNameToItemMap* CBLAST_Dlg_Item::GetChildItems ( )

◆ GetCurrDatabase() [2/2]

const string & CBLASTParams::GetCurrDatabase ( ) const

Definition at line 330 of file blast_search_params.cpp.

References CBLASTParams::GetCurrProgram(), CBLASTParams::GetDatabase(), and CBLASTParams::IsNucDatabase().

◆ GetCurrentPanel() [1/5]

wxPanel * CBLASTToolManager::GetCurrentPanel ( )

virtual

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

Implements IUIToolManager.

Definition at line 136 of file blast_tool_manager.cpp.

References CBLASTToolManager::eOptions, CBLASTToolManager::eParams, CBLASTToolManager::m_OptionsPanel, CBLASTToolManager::m_ParamsPanel, CBLASTToolManager::m_State, and NULL.

Referenced by CBLASTToolManager::RestoreDefaults().

◆ GetCurrentPanel() [2/5]

wxPanel * CNetBLASTUILoadManager::GetCurrentPanel ( )

virtual

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

Implements IUIToolManager.

Definition at line 99 of file net_blast_ui_load_manager.cpp.

◆ GetCurrentPanel() [3/5]

wxPanel * CNGAlignTool::GetCurrentPanel ( )

protectedvirtual

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

Reimplemented from CAlgoToolManagerBase.

Definition at line 160 of file ngalign_tool.cpp.

References CAlgoToolManagerBase::eParams, CAlgoToolManagerBase::eSelectProject, CAlgoToolManagerBase::m_ProjectSelPanel, CAlgoToolManagerBase::m_State, NULL, and CNGAlignTool::x_GetCurrentPage().

◆ GetCurrentPanel() [4/5]

wxPanel * CPslLoadManager::GetCurrentPanel ( )

virtual

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

Implements IUIToolManager.

Definition at line 114 of file psl_load_manager.cpp.

References CPslLoadManager::eParams, CPslLoadManager::m_State, NULL, and CPslLoadManager::x_GetParamsPanel().

◆ GetCurrentPanel() [5/5]

wxPanel * CTextAlignLoaderManager::GetCurrentPanel ( )

virtual

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

Implements IUIToolManager.

Definition at line 112 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::eParams, CTextAlignLoaderManager::m_State, NULL, and CTextAlignLoaderManager::x_GetParamsPanel().

◆ GetCurrMRUDatabases()

CBLASTParams::TMRUDatabases & CBLASTParams::GetCurrMRUDatabases ( )

returns MRU databases for the current program

Definition at line 349 of file blast_search_params.cpp.

References CBLASTParams::GetCurrProgram(), CBLASTParams::GetMRUDatabases(), and CBLASTParams::IsNucDatabase().

Referenced by CBLASTSearchOptionsPanel::OnBrowseDatabases(), and CBLASTSearchOptionsPanel::OnDatabaseComboSelected().

◆ GetCurrParams() [1/2]

CBLASTParams::SProgParams & CBLASTParams::GetCurrParams ( )

returns params for the current program

Definition at line 441 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), CBLASTParams::GetCurrProgram(), and CBLASTParams::m_ProgToParams.

Referenced by CBLASTParams::GetCurrParams(), CBLASTParams::PrintParams(), CBLASTSearchParamsPanel::TaxonsLoaded(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), and CBLASTSearchParamsPanel::x_InitTaxons().

◆ GetCurrParams() [2/2]

const CBLASTParams::SProgParams & CBLASTParams::GetCurrParams ( ) const

Definition at line 450 of file blast_search_params.cpp.

References CBLASTParams::GetCurrParams().

◆ GetCurrProgram() [1/2]

blast::EProgram & CBLASTParams::GetCurrProgram ( )

returns the current program for the currently selected input type

Definition at line 299 of file blast_search_params.cpp.

References CBLASTParams::GetProgram(), and CBLASTParams::m_NucInput.

string & CBLASTParams::GetDatabase ( bool nuc_db )

returns the database of the specified type

Definition at line 337 of file blast_search_params.cpp.

References CBLASTParams::m_NucDatabase, and CBLASTParams::m_ProtDatabase.

Referenced by CBLASTParams::GetCurrDatabase(), and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

◆ GetDatabase() [2/2]

const string & CBLASTParams::GetDatabase ( bool nuc_db ) const

Definition at line 343 of file blast_search_params.cpp.

References CBLASTParams::m_NucDatabase, and CBLASTParams::m_ProtDatabase.

◆ GetDbGeneticCode()

wxString CBLASTSearchParamsPanel::GetDbGeneticCode ( void ) const

inline

Definition at line 141 of file blast_search_params_panel.hpp.

References CBLASTSearchParamsPanel::m_DbGeneticCode.

◆ GetDbNames()

void CNetBLAST_DMSearchTool::GetDbNames ( vector< string > & name )

string CNetBlastSubmittingJob::GetDescr ( ) const

virtual

Returns a human readable description of the Job (optional)

Implements IAppJob.

Definition at line 235 of file blast_jobs.cpp.

References CNetBlastSubmittingJob::m_Descr.

Referenced by CNetBlastSubmittingJob::Run().

◆ GetDescr() [4/4]

string CNetBlastMonitoringJob::GetDescr ( ) const

virtual

Returns a human readable description of the Job (optional)

Implements IAppJob.

Definition at line 463 of file blast_jobs.cpp.

References CNetBlastMonitoringJob::m_Descr.

Referenced by CNetBlastMonitoringJob::Run().

◆ GetDescription() [1/3]

string CNetBLAST_DMSearchTool::GetDescription ( ) const

virtual

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

Implements CSearchToolBase.

Definition at line 162 of file net_blast_dm_search_tool.cpp.

◆ GetDescription() [2/3]

string CNetBlastJobDescriptor::GetDescription ( void ) const

Definition at line 171 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::m_Description, and CNetBlastJobDescriptor::m_Mutex.

void CNetBlastSubmittingJob::GetDescriptors ( TDescriptors & descriptors )

Definition at line 241 of file blast_jobs.cpp.

References CNetBlastSubmittingJob::m_Descriptors.

Referenced by CBlastSearchTask::x_NextSubTask().

◆ GetDiscType()

int CSplignParams::GetDiscType ( ) const

inline

Definition at line 80 of file splign_params.hpp.

References CSplignParams::m_DiscType.

Referenced by CSplignJob::x_CreateProjectItems().

◆ GetDistanceMethod()

wxString CTreeBuilderParams::GetDistanceMethod ( ) const

inline

Definition at line 81 of file tree_builder_params.hpp.

References CTreeBuilderParams::m_DistanceMethod.

Referenced by CTreeBuilderJob::x_CreateProjectItems().

◆ GetEndGapDetect()

bool CSplignParams::GetEndGapDetect ( ) const

inline

Definition at line 83 of file splign_params.hpp.

References CSplignParams::m_EndGapDetect.

Referenced by CSplignJob::x_CreateProjectItems().

◆ GetEntrezQuery() [1/2]

string & CBLASTParams::GetEntrezQuery ( void )

Definition at line 411 of file blast_search_params.cpp.

References CBLASTParams::m_EntrezQuery.

Referenced by CNetBlastJobDescriptor::Init(), CBLASTParams::PrintParams(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ GetEntrezQuery() [2/2]

string CBLASTParams::GetEntrezQuery ( void ) const

Definition at line 417 of file blast_search_params.cpp.

References CBLASTParams::m_EntrezQuery.

◆ GetError() [1/2]

CConstIRef< IAppJobError > CNetBlastSubmittingJob::GetError ( )

virtual

Returns IAppJobError object describing internal error that caused the Job to fail.

Result shall be returned only if the Job did fail.

Implements IAppJob.

Definition at line 229 of file blast_jobs.cpp.

References CRef< C, Locker >::GetPointer(), and CNetBlastSubmittingJob::m_Error.

◆ GetError() [2/2]

CConstIRef< IAppJobError > CNetBlastMonitoringJob::GetError ( )

virtual

Returns IAppJobError object describing internal error that caused the Job to fail.

Result shall be returned only if the Job did fail.

Implements IAppJob.

Definition at line 457 of file blast_jobs.cpp.

References CRef< C, Locker >::GetPointer(), and CNetBlastMonitoringJob::m_Error.

◆ GetErrors() [1/3]

string CNetBlastJobDescriptor::GetErrors ( void ) const

Definition at line 178 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::m_Errors, and CNetBlastJobDescriptor::m_Mutex.

Referenced by CNetBlastSubmittingJob::GetErrors(), and CNetBlastLoadingJob::x_CreateProjectItems().

◆ GetErrors() [2/3]

void CNetBlastSubmittingJob::GetErrors ( vector< string > & errors ) const

Definition at line 247 of file blast_jobs.cpp.

References CNetBlastJobDescriptor::GetErrors(), i, and CNetBlastSubmittingJob::m_Descriptors.

Referenced by CBlastSearchTask::x_RunCurrentSubTask().

◆ GetErrors() [3/3]

void CNetBlastLoadingJob::GetErrors ( vector< string > & errors ) const

Definition at line 517 of file blast_jobs.cpp.

References CNetBlastLoadingJob::m_Errors.

Referenced by CBlastSearchTask::x_RunCurrentSubTask().

string CNetBLASTUIDataSourceType::GetExtensionLabel ( ) const

void CPslLoadManager::GetFilenames ( vector< wxString > & filenames ) const

virtual

get actual filenames that will be opened

Implements IFileFormatLoaderManager.

Definition at line 205 of file psl_load_manager.cpp.

References filenames, and CPslLoadManager::m_FileNames.

◆ GetFilenames() [2/2]

void CTextAlignLoaderManager::GetFilenames ( vector< wxString > & filenames ) const

virtual

get actual filenames that will be opened

Implements IFileFormatLoaderManager.

Definition at line 201 of file text_align_load_manager.cpp.

References filenames, and CTextAlignLoaderManager::m_FileNames.

IDMSearchTool::TUIToolFlags CNetBLAST_DMSearchTool::GetFlags ( void )

virtual

special flags

Reimplemented from CSearchToolBase.

Definition at line 232 of file net_blast_dm_search_tool.cpp.

References IDMSearchTool::eAutorun.

◆ GetFormatWildcard() [1/4]

wxString CPslLoadManager::GetFormatWildcard ( )

virtual

IFileFormatLoaderManager - additional members

Implements IFileFormatLoaderManager.

Definition at line 186 of file psl_load_manager.cpp.

References CFileExtensions::GetDialogFilter(), CFileExtensions::kAllFiles, CFileExtensions::kPSL, and wxT.

◆ GetFormatWildcard() [2/4]

wxString CTextAlignLoaderManager::GetFormatWildcard ( )

virtual

IFileFormatLoaderManager - additional members

Implements IFileFormatLoaderManager.

Definition at line 183 of file text_align_load_manager.cpp.

References CFileExtensions::GetDialogFilter(), and CFileExtensions::kAllFiles.

◆ GetFormatWildcard() [3/4]

wxString CPslLoadManager::GetFormatWildcard ( ) const

virtual

return file wildcard for the format (example - "*.txt;*.tab" )

Implements IFileLoadPanelClient.

Definition at line 73 of file psl_load_manager.cpp.

References CFileExtensions::GetDialogFilter(), CFileExtensions::kAllFiles, CFileExtensions::kPSL, and wxT.

◆ GetFormatWildcard() [4/4]

wxString CTextAlignLoaderManager::GetFormatWildcard ( ) const

Definition at line 358 of file blast_search_params_panel.cpp.

◆ GetIconResource() [4/14]

wxIcon CCleanupAlignmentsParamsPanel::GetIconResource ( const wxString & name )

Definition at line 252 of file cleanup_alignments_params_panel.cpp.

◆ GetIconResource() [5/14]

wxIcon CFindOverlapPanel::GetIconResource ( const wxString & name )

Definition at line 176 of file find_overlap_panel.cpp.

◆ GetIconResource() [6/14]

wxIcon CGroupAlignmentsParamsPanel::GetIconResource ( const wxString & name )

Definition at line 273 of file group_alignments_params_panel.cpp.

◆ GetIconResource() [7/14]

wxIcon CMergeAlignmentsParamsPanel::GetIconResource ( const wxString & name )

Definition at line 225 of file merge_alignments_params_panel.cpp.

◆ GetIconResource() [8/14]

wxIcon CNetBlastDMSearchFormPanel::GetIconResource ( const wxString & name )

Definition at line 188 of file net_blast_dm_search_form_panel.cpp.

◆ GetIconResource() [9/14]

wxIcon CNetBLASTLoadOptionPanel::GetIconResource ( const wxString & name )

Definition at line 220 of file net_blast_load_option_panel.cpp.

◆ GetIconResource() [10/14]

wxIcon CSplignPanel::GetIconResource ( const wxString & name )

Definition at line 314 of file splign_panel.cpp.

◆ GetIconResource() [11/14]

wxIcon CTreeBuilderPanel::GetIconResource ( const wxString & name )

Definition at line 191 of file tree_builder_panel.cpp.

◆ GetIconResource() [12/14]

wxIcon CMuscleToolPanel::GetIconResource ( const wxString & name )

Definition at line 198 of file muscle_tool_panel.cpp.

◆ GetIconResource() [13/14]

wxIcon CNGAlignPanel::GetIconResource ( const wxString & name )

Definition at line 146 of file ngalign_panel.cpp.

◆ GetIconResource() [14/14]

wxIcon CTaxTreeToolPanel::GetIconResource ( const wxString & name )

Definition at line 135 of file taxtree_tool_panel.cpp.

◆ GetId()

const wxTreeItemId& CBLAST_Dlg_Item::GetId ( void ) const

inline

Definition at line 101 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_Id.

Referenced by CBLAST_DB_Dialog::OnInitDialog(), and CBLAST_DB_Dialog::x_BuildTreeItems().

◆ GetID()

CConstRef< CSeq_id > SGeneCdsmRnaFeats::GetID ( objects::CScope * scope ) const

SGeneCdsmRnaFeats.

Definition at line 197 of file create_gene_model_tool_manager.cpp.

References SGeneCdsmRnaFeats::cds, SGeneCdsmRnaFeats::gene, GetIdHandle(), CSeq_id_Handle::GetSeqId(), CSeq_id::Match(), SGeneCdsmRnaFeats::mRNA, and NCBI_USER_THROW.

◆ GetInput()

string CNetBLASTLoadOptionPanel::GetInput ( ) const

Definition at line 169 of file net_blast_load_option_panel.cpp.

References _ASSERT, CNetBLASTLoadOptionPanel::ID_TEXTCTRL1, and string.

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

◆ GetJobDescriptors()

void CNetBLASTUIDataSource::GetJobDescriptors ( TJobDescrVec & descriptors )

returns Job Descriptors not marked as Deleted

Definition at line 420 of file net_blast_ui_data_source.cpp.

References i, CNetBLASTUIDataSource::m_JobDescrMutex, and CNetBLASTUIDataSource::m_JobDescrs.

Referenced by CNetBLAST_DMSearchJob::x_DoSearch().

◆ GetJobTitle() [1/5]

string & CBLASTParams::GetJobTitle ( )

Definition at line 477 of file blast_search_params.cpp.

References CBLASTParams::m_JobTitle.

Referenced by CNetBlastJobDescriptor::Init(), CBlastSearchTask::Init_SubmitSearch(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

wxString CBLAST_Dlg_Item::GetLabel ( void ) const

Definition at line 90 of file blast_db_dialog.cpp.

References CBLAST_Dlg_Item::m_LabelLength, CBLAST_Dlg_Item::m_LabelPos, CBLAST_Dlg_Item::m_Path, and wxT.

Referenced by CBLAST_Dlg_Item::AddChild(), CBLAST_DB_Dialog::x_BuildTreeItems(), and CBLAST_DB_Dialog::x_FilterItems().

◆ GetLabel() [2/3]

string CPslLoadManager::GetLabel ( void ) const

virtual

Implements IFileLoadPanelClient.

Definition at line 68 of file psl_load_manager.cpp.

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

◆ GetLabel() [3/3]

string CTextAlignLoaderManager::GetLabel ( void ) const

virtual

Implements IFileLoadPanelClient.

Definition at line 67 of file text_align_load_manager.cpp.

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

◆ GetLeafLabels()

wxString CTreeBuilderParams::GetLeafLabels ( ) const

Definition at line 341 of file mp_cross_align_view.cpp.

References _ASSERT, CMPCrossAlignView::m_MainSplitter, CMPCrossAlignView::x_GetOrigObject(), CProjectViewBase::x_GetScope(), and CProjectViewBase::x_HasProject().

◆ GetMatchCost()

int CNeedlemanWunschToolParams::GetMatchCost ( ) const

inline

Definition at line 97 of file needlemanwunsch_tool_params.hpp.

References CNeedlemanWunschToolParams::m_MatchCost.

Referenced by CCreateNeedlemanWunschJob::x_CreateProjectItems().

◆ GetMaxGenomicExtent()

long CSplignParams::GetMaxGenomicExtent ( void ) const

inline

Definition at line 86 of file splign_params.hpp.

References CSplignParams::m_MaxGenomicExtent.

Referenced by CSplignJob::x_CreateProjectItems().

wxPanel * CAdvancedCleanupTool::GetMaxPanel ( )

virtual

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

Reimplemented from IUIToolManager.

Definition at line 113 of file advanced_cleanup_tool.cpp.

References CAdvancedCleanupParamsPanel::Create(), and CAlgoToolManagerBase::m_ParentWindow.

◆ GetMaxSlop()

wxString CFindOverlapParams::GetMaxSlop ( ) const

inline

Definition at line 89 of file find_overlap_params.hpp.

References CFindOverlapParams::m_MaxSlop.

Referenced by CFindOverlapJob::x_CreateProjectItems(), and CFindOverlapJob::x_PrepareAligner().

◆ GetMenu() [1/2]

IObjectCmdContributor::TContribution CNetBLASTUIDataSource::GetMenu ( TConstScopedObjects & objects )

virtual

returns a menu with commands applicable to the objects and optional command handler for the commands caller assumes ownership of the returned objects

Implements IObjectCmdContributor.

Definition at line 307 of file net_blast_ui_data_source.cpp.

References CUICommandRegistry::AppendMenuItem(), CNetBLASTUIDataSource::CNetBlastDSEvtHandler, eCmdDeleteBlastJobs, eCmdMonitorBlastJobs, eCmdRetriveBlastJobs, CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eRetrieved, CNetBlastJobDescriptor::eSubmitted, CUICommandRegistry::GetInstance(), CNetBlastJobDescriptor::GetState(), NON_CONST_ITERATE, NULL, and wxT.

◆ GetMenu() [2/2]

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

virtual

for the given set of items returns a contribution

Implements IExplorerItemCmdContributor.

Definition at line 364 of file net_blast_ui_data_source.cpp.

References CUICommandRegistry::AppendMenuItem(), CNetBLASTUIDataSource::CNetBlastDSEvtHandler, eCmdExploreNetBLAST, eCmdLoadRIDs, PT::eDataSource, PT::TPTItem< TData, Type >::GetData(), CUICommandRegistry::GetInstance(), CRef< C, Locker >::GetPointer(), PT::CItem::GetType(), and wxT.

◆ GetMenuDef()

const SwxMenuItemRec * CMultiAlignView::GetMenuDef ( ) const

protectedvirtual

simpler way to provide a static menu using macros defined earlier in this file

Reimplemented from IMenuContributor.

Definition at line 157 of file multi_align_view.cpp.

◆ GetMinCompIdentity()

double CSplignParams::GetMinCompIdentity ( ) const

inline

Definition at line 92 of file splign_params.hpp.

References CSplignParams::m_MinCompIdentity.

Referenced by CSplignJob::x_CreateProjectItems().

◆ GetMinExonIdentity()

double CSplignParams::GetMinExonIdentity ( void ) const

inline

Definition at line 95 of file splign_params.hpp.

References CSplignParams::m_MinExonIdentity.

Referenced by CSplignJob::x_CreateProjectItems().

◆ GetMismatchCost()

int CNeedlemanWunschToolParams::GetMismatchCost ( ) const

inline

Definition at line 100 of file needlemanwunsch_tool_params.hpp.

References CNeedlemanWunschToolParams::m_MismatchCost.

Referenced by CCreateNeedlemanWunschJob::x_CreateProjectItems().

◆ GetMRUDatabases()

CBLASTParams::TMRUDatabases & CBLASTParams::GetMRUDatabases ( bool nuc_db )

Definition at line 356 of file blast_search_params.cpp.

References CBLASTParams::m_NucMRUDatabases, and CBLASTParams::m_ProtMRUDatabases.

Referenced by CBLASTParams::GetCurrMRUDatabases(), and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

◆ GetMuscleExecutable()

wxString CMuscleToolParams::GetMuscleExecutable ( ) const

Definition at line 91 of file muscle_tool_params.cpp.

References FindExeFile(), and CMuscleToolParams::m_MusclePath.

Referenced by CMuscleToolJob::x_GetCommandLine().

◆ GetMusclePath()

wxString CMuscleToolParams::GetMusclePath ( ) const

inline

Definition at line 86 of file muscle_tool_params.hpp.

References CMuscleToolParams::m_MusclePath.

◆ GetName()

string CNetBLAST_DMSearchTool::GetName ( ) const

virtual

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

Implements CSearchToolBase.

Definition at line 155 of file net_blast_dm_search_tool.cpp.

References NET_BLAST_DM_TOOL_NAME.

◆ GetNumrow()

IAlnExplorer::TNumrow CSelRowHandle::GetNumrow ( ) const

inline

Definition at line 191 of file multi_align_view.hpp.

References CSelRowHandle::m_Numrow.

Referenced by CMultiAlignView::x_OnSetSelection().

◆ GetObject()

const SConstScopedObject& CTreeBuilderParams::GetObject ( void ) const

inline

Definition at line 78 of file tree_builder_params.hpp.

References CTreeBuilderParams::m_Object.

Referenced by CTreeBuilderJob::x_CreateProjectItems().

◆ GetObjects() [1/8]

IObjectLoader::TObjects & CTextAlignObjectLoader::GetObjects ( )

virtual IOpenViewManager* CDotMatrixViewFactory::GetOpenViewManager ( )

inlinevirtual

Reimplemented from IProjectViewFactory.

Definition at line 151 of file dot_matrix_view.hpp.

References CDotMatrixViewFactory::m_ViewManager.

◆ GetOpenViewManager() [2/2]

virtual IOpenViewManager* CMultiAlignViewFactory::GetOpenViewManager ( )

inlinevirtual

Reimplemented from IProjectViewFactory.

Definition at line 179 of file multi_align_view.hpp.

References CMultiAlignViewFactory::m_ViewManager.

◆ GetOptionsPage()

virtual IWizardPage* CTextAlignLoaderManager::GetOptionsPage ( )

blast::EProgram & CBLASTParams::GetProgram ( bool nuc )

returns the selected programs for the given input type

Definition at line 311 of file blast_search_params.cpp.

References CBLASTParams::m_NucProgram, CBLASTParams::m_ProtProgram, and nuc.

Referenced by CBLASTParams::GetCurrProgram().

◆ GetProgram() [2/2]

const blast::EProgram CBLASTParams::GetProgram ( bool nuc ) const

Definition at line 317 of file blast_search_params.cpp.

References CBLASTParams::m_NucProgram, CBLASTParams::m_ProtProgram, and nuc.

◆ GetProgramByLabel()

blast::EProgram CBLASTParams::GetProgramByLabel ( const string & str )

static

Definition at line 706 of file blast_search_params.cpp.

References eBlastNotSet, ITERATE, label, and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTParams::FromUserObject(), CBLASTSearchOptionsPanel::OnProgramComboSelected(), and CBLASTSearchOptionsPanel::TransferDataFromWindow().

◆ GetProgramLabel()

string CBLASTParams::GetProgramLabel ( blast::EProgram program )

static

Definition at line 694 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), kEmptyStr, and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTParams::FromUserObject(), CBLASTParams::PrintParams(), CBLASTParams::ToUserObject(), and CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ GetProgramLabels()

void CBLASTParams::GetProgramLabels	(	bool	nuc_input,
		vector< string > &	labels
	)

static

Definition at line 683 of file blast_search_params.cpp.

References info, ITERATE, and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ GetProgress() [1/3]

CConstIRef< IAppJobProgress > CNetBlastSubmittingJob::GetProgress ( )

virtual

return progress object, the function shall be synchronized internally.

the returned object should not be modified by the job (job shall create a new instance of Progress object on every GetProgress() invocation).

Implements IAppJob.

Definition at line 215 of file blast_jobs.cpp.

References CNetBlastSubmittingJob::m_Mutex, and CNetBlastSubmittingJob::m_Status.

◆ GetProgress() [2/3]

CConstIRef< IAppJobProgress > CNetBlastMonitoringJob::GetProgress ( )

const CProjectViewTypeDescriptor & CPhyTreeViewFactory::GetProjectViewTypeDescriptor ( ) const

virtual

returns a Descriptor for the View Type supported by the Factory

Implements IProjectViewFactory.

Definition at line 1854 of file phy_tree_view.cpp.

References s_PhyTreeViewTypeDescr.

CRef< blast::CRemoteBlast > CNetBlastJobDescriptor::GetRemoteBlast ( )

Definition at line 356 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eRetrieved, eUnknown, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_State, NCBI_THROW, result, CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded(), and CNetBlastJobDescriptor::x_NotifyDataSource().

Referenced by CNetBlastLoadingJob::x_CreateProjectItems().

◆ GetRepeatDb()

string CBLASTParams::GetRepeatDb ( const string & repeat_lib )

static

Definition at line 402 of file blast_search_params.cpp.

References kEmptyStr.

Referenced by CBLASTParams::ToArgVec().

◆ GetRepeatLib()

string CBLASTParams::GetRepeatLib ( const string & repeat_db )

static

Definition at line 392 of file blast_search_params.cpp.

References NStr::EqualNocase(), ITERATE, and kEmptyStr.

◆ GetResult() [1/2]

CRef< CObject > CNetBlastSubmittingJob::GetResult ( )

virtual

Returns the Job Result.

Derive your own object from CObject and return it from your Job class. Result shall be returned only if Job finished succesfully.

Implements IAppJob.

Definition at line 223 of file blast_jobs.cpp.

◆ GetResult() [2/2]

CRef< CObject > CNetBlastMonitoringJob::GetResult ( )

virtual

Returns the Job Result.

Derive your own object from CObject and return it from your Job class. Result shall be returned only if Job finished succesfully.

Implements IAppJob.

Definition at line 451 of file blast_jobs.cpp.

◆ GetRetrieved()

bool CNetBlastDMSearchFormPanel::GetRetrieved ( ) const

inline

Definition at line 108 of file net_blast_dm_search_form_panel.hpp.

References CNetBlastDMSearchFormPanel::m_Retrieved.

Referenced by CNetBLAST_DMSearchForm::ConstructQuery().

◆ GetRID()

string CNetBlastJobDescriptor::GetRID ( void ) const

Definition at line 155 of file net_blast_job_descr.cpp.

References _ASSERT, CNetBlastJobDescriptor::m_Mutex, and CNetBlastJobDescriptor::m_RID.

Referenced by CNetBlastJobDescriptorLabelHandler::GetLabel(), GetNetBlastJobDescription(), CNetBLASTUIDataSource::StartRetrievingTask(), and CNetBlastLoadingJob::x_CreateProjectItems().

◆ GetRIDs()

void CNetBLASTLoadOptionPanel::GetRIDs ( vector< string > & rids )

Definition at line 192 of file net_blast_load_option_panel.cpp.

References _ASSERT, NStr::fSplit_Tokenize, CNetBLASTLoadOptionPanel::ID_TEXTCTRL1, sDelim(), NStr::Split(), text(), and ToStdString().

Referenced by CNetBLASTUILoadManager::GetTask().

void CBLAST_DB_Dialog::GetSelectedDatabases ( vector< string > & databases )

Definition at line 293 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::m_SelDatabase.

Referenced by CBLASTSearchOptionsPanel::OnBrowseDatabases().

◆ GetSelection() [1/14]

void CAlignSpanView::GetSelection ( CSelectionEvent & evt ) const

virtual

get selection for broadcasting

Reimplemented from CProjectView.

Definition at line 514 of file align_span_view.cpp.

References CSelectionEvent::AddRangeSelection(), GetIdHandle(), CAlnSpanWidget::GetSelection(), ITERATE, CAlignSpanView::m_AlnWidget, NULL, compile_time_bits::range(), and CProjectViewBase::x_HasProject().

void CPhyTreeView::GetSelection ( CSelectionEvent & evt ) const

virtual

◆ GetSelection() [8/14]

void CAlignSpanView::GetSelection ( TConstScopedObjects & objects ) const

virtual

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 479 of file align_span_view.cpp.

References _ASSERT, GetIdHandle(), CProjectViewBase::GetScope(), CAlnSpanWidget::GetSelection(), CRef< C, Locker >::IsNull(), ITERATE, CAlignSpanView::m_AlnWidget, NULL, compile_time_bits::range(), CSeq_loc::SetId(), CSeq_loc::SetInt(), and CProjectViewBase::x_HasProject().

const SConstScopedObject& CFindOverlapParams::GetSeq1 ( void ) const

inline

Definition at line 76 of file find_overlap_params.hpp.

References CFindOverlapParams::m_Seq1.

Referenced by CFindOverlapJob::x_CreateProjectItems().

◆ GetSeq2()

const SConstScopedObject& CFindOverlapParams::GetSeq2 ( void ) const

inline

Definition at line 79 of file find_overlap_params.hpp.

References CFindOverlapParams::m_Seq2.

Referenced by CFindOverlapJob::x_CreateProjectItems().

◆ GetSeqLocs() [1/2]

TConstScopedObjects & CBLASTParams::GetSeqLocs ( )

Definition at line 287 of file blast_search_params.cpp.

References CBLASTParams::m_SeqLocs.

Referenced by CNetBlastSubmittingJob::CNetBlastSubmittingJob(), CBlastSearchTask::Init_SubmitSearch(), CBLASTToolManager::QuickLaunch(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSeqToolJob::x_CreateProjectItems().

◆ GetSeqLocs() [2/2]

const TConstScopedObjects & CBLASTParams::GetSeqLocs ( ) const

Definition at line 293 of file blast_search_params.cpp.

References CBLASTParams::m_SeqLocs.

◆ GetState()

CNetBlastJobDescriptor::EState CNetBlastJobDescriptor::GetState ( void ) const

Definition at line 149 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::m_State.

Referenced by CNetBlastJobDescriptorLabelHandler::GetLabel(), CNetBLASTUIDataSource::GetMenu(), GetNetBlastJobDescription(), CNetBlastLoadingJob::x_CreateProjectItems(), and CNetBLAST_DMSearchJob::x_DoSearch().

◆ GetStateLabel()

string CNetBlastJobDescriptor::GetStateLabel ( EState state )

static

Definition at line 140 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::eExpired, and i.

Referenced by CNetBlastJobDescriptorLabelHandler::GetLabel(), and GetNetBlastJobDescription().

◆ GetStatusText()

string CBlastSearchTask::GetStatusText ( void ) const

virtual

overriding CAppTask::GetStatusText()

Reimplemented from CAppTask.

Definition at line 174 of file blast_search_task.cpp.

References _ASSERT, CBlastSearchTask::eFinished, CBlastSearchTask::eMonitor, CBlastSearchTask::eRetrieve, CBlastSearchTask::eSubmit, and CBlastSearchTask::m_Stage.

◆ GetSubject() [1/2]

const SConstScopedObject& CNGAlignParams::GetSubject ( ) const

inline

Definition at line 77 of file ngalign_params.hpp.

References CNGAlignParams::m_Subject.

Referenced by CNGAlignJob::x_CreateProjectItems().

◆ GetSubject() [2/2]

const SConstScopedObject& CNGAlignPanel::GetSubject ( void ) const

inline

Definition at line 101 of file ngalign_panel.hpp.

References CNGAlignPanel::m_Subject.

Referenced by CNGAlignTool::x_CreateLoadingJob().

◆ GetSubjectType()

ESubjectType CBLASTParams::GetSubjectType ( ) const

inline

Definition at line 204 of file blast_search_params.hpp.

Referenced by CBLASTToolManager::CanQuickLaunch(), CBLASTToolManager::GetTask(), CBLASTToolManager::QuickLaunch(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTSearchParamsPanel::x_HideShowInputs(), CBLASTSearchOptionsPanel::x_UpdateSubjects(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ GetSubjSeqLocs() [1/2]

TConstScopedObjects & CBLASTParams::GetSubjSeqLocs ( )

Definition at line 429 of file blast_search_params.cpp.

References CBLASTParams::m_SubjSeqLocs.

Referenced by CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSeqToolJob::x_CreateProjectItems().

◆ GetSubjSeqLocs() [2/2]

const TConstScopedObjects & CBLASTParams::GetSubjSeqLocs ( ) const

Definition at line 435 of file blast_search_params.cpp.

References CBLASTParams::m_SubjSeqLocs.

◆ GetSubmitted()

bool CNetBlastDMSearchFormPanel::GetSubmitted ( ) const

inline

Definition at line 102 of file net_blast_dm_search_form_panel.hpp.

References CNetBlastDMSearchFormPanel::m_Submitted.

Referenced by CNetBLAST_DMSearchForm::ConstructQuery().

◆ GetSubmitTime()

time_t CNetBlastJobDescriptor::GetSubmitTime ( ) const

Definition at line 185 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::m_Mutex, and CNetBlastJobDescriptor::m_SubmitTime.

Referenced by GetNetBlastJobDescription().

◆ GetTask() [1/5]

IAppTask * CBLASTToolManager::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 269 of file blast_tool_manager.cpp.

References CBLASTParams::eNCBIDB, CBLASTToolManager::GetBLASTDataSource(), CUIObject::GetLabel(), IServiceLocator::GetServiceByType(), CBLASTParams::GetSubjectType(), CBLASTToolManager::m_Descriptor, CBLASTToolManager::m_Params, CBLASTToolManager::m_ProjectParams, CBLASTToolManager::m_SrvLocator, CBLASTParams::PrintParams(), CRef< C, Locker >::Release(), and SProjectSelectorParams::ToLoadingOptions().

Referenced by CBLASTToolManager::QuickLaunch().

◆ GetTask() [2/5]

IAppTask * CCreateGeneModelToolManager::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.

Reimplemented from CAlgoToolManagerBase.

Definition at line 182 of file create_gene_model_tool_manager.cpp.

References CProjectSelectorPanel::GetParams(), IServiceLocator::GetServiceByType(), CCreateGeneModelToolManager::m_Params, CAlgoToolManagerBase::m_ProjectParams, CAlgoToolManagerBase::m_ProjectSelPanel, CAlgoToolManagerBase::m_SrvLocator, and SProjectSelectorParams::ToLoadingOptions().

◆ GetTask() [3/5]

IAppTask * CNetBLASTUILoadManager::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 177 of file net_blast_ui_load_manager.cpp.

References CUIObject::GetLabel(), CProjectSelectorPanel::GetParams(), CNetBLASTLoadOptionPanel::GetRIDs(), i, Info(), CBlastSearchTask::Init_RetrieveRID(), LOG_POST, SProjectSelectorParams::m_CreateFolder, CNetBLASTUILoadManager::m_DataSource, CNetBLASTUILoadManager::m_Descriptor, SProjectSelectorParams::m_FolderName, CNetBLASTUILoadManager::m_OptionPanel, CNetBLASTUILoadManager::m_ProjectParams, CNetBLASTUILoadManager::m_ProjectSelPanel, CNetBLASTUILoadManager::m_SrvLocator, CBlastSearchTask::SetLoadingOptions(), and SProjectSelectorParams::ToLoadingOptions().

◆ GetTask() [4/5]

IAppTask * CPslLoadManager::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 175 of file psl_load_manager.cpp.

◆ GetTask() [5/5]

IAppTask * CTextAlignLoaderManager::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 172 of file text_align_load_manager.cpp.

◆ GetThreshold()

long CBLASTSearchParamsPanel::GetThreshold ( ) const

inline

Definition at line 156 of file blast_search_params_panel.hpp.

References CBLASTSearchParamsPanel::m_Threshold.

void CAlignSpanView::GetVisibleRanges ( CVisibleRange & vrange ) const

virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 554 of file align_span_view.cpp.

References CVisibleRange::AddLocation(), CAlnSpanWidget::GetSelection(), ITERATE, CAlignSpanView::m_AlnWidget, and CProjectViewBase::x_HasProject().

void CMPCrossAlignView::GetVisibleRanges ( CVisibleRange & vrange ) const

virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 368 of file mp_cross_align_view.cpp.

◆ GetVisibleRanges() [6/6]

void CPhyTreeView::GetVisibleRanges ( CVisibleRange & vrange ) const

virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 1433 of file phy_tree_view.cpp.

◆ GetWaitPeriod()

CTimeSpan CNetBlastMonitoringJob::GetWaitPeriod ( )

virtual

returns a period of time after which the task shall be executed again

Implements IWaitPeriod.

Definition at line 469 of file blast_jobs.cpp.

References CNetBlastMonitoringJob::m_WaitPeriodIndex, min(), and t.

◆ GetWidget() [1/2]

CPhyloTreeWidget * CPhyTreeView::GetWidget ( ) const

Definition at line 816 of file phy_tree_view.cpp.

References CPhyTreeView::kPhylpWidgetID, and CPhyTreeView::m_Panel.

Referenced by CChangePhyloPropertyCmd::CChangePhyloPropertyCmd(), CPhyTreeView::GetSelection(), CPhyTreeView::InitView(), CPhyTreeView::LoadSettings(), CPhyTreeView::OnBioTreeChanged(), CPhyTreeView::OnCreateSelectedSubtree(), CPhyTreeView::OnExportTree(), CPhyTreeView::OnProjectChanged(), CPhyTreeView::OnSomethingEdited(), CChangePhyloPropertyCmd::PerformEdit(), CPhyTreeView::SaveSettings(), CPhyTreeView::SetRegistryPath(), and CPhyTreeView::x_OnSetSelection().

◆ GetWidget() [2/2]

wxSizer * CNetBLAST_DMSearchForm::GetWidget ( wxWindow * )

virtual

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

Reimplemented from CSearchFormBase.

Definition at line 289 of file net_blast_dm_search_tool.cpp.

References CNetBLAST_DMSearchForm::m_Panel, and CSearchFormBase::m_Sizer.

◆ GetWindow() [1/7]

wxWindow * CAlignSpanView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 98 of file align_span_view.cpp.

References _ASSERT, and CAlignSpanView::m_Panel.

Referenced by CAlignSpanView::DestroyViewWindow().

◆ GetWindow() [2/7]

wxWindow * CAnnotCompareView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 77 of file annot_compare_view.cpp.

References _ASSERT, and CAnnotCompareView::m_AnnWidget.

◆ GetWindow() [3/7]

wxWindow * CCrossAlignView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 76 of file cross_align_view.cpp.

References _ASSERT, and CCrossAlignView::m_AlnWidget.

◆ GetWindow() [4/7]

wxWindow * CDotMatrixView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 87 of file dot_matrix_view.cpp.

References _ASSERT, and CDotMatrixView::m_AlnWidget.

◆ GetWindow() [5/7]

wxWindow * CMPCrossAlignView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 78 of file mp_cross_align_view.cpp.

References _ASSERT, and CMPCrossAlignView::m_MainSplitter.

Referenced by CMPCrossAlignView::InitView().

◆ GetWindow() [6/7]

wxWindow * CMultiAlignView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 104 of file multi_align_view.cpp.

References _ASSERT, and CMultiAlignView::m_AlnWidget.

◆ GetWindow() [7/7]

wxWindow * CPhyTreeView::GetWindow ( )

virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 748 of file phy_tree_view.cpp.

References _ASSERT, and CPhyTreeView::m_Panel.

long CBLASTSearchParamsPanel::GetWordSize ( ) const

inline

Definition at line 159 of file blast_search_params_panel.hpp.

References CBLASTSearchParamsPanel::m_WordSize.

◆ GetWordSize() [2/2]

long CNGAlignParams::GetWordSize ( ) const

inline

Definition at line 87 of file ngalign_params.hpp.

References CNGAlignParams::m_WordSize.

Referenced by s_CallAligner().

◆ HasErrors()

bool CNetBlastLoadingJob::HasErrors ( ) const

Definition at line 511 of file blast_jobs.cpp.

References CNetBlastLoadingJob::m_Errors.

◆ Id() [1/2]

static string CPslLoadManager::Id ( void )

inlinestatic

Definition at line 120 of file psl_load_manager.hpp.

Referenced by CPslLoadManager::GetFileLoaderId().

◆ Id() [2/2]

static string CTextAlignLoaderManager::Id ( void )

inlinestatic

Definition at line 122 of file text_align_load_manager.hpp.

Referenced by CTextAlignLoaderManager::GetFileLoaderId().

◆ Init() [1/32]

void CBLAST_DB_Dialog::Init ( void )

Definition at line 186 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::m_DbMap, CBLAST_DB_Dialog::m_OKBtn, CBLAST_DB_Dialog::m_SearchCtrl, CBLAST_DB_Dialog::m_StatusText, CBLAST_DB_Dialog::m_TreeCtrl, and NULL.

Referenced by CBLAST_DB_Dialog::CBLAST_DB_Dialog().

◆ Init() [2/32]

void CBLASTSearchOptionsPanel::Init ( void )

Definition at line 166 of file blast_search_options_panel.cpp.

Referenced by CBLASTSearchOptionsPanel::CBLASTSearchOptionsPanel().

◆ Init() [3/32]

void CBLASTSearchParamsPanel::Init ( void )

Definition at line 126 of file blast_search_params_panel.cpp.

Referenced by CBLASTSearchParamsPanel::CBLASTSearchParamsPanel().

◆ Init() [4/32]

void SCleanupAlignmentsParams::Init ( void )

Definition at line 53 of file cleanup_alignments_params_panel.cpp.

References SCleanupAlignmentsParams::eAlignmentManager, SCleanupAlignmentsParams::m_Algo, SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned, SCleanupAlignmentsParams::m_AlnMgr_PreserveRows, SCleanupAlignmentsParams::m_AlnMgr_Sort, SCleanupAlignmentsParams::m_AlnMgr_Transloc, SCleanupAlignmentsParams::m_HitFilter_MinIdentity, and SCleanupAlignmentsParams::m_HitFilter_MinLength.

Referenced by CCleanupAlignmentsParamsPanel::RestoreDefaults(), and SCleanupAlignmentsParams::SCleanupAlignmentsParams().

◆ Init() [5/32]

void CCleanupAlignmentsParamsPanel::Init ( void )

Definition at line 129 of file cleanup_alignments_params_panel.cpp.

References CCleanupAlignmentsParamsPanel::m_AlgoSelector, CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned, CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows, CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort, CCleanupAlignmentsParamsPanel::m_AlnMgr_Transloc, CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity, CCleanupAlignmentsParamsPanel::m_HitFilter_MinLength, CCleanupAlignmentsParamsPanel::m_ObjectList, CCleanupAlignmentsParamsPanel::m_ParamsPanel, and NULL.

Referenced by CCleanupAlignmentsParamsPanel::CCleanupAlignmentsParamsPanel().

◆ Init() [6/32]

void CClustalOmegaToolParams::Init ( void )

Definition at line 85 of file clustal_omega_tool_params.cpp.

References CClustalOmegaToolParams::m_GenerateTree.

Referenced by CClustalOmegaToolParams::CClustalOmegaToolParams(), and CClustalOmegaToolPanel::RestoreDefaults().

◆ Init() [7/32]

void CClustalwToolParams::Init ( void )

Definition at line 75 of file clustalw_tool_params.cpp.

References CClustalwToolParams::m_GenerateTree.

Referenced by CClustalwToolParams::CClustalwToolParams(), and CClustalwToolPanel::RestoreDefaults().

◆ Init() [8/32]

void CFindOverlapPanel::Init ( void )

Definition at line 97 of file find_overlap_panel.cpp.

References CFindOverlapPanel::m_Seq1List, CFindOverlapPanel::m_Seq2List, and NULL.

Referenced by CFindOverlapPanel::CFindOverlapPanel().

◆ Init() [9/32]

void CFindOverlapParams::Init ( void )

Definition at line 75 of file find_overlap_params.cpp.

References CFindOverlapParams::m_BlastParams, CFindOverlapParams::m_FilterQty, CFindOverlapParams::m_MaxSlop, and wxT.

Referenced by CFindOverlapParams::CFindOverlapParams(), and CFindOverlapPanel::RestoreDefaults().

◆ Init() [10/32]

void SGroupAlignmentsParams::Init ( void )

Definition at line 67 of file group_alignments_params_panel.cpp.

References SGroupAlignmentsParams::m_GroupByEST, SGroupAlignmentsParams::m_GroupByGenBank, SGroupAlignmentsParams::m_GroupByHTGS, SGroupAlignmentsParams::m_GroupByLikeTaxId, SGroupAlignmentsParams::m_GroupByPatent, SGroupAlignmentsParams::m_GroupByPredictedRefSeq, SGroupAlignmentsParams::m_GroupByRefSeq, SGroupAlignmentsParams::m_GroupBySeqId, SGroupAlignmentsParams::m_GroupByStrand, SGroupAlignmentsParams::m_GroupByTaxId, and SGroupAlignmentsParams::m_GroupByWGS.

Referenced by CGroupAlignmentsParamsPanel::RestoreDefaults().

◆ Init() [11/32]

void CGroupAlignmentsParamsPanel::Init ( void )

Definition at line 175 of file group_alignments_params_panel.cpp.

Referenced by CGroupAlignmentsParamsPanel::CGroupAlignmentsParamsPanel().

◆ Init() [12/32]

void CKalignToolParams::Init ( void )

Definition at line 81 of file kalign_tool_params.cpp.

References CKalignToolParams::m_QuietFlag.

Referenced by CKalignToolParams::CKalignToolParams(), and CKalignToolPanel::RestoreDefaults().

◆ Init() [13/32]

void CMafftToolParams::Init ( void )

Definition at line 83 of file mafft_tool_params.cpp.

References CMafftToolParams::m_AutoFlag, and CMafftToolParams::m_QuietFlag.

Referenced by CMafftToolParams::CMafftToolParams(), and CMafftToolPanel::RestoreDefaults().

◆ Init() [14/32]

void SMergeAlignmentsParams::Init ( void )

Definition at line 61 of file merge_alignments_params_panel.cpp.

References CAlnUserOptions::eBothDirections, CAlnUserOptions::eMergeAllSeqs, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, and SMergeAlignmentsParams::m_MergeFlags.

Referenced by CMergeAlignmentsParamsPanel::RestoreDefaults(), and SMergeAlignmentsParams::SMergeAlignmentsParams().

◆ Init() [15/32]

void CMergeAlignmentsParamsPanel::Init ( void )

Definition at line 154 of file merge_alignments_params_panel.cpp.

References CMergeAlignmentsParamsPanel::m_AssumeNegStrand, CMergeAlignmentsParamsPanel::m_FillUnaligned, CMergeAlignmentsParamsPanel::m_InputListDirty, CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly, CMergeAlignmentsParamsPanel::m_ObjectListCtrl, CMergeAlignmentsParamsPanel::m_Params, CMergeAlignmentsParamsPanel::m_SortInput, CMergeAlignmentsParamsPanel::m_TruncateOverlap, and NULL.

Referenced by CMergeAlignmentsParamsPanel::CMergeAlignmentsParamsPanel().

◆ Init() [16/32]

void CMuscleToolParams::Init ( void )

Definition at line 83 of file muscle_tool_params.cpp.

References CMuscleToolParams::m_GenerateTree, and CMuscleToolParams::m_ScoringMethod.

Referenced by CMuscleToolParams::CMuscleToolParams(), and CMuscleToolPanel::RestoreDefaults().

◆ Init() [17/32]

void CNeedlemanWunschToolParams::Init ( void )

Definition at line 82 of file needlemanwunsch_tool_params.cpp.

References CNeedlemanWunschToolParams::m_BandSize, CNeedlemanWunschToolParams::m_FirstSeqFreeEnds, CNeedlemanWunschToolParams::m_GapExtendCost, CNeedlemanWunschToolParams::m_GapOpenCost, CNeedlemanWunschToolParams::m_MatchCost, CNeedlemanWunschToolParams::m_MismatchCost, and CNeedlemanWunschToolParams::m_SecondSeqFreeEnds.

Referenced by CNeedlemanWunschToolParams::CNeedlemanWunschToolParams(), and CAlignNeedlemanWunschPanel::RestoreDefaults().

◆ Init() [18/32]

void CNetBlastDMSearchFormPanel::Init ( void )

Definition at line 107 of file net_blast_dm_search_form_panel.cpp.

References CNetBlastDMSearchFormPanel::m_Completed, CNetBlastDMSearchFormPanel::m_Expired, CNetBlastDMSearchFormPanel::m_Failed, CNetBlastDMSearchFormPanel::m_ResetBtn, CNetBlastDMSearchFormPanel::m_Retrieved, CNetBlastDMSearchFormPanel::m_SearchCtrl, CNetBlastDMSearchFormPanel::m_Submitted, and NULL.

Referenced by CNetBlastDMSearchFormPanel::CNetBlastDMSearchFormPanel().

◆ Init() [19/32]

void CNetBLAST_DMSearchForm::Init ( void )

virtual

Reimplemented from IDMSearchForm.

Definition at line 264 of file net_blast_dm_search_tool.cpp.

References IDMSearchForm::Init().

◆ Init() [20/32]

void CNetBLASTLoadOptionPanel::Init ( void )

Definition at line 93 of file net_blast_load_option_panel.cpp.

Referenced by CNetBLASTLoadOptionPanel::CNetBLASTLoadOptionPanel().

◆ Init() [21/32]

void CNGAlignParams::Init ( void )

Definition at line 95 of file ngalign_params.cpp.

References CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_WM_TaxId, and CNGAlignParams::m_WordSize.

Referenced by CNGAlignParams::CNGAlignParams(), and CNGAlignBLASTPanel::RestoreDefaults().

◆ Init() [22/32]

void CSplignPanel::Init ( void )

Definition at line 193 of file splign_panel.cpp.

References CSplignPanel::m_cDNAList, CSplignPanel::m_GenomicList, and NULL.

Referenced by CSplignPanel::CSplignPanel().

◆ Init() [23/32]

void CSplignParams::Init ( void )

Definition at line 85 of file splign_params.cpp.

References CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, and CSplignParams::m_PolyADetect.

Referenced by CSplignParams::CSplignParams(), and CSplignPanel::RestoreDefaults().

◆ Init() [24/32]

void CTaxTreeToolParams::Init ( void )

Definition at line 68 of file taxtree_tool_params.cpp.

Referenced by CTaxTreeToolParams::CTaxTreeToolParams(), and CTaxTreeToolPanel::RestoreDefaults().

◆ Init() [25/32]

void CTreeBuilderPanel::Init ( void )

Definition at line 106 of file tree_builder_panel.cpp.

References CTreeBuilderPanel::m_Seq1List, and NULL.

Referenced by CTreeBuilderPanel::CTreeBuilderPanel().

◆ Init() [26/32]

void CTreeBuilderParams::Init ( void )

Definition at line 74 of file tree_builder_params.cpp.

Referenced by CTreeBuilderParams::CTreeBuilderParams(), and CTreeBuilderPanel::RestoreDefaults().

◆ Init() [27/32]

void CTextAlignObjectLoader::Init ( void )

Definition at line 129 of file text_align_object_loader.cpp.

References CObjectManager::GetInstance(), CTextAlignObjectLoader::m_Scope, and CRef< C, Locker >::Reset().

Referenced by CTextAlignObjectLoader::Execute().

◆ Init() [28/32]

void CMuscleToolPanel::Init ( void )

Definition at line 106 of file muscle_tool_panel.cpp.

References CMuscleToolPanel::m_LocationSel, and NULL.

Referenced by CMuscleToolPanel::CMuscleToolPanel().

◆ Init() [29/32]

void CNGAlignPanel::Init ( void )

Definition at line 101 of file ngalign_panel.cpp.

References CNGAlignPanel::m_QueryListCtrl, CNGAlignPanel::m_SubjectListCtrl, and NULL.

Referenced by CNGAlignPanel::CNGAlignPanel().

◆ Init() [30/32]

void CTaxTreeToolPanel::Init ( void )

Definition at line 94 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::m_SeqIds, and NULL.

Referenced by CTaxTreeToolPanel::CTaxTreeToolPanel().

◆ Init() [31/32]

void CNetBlastJobDescriptor::Init	(	const CBLASTParams &	params,
		CNetBLASTUIDataSource &	ds
	)

◆ Init() [32/32]

void CNetBlastJobDescriptor::Init	(	const string &	rid,
		CNetBLASTUIDataSource &	ds
	)

Definition at line 264 of file net_blast_job_descr.cpp.

References _ASSERT, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eInvalidState, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_NetBlastDS, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_RID, and CNetBlastJobDescriptor::m_State.

◆ Init_Monitoring()

void CBlastSearchTask::Init_Monitoring ( TDescriptors & descriptors )

virtual

setup the task for monitoring BLAST jobs and for retrieving results

Definition at line 89 of file blast_search_task.cpp.

References CBlastSearchTask::eMonitor, CBlastSearchTask::m_Command, CAppTask::m_Descr, CBlastSearchTask::m_ToolName, n, NStr::NumericToString(), and CBlastSearchTask::x_InitMonitoringStage().

◆ Init_RetrieveRID()

void CBlastSearchTask::Init_RetrieveRID ( const vector< string > & RIDs )

virtual

setup the task for retrieving results

Definition at line 101 of file blast_search_task.cpp.

Referenced by CNetBLASTUILoadManager::GetTask().

◆ Init_SubmitSearch()

void CBlastSearchTask::Init_SubmitSearch ( const CBLASTParams & params )

virtual

setup the task for submitting and monitoring BLAST jobs, and for retrieving results

Definition at line 63 of file blast_search_task.cpp.

References CBlastSearchTask::eSubmit, CBLASTParams::GetJobTitle(), CBLASTParams::GetSeqLocs(), CBlastSearchTask::m_Command, CBlastSearchTask::m_CurrTask, CAppTask::m_Descr, CBlastSearchTask::m_NetBlastDS, CBlastSearchTask::m_Stage, CBlastSearchTask::m_SubmittingJob, CBlastSearchTask::m_ToolName, n, NStr::NumericToString(), CRef< C, Locker >::Reset(), and CAppJobTask::SetReportErrors().

◆ InitUI() [1/21]

void CBLASTToolManager::InitUI ( )

bool CMPCrossAlignView::InitView	(	TConstScopedObjects &	objects,
		const objects::CUser_object *	params
	)

virtual

initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project

Reimplemented from CProjectView.

Definition at line 135 of file mp_cross_align_view.cpp.

References _ASSERT, IWindowManagerService::ActivateClient(), IViewManagerService::CreateViewInstance(), CProjectViewBase::CreateViewWindow(), CSeq_id_Handle::GetHandle(), IServiceLocator::GetServiceByType(), IWorkbench::GetViewManagerService(), CMPCrossAlignView::GetWindow(), CProjectViewBase::GetWindow(), IWorkbench::GetWindowManagerService(), i, CMPCrossAlignView::m_MainSplitter, CMPCrossAlignView::m_OrigAlign, CMPCrossAlignView::m_OrigAnnot, CMPCrossAlignView::m_Views, CProjectViewBase::m_Workbench, IWindowManagerService::RegisterActiveClient(), CConstRef< C, Locker >::Reset(), CProjectView::SetVisibleRangeService(), IWindowManagerService::UnRegisterActiveClient(), wxID_ANY, CProjectViewBase::x_AttachToProject(), CProjectViewBase::x_ReportInvalidInputData(), and CProjectViewBase::x_UpdateContentLabel().

◆ InitView() [2/3]

bool CMultiAlignView::InitView	(	TConstScopedObjects &	objects,
		const objects::CUser_object *	params
	)

virtual

initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project

Reimplemented from CProjectView.

Definition at line 211 of file multi_align_view.cpp.

References _ASSERT, IServiceLocator::GetServiceByType(), CProjectViewBase::m_Workbench, NULL, CMultiAlignView::OnProjectChanged(), CProjectViewBase::x_AttachToProject(), CMultiAlignView::x_GetValidInputData(), CMultiAlignView::x_MergeObjects(), and CProjectViewBase::x_ReportInvalidInputData().

◆ InitView() [3/3]

bool CPhyTreeView::InitView	(	TConstScopedObjects &	objects,
		const objects::CUser_object *	params
	)

virtual

initialize view with data, inside this function the view must call CProjectService::AttachView to connect to a project

Reimplemented from CProjectView.

Definition at line 839 of file phy_tree_view.cpp.

References _ASSERT, CProjectViewEvent::eData, Error(), CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetInt(), CPhyloTreeScheme::GetLayoutIdx(), CException::GetMsg(), CPhyloTreeWidget::GetScheme(), IServiceLocator::GetServiceByType(), CPhyTreeView::GetWidget(), CUser_object::HasField(), CPhyloTreeWidget::HasScheme(), CUser_field_Base::C_Data::IsBool(), CUser_field_Base::C_Data::IsInt(), ITERATE, CPhyloTreeWidget::LoadSettings(), LOG_POST, CPhyTreeView::m_BioTreeContainer, CPhyTreeView::m_InitialLayout, CPhyTreeView::m_InitialRotateLabels, CPhyTreeView::m_InitialUseDistances, CProjectViewBase::m_Workbench, CProjectViewBase::OnProjectChanged(), CConstRef< C, Locker >::Reset(), CProjectViewBase::x_AttachToProject(), and CProjectViewBase::x_ReportInvalidInputData().

◆ IsCompartmentsRequested()

bool CBLASTParams::IsCompartmentsRequested ( ) const

inline

Definition at line 162 of file blast_search_params.hpp.

Referenced by CBLASTSearchParamsPanel::TransferDataToWindow(), and CBLASTSeqToolJob::x_CreateProjectItems().

◆ IsCompatible()

bool CNetBLAST_DMSearchTool::IsCompatible ( IDataMiningContext * context )

virtual

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

Implements CSearchToolBase.

Definition at line 180 of file net_blast_dm_search_tool.cpp.

◆ IsCompatibleWith() [1/2]

bool CMPCrossAlignViewFactory::IsCompatibleWith	(	const CObject &	object,
		objects::CScope &	scope
	)

virtual

Reimplemented from IProjectViewFactory.

Definition at line 449 of file mp_cross_align_view.cpp.

Referenced by CMPCrossAlignViewFactory::TestInputObjects().

◆ IsCompatibleWith() [2/2]

bool CMultiAlignViewFactory::IsCompatibleWith	(	const CObject &	object,
		objects::CScope &	scope
	)

virtual

Reimplemented from IProjectViewFactory.

Definition at line 644 of file multi_align_view.cpp.

References CSeq_annot::IsAlign(), and type.

Referenced by CMultiAlignViewFactory::TestInputObjects().

◆ IsCompletedState() [1/4]

bool CBLASTToolManager::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 215 of file blast_tool_manager.cpp.

References CBLASTToolManager::eCompleted, and CBLASTToolManager::m_State.

◆ IsCompletedState() [2/4]

bool CNetBLASTUILoadManager::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 146 of file net_blast_ui_load_manager.cpp.

References CNetBLASTUILoadManager::eCompleted, and CNetBLASTUILoadManager::m_State.

◆ IsCompletedState() [3/4]

bool CPslLoadManager::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 150 of file psl_load_manager.cpp.

References CPslLoadManager::eCompleted, and CPslLoadManager::m_State.

◆ IsCompletedState() [4/4]

bool CTextAlignLoaderManager::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 147 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::eCompleted, and CTextAlignLoaderManager::m_State.

◆ IsDatabase()

bool CBLAST_Dlg_Item::IsDatabase ( ) const

inline

Definition at line 86 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_IsDatabase.

Referenced by CBLAST_DB_Dialog::OnTreectrlSelChanged(), and CBLAST_DB_Dialog::x_GetSelectedDBItem().

◆ IsDeleted()

bool CNetBlastJobDescriptor::IsDeleted ( ) const

Definition at line 202 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::m_Deleted.

Referenced by CNetBLASTUIDataSource::x_SaveJobDescriptors().

◆ IsExpanded()

bool CBLAST_Dlg_Item::IsExpanded ( ) const

inline

Definition at line 91 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_Expanded.

Referenced by CBLAST_DB_Dialog::x_BuildTreeItems().

◆ IsFinalState() [1/5]

bool CBLASTToolManager::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 209 of file blast_tool_manager.cpp.

References CBLASTToolManager::eParams, and CBLASTToolManager::m_State.

◆ IsFinalState() [2/5]

bool CNetBLASTUILoadManager::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 140 of file net_blast_ui_load_manager.cpp.

References CNetBLASTUILoadManager::eSelectProject, and CNetBLASTUILoadManager::m_State.

◆ IsFinalState() [3/5]

bool CNGAlignTool::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.

Reimplemented from CAlgoToolManagerBase.

Definition at line 93 of file ngalign_tool.cpp.

References CAlgoToolManagerBase::eParams, CAlgoToolManagerBase::eSelectProject, CNGAlignTool::m_CurrentPage, CAlgoToolManagerBase::m_State, and IUIToolManager::UsesSingleOMScope().

◆ IsFinalState() [4/5]

bool CPslLoadManager::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 144 of file psl_load_manager.cpp.

References CPslLoadManager::eParams, and CPslLoadManager::m_State.

◆ IsFinalState() [5/5]

bool CTextAlignLoaderManager::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 141 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::eParams, and CTextAlignLoaderManager::m_State.

◆ IsInitialState() [1/2]

bool CPslLoadManager::IsInitialState ( )

virtual

return true if the current state of the loader UI is the first valid state (first step in a wizard-like sequence)

Implements IFileFormatLoaderManager.

Definition at line 210 of file psl_load_manager.cpp.

References CPslLoadManager::eParams, and CPslLoadManager::m_State.

◆ IsInitialState() [2/2]

bool CTextAlignLoaderManager::IsInitialState ( )

virtual

return true if the current state of the loader UI is the first valid state (first step in a wizard-like sequence)

Implements IFileFormatLoaderManager.

Definition at line 206 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::eParams, and CTextAlignLoaderManager::m_State.

◆ IsInputValid()

bool CNetBLASTLoadOptionPanel::IsInputValid ( )

Definition at line 185 of file net_blast_load_option_panel.cpp.

Referenced by CNetBLASTUILoadManager::DoTransition().

◆ IsMultiScopeInputAccepted()

virtual bool CNGAlignTool::IsMultiScopeInputAccepted ( ) const

inlineprotectedvirtual

Definition at line 82 of file ngalign_tool.hpp.

◆ IsNucDatabase()

bool CBLASTParams::IsNucDatabase ( blast::EProgram program )

static

Definition at line 134 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrMRUDatabases(), CBLASTParams::IsSubjNucInput(), and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

◆ IsNucInput() [1/3]

bool & CBLASTParams::IsNucInput ( )

Definition at line 275 of file blast_search_params.cpp.

References CBLASTParams::m_NucInput.

Referenced by CBLASTToolManager::QuickLaunch(), CBLASTToolManager::SaveSettings(), CBLASTParams::ToArgVec(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTToolManager::x_CreateOptionsPanelIfNeeded(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTSearchOptionsPanel::x_FillQueryList(), CBLASTSearchParamsPanel::x_HideShowInputs(), CBLASTSearchOptionsPanel::x_OnInputTypeChanged(), and CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet().

◆ IsNucInput() [2/3]

bool CBLASTParams::IsNucInput ( ) const

Definition at line 281 of file blast_search_params.cpp.

References CBLASTParams::m_NucInput.

◆ IsNucInput() [3/3]

bool CBLASTParams::IsNucInput ( blast::EProgram program )

static

Definition at line 110 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), and CBLASTParams::sm_ProgramToAttr.

◆ IsOpen()

bool CNetBLASTUIDataSource::IsOpen ( )

virtual

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

Implements IUIDataSource.

Definition at line 218 of file net_blast_ui_data_source.cpp.

References CNetBLASTUIDataSource::m_Open.

◆ IsStandaloneRequested()

bool CBLASTParams::IsStandaloneRequested ( ) const

inline

Definition at line 159 of file blast_search_params.hpp.

Referenced by CBLASTSearchParamsPanel::TransferDataToWindow(), and CBLASTSeqToolJob::x_CreateProjectItems().

◆ IsSubjNucInput()

bool CBLASTParams::IsSubjNucInput ( ) const

Definition at line 423 of file blast_search_params.cpp.

References CBLASTParams::GetCurrProgram(), and CBLASTParams::IsNucDatabase().

Referenced by CNetBlastJobDescriptor::Init(), CBLASTSearchOptionsPanel::OnBrowseDatabases(), CBLASTSearchOptionsPanel::OnProgramComboSelected(), CBLASTSearchOptionsPanel::OnSelectLocalDB(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTSearchOptionsPanel::x_FillSubjectList(), CBLASTSearchOptionsPanel::x_UpdateSubjects(), and CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet().

◆ IsVisible()

bool CBLAST_Dlg_Item::IsVisible ( void ) const

inline

Definition at line 88 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_Visible.

Referenced by CBLAST_DB_Dialog::x_BuildTreeItems(), and CBLAST_DB_Dialog::x_FilterItems().

◆ Label() [1/2]

static string CPslLoadManager::Label ( )

inlinestatic

Definition at line 121 of file psl_load_manager.hpp.

◆ Label() [2/2]

static string CTextAlignLoaderManager::Label ( )

inlinestatic

Definition at line 123 of file text_align_load_manager.hpp.

◆ LoadFromStream()

void CTextAlignObjectLoader::LoadFromStream	(	CNcbiIstream &	istr,
		TObjects &	objects,
		string &	errMsg
	)

Definition at line 136 of file text_align_object_loader.cpp.

References _ASSERT, _DEBUG_ARG, _TRACE, CMessageListenerBase::Count(), CAlnReader::eAlpha_Nucleotide, CAlnReader::eAlpha_Protein, CLabel::eDefault, CTextAlignParams::GetBegin(), CTextAlignParams::GetEnd(), CMessageListenerBase::GetError(), CTextAlnReader::GetFilteredSeqEntry(), CLabel::GetLabel(), CTextAlignParams::GetMatch(), CTextAlignParams::GetMiddle(), CTextAlignParams::GetSeqType(), ILineError::GetText(), CTextAlignParams::GetUnknown(), i, NStr::IsBlank(), label, CTextAlignObjectLoader::m_Params, CTextAlignObjectLoader::m_Scope, CAlnReader::Read(), CAlnReader::SetAlphabet(), CAlnReader::SetBeginningGap(), CSeq_annot_Base::SetData(), CAlnReader::SetEndGap(), CAlnReader::SetMatch(), CAlnReader::SetMiddleGap(), CAlnReader::SetMissing(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and ToStdString().

Referenced by CTextAlignObjectLoader::Execute().

◆ LoadSettings() [1/33]

void CAlignSpanView::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 190 of file align_span_view.cpp.

References CGuiRegistry::GetInstance(), CwxTableListCtrl::GetModel(), CGuiRegistry::GetReadView(), CwxTableListCtrl::LoadTableSettings(), CAlignSpanView::m_AlnWidget, CAlignSpanView::m_RegPath, and NULL.

Referenced by CAlignSpanView::x_PostAttachToProject().

◆ LoadSettings() [2/33]

void CBLASTSearchOptionsPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 410 of file blast_search_options_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kTableTag, CwxTableListCtrl::LoadTableSettings(), CBLASTSearchOptionsPanel::m_QueryListCtrl, CAlgoToolManagerParamsPanel::m_RegPath, CBLASTSearchOptionsPanel::m_SubjectListCtrl, and CGuiRegistryUtil::MakeKey().

Referenced by CBLASTToolManager::x_CreateOptionsPanelIfNeeded().

◆ LoadSettings() [3/33]

virtual void CBLASTSearchParamsPanel::LoadSettings ( )

inlinevirtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 119 of file blast_search_params_panel.hpp.

◆ LoadSettings() [4/33]

void CBLASTToolManager::LoadSettings ( )

virtual

◆ LoadSettings() [5/33]

void SCleanupAlignmentsParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 68 of file cleanup_alignments_params_panel.cpp.

◆ LoadSettings() [6/33]

void CCleanupAlignmentsParamsPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 282 of file cleanup_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kTableTag, CwxTableListCtrl::LoadTableSettings(), CCleanupAlignmentsParamsPanel::m_ObjectList, CCleanupAlignmentsParamsPanel::m_RegPath, and CGuiRegistryUtil::MakeKey().

Referenced by CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ LoadSettings() [7/33]

void CClustalOmegaToolParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 114 of file clustal_omega_tool_params.cpp.

References FnToWxString(), CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kClustalwPath, kCommandLine, kGenerateTree, CClustalOmegaToolParams::m_ClustalOmegaPath, CClustalOmegaToolParams::m_CommandLine, CClustalOmegaToolParams::m_GenerateTree, CClustalOmegaToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [8/33]

void CClustalwToolParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 104 of file clustalw_tool_params.cpp.

References FnToWxString(), CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kClustalwPath, kCommandLine, kGenerateTree, CClustalwToolParams::m_ClustalWPath, CClustalwToolParams::m_CommandLine, CClustalwToolParams::m_GenerateTree, CClustalwToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [9/33]

void CFindOverlapPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 244 of file find_overlap_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kTable1Tag, kTable2Tag, CwxTableListCtrl::LoadTableSettings(), CAlgoToolManagerParamsPanel::m_RegPath, CFindOverlapPanel::m_Seq1List, CFindOverlapPanel::m_Seq2List, and CGuiRegistryUtil::MakeKey().

Referenced by CFindOverlapTool::x_CreateParamsPanelIfNeeded().

◆ LoadSettings() [10/33]

void CFindOverlapParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 101 of file find_overlap_params.cpp.

References CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), kBlastParamsTag, kFilterTag, kMaxSlopTag, CFindOverlapParams::m_BlastParams, CFindOverlapParams::m_FilterQty, CFindOverlapParams::m_MaxSlop, CFindOverlapParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [11/33]

void SGroupAlignmentsParams::LoadSettings ( )

virtual

◆ LoadSettings() [12/33]

void CGroupAlignmentsParamsPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 303 of file group_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kTableTag, CwxTableListCtrl::LoadTableSettings(), CGroupAlignmentsParamsPanel::m_ObjectList, CGroupAlignmentsParamsPanel::m_RegPath, and CGuiRegistryUtil::MakeKey().

Referenced by CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ LoadSettings() [13/33]

void CKalignToolParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 110 of file kalign_tool_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kAlignPath, kCommandLine, kQuietMode, CKalignToolParams::m_CommandLine, CKalignToolParams::m_KalignPath, CKalignToolParams::m_QuietFlag, CKalignToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [14/33]

void CMafftToolParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 115 of file mafft_tool_params.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), CRegistryReadView::GetString(), CGuiRegistry::GetString(), kAutoFlag, kCommandLine, kMafftPath, kQuietMode, CMafftToolParams::m_AutoFlag, CMafftToolParams::m_CommandLine, CMafftToolParams::m_MafftPath, CMafftToolParams::m_QuietFlag, CMafftToolParams::m_RegPath, ToStdString(), and ToWxString().

◆ LoadSettings() [15/33]

void SMergeAlignmentsParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 93 of file merge_alignments_params_panel.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CRegistryReadView::GetInt(), CGuiRegistry::GetReadView(), kDirectionTag, kFillUnalignedTag, kMergeAlgoTag, kMergeFlagsTag, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, and SMergeAlignmentsParams::m_RegPath.

◆ LoadSettings() [16/33]

void CMergeAlignmentsParamsPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 309 of file merge_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kTableTag, CwxTableListCtrl::LoadTableSettings(), CMergeAlignmentsParamsPanel::m_ObjectListCtrl, CMergeAlignmentsParamsPanel::m_RegPath, and CGuiRegistryUtil::MakeKey().

Referenced by CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ LoadSettings() [17/33]

void CMultiAlignView::LoadSettings ( )

virtual

Implements IRegSettings.

void CSplignPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 351 of file splign_panel.cpp.

References CObjectListWidgetSel::LoadSettings(), CSplignPanel::m_cDNAList, and CSplignPanel::m_GenomicList.

Referenced by CSplignTool::x_CreateParamsPanelIfNeeded().

◆ LoadSettings() [25/33]

void CSplignParams::LoadSettings ( )

virtual

◆ LoadSettings() [26/33]

void CTaxTreeToolParams::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 81 of file taxtree_tool_params.cpp.

◆ LoadSettings() [27/33]

void CTreeBuilderPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 245 of file tree_builder_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kTable1Tag, CwxTableListCtrl::LoadTableSettings(), CAlgoToolManagerParamsPanel::m_RegPath, CTreeBuilderPanel::m_Seq1List, and CGuiRegistryUtil::MakeKey().

Referenced by CTreeBuilderTool::x_CreateParamsPanelIfNeeded().

void CPslLoadManager::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 252 of file psl_load_manager.cpp.

References CPslLoadParams::LoadSettings(), and CPslLoadManager::m_Params.

◆ LoadSettings() [32/33]

void CTaxTreeToolPanel::LoadSettings ( )

virtual

Implements CAlgoToolManagerParamsPanel.

Definition at line 168 of file taxtree_tool_panel.cpp.

References CObjectListWidgetSel::LoadSettings(), and CTaxTreeToolPanel::m_SeqIds.

Referenced by CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded().

◆ LoadSettings() [33/33]

void CTextAlignLoaderManager::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 253 of file text_align_load_manager.cpp.

References CTextAlignParams::LoadSettings(), and CTextAlignLoaderManager::m_Params.

◆ LogDump()

void CNGAlignParams::LogDump ( )

Definition at line 147 of file ngalign_params.cpp.

References CSeq_id::eContent, CSeq_id::GetLabel(), CConstRef< C, Locker >::GetPointer(), Info(), LOG_POST, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_Queries, CNGAlignParams::m_Subject, CNGAlignParams::m_WM_TaxId, CNGAlignParams::m_WordSize, NON_CONST_ITERATE, NULL, and SConstScopedObject::object.

Referenced by CNGAlignJob::x_CreateProjectItems().

◆ MarkDeleted()

void CNetBlastJobDescriptor::MarkDeleted ( bool deleted )

Definition at line 192 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::m_Deleted, CNetBlastJobDescriptor::m_Mutex, and CNetBlastJobDescriptor::x_NotifyDataSource().

Referenced by CNetBLASTUIDataSource::DeleteJobDescriptors().

◆ NeedsDbGeneticCode()

bool CBLASTParams::NeedsDbGeneticCode ( blast::EProgram program )

static

Definition at line 169 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTParams::x_FromUserObject(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTParams::x_ToUserObject().

◆ NeedsQueryGeneticCode()

bool CBLASTParams::NeedsQueryGeneticCode ( blast::EProgram program )

static

Definition at line 158 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTParams::x_FromUserObject(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTParams::x_ToUserObject().

◆ NeedsThreshold()

bool CBLASTParams::NeedsThreshold ( blast::EProgram program )

static

Definition at line 146 of file blast_search_params.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::find(), and CBLASTParams::sm_ProgramToAttr.

Referenced by CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTParams::x_FromUserObject(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTParams::x_ToUserObject().

◆ OnAlnWidgetSelChanged()

void CMultiAlignView::OnAlnWidgetSelChanged ( CEvent * evt )

Definition at line 535 of file multi_align_view.cpp.

References _ASSERT, CAlnMultiPane::eLinearSelChanged, CAlnMultiPane::eSelRowChanged, CEvent::GetID(), CProjectViewBase::m_SelectionService, and ISelectionService::OnSelectionChanged().

◆ OnBioTreeChanged()

void CPhyTreeView::OnBioTreeChanged ( )

Definition at line 967 of file phy_tree_view.cpp.

Referenced by CPhyTreeView::OnProjectChanged(), and CChangePhyloTreeCommand::Unexecute().

◆ OnBrowseDatabases()

void CBLASTSearchOptionsPanel::OnBrowseDatabases ( wxCommandEvent & event )

◆ OnComboboxSelected()

void CCleanupAlignmentsParamsPanel::OnComboboxSelected ( wxCommandEvent & event )

Definition at line 219 of file cleanup_alignments_params_panel.cpp.

References CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector().

◆ OnCreateSelectedSubtree()

void CPhyTreeView::OnCreateSelectedSubtree ( CEvent * evt )

◆ OnDatabaseComboSelected()

void CBLASTSearchOptionsPanel::OnDatabaseComboSelected ( wxCommandEvent & event )

Definition at line 663 of file blast_search_options_panel.cpp.

References CMRUList< T >::AddItem(), database, CBLASTParams::GetCurrDatabase(), CBLASTParams::GetCurrMRUDatabases(), CBLASTSearchOptionsPanel::m_DatabaseCombo, CBLASTSearchOptionsPanel::m_Params, and ToStdString().

◆ OnDSChanged()

void CMultiAlignView::OnDSChanged ( CDataChangeNotifier::CUpdate & update )

virtual

Implements CDataChangeNotifier::IListener.

Definition at line 315 of file multi_align_view.cpp.

References CDataChangeNotifier::eChanged, CDataChangeNotifier::CUpdate::GetType(), CMultiAlignView::m_AlnWidget, CAlnMultiWidget::OnDSChanged(), CMultiAlignView::x_RebuildObjectIndex(), and CProjectViewBase::x_UpdateContentLabel().

◆ OnExplore()

void CNetBLASTUIDataSource::OnExplore ( )

Definition at line 566 of file net_blast_ui_data_source.cpp.

References IServiceLocator::GetServiceByType(), CNetBLASTUIDataSource::m_SrvLocator, NET_BLAST_DM_TOOL_NAME, CDataMiningView::SelectToolByName(), and IViewManagerService::ShowSingletonView().

Referenced by CNetBlastDSEvtHandler::OnExplore().

◆ OnExportTree()

void CPhyTreeView::OnExportTree ( CEvent * evt )

Definition at line 1566 of file phy_tree_view.cpp.

References _ASSERT, CAppTaskService::AddTask(), IWorkbench::GetAppTaskService(), CExportTreeDlg::GetData(), CPhyloTreeWidget::GetScheme(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::GetWidget(), CPhyloTreeWidget::HasScheme(), CPhyTreeView::m_DataSource, CProjectViewBase::m_Workbench, CPhyExportParams::SetBioTree(), CPhyExportParams::SetLabelFormat(), CPhyloTreeScheme::SetLabelFormat(), and TreeConvert2Container().

◆ OnFilterInputTextUpdated()

void CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated ( wxCommandEvent & event )

Definition at line 198 of file net_blast_dm_search_form_panel.cpp.

References CNetBlastDMSearchFormPanel::m_BlockEvents, CNetBlastDMSearchFormPanel::m_SearchCtrl, CNetBlastDMSearchFormPanel::m_SearchValue, and CNetBlastDMSearchFormPanel::RestartSearch().

◆ OnInitDialog()

void CBLAST_DB_Dialog::OnInitDialog ( wxInitDialogEvent & event )

Definition at line 315 of file blast_db_dialog.cpp.

References CBLAST_Dlg_Item::GetId(), CBLAST_Dlg_Item::GetPath(), GUI_AsyncExec(), kEmptyStr, CBLAST_DB_Dialog::m_DbItems, CBLAST_DB_Dialog::m_SelDatabase, CBLAST_DB_Dialog::m_TreeCtrl, NON_CONST_ITERATE, wxT, CBLAST_DB_Dialog::x_CreateItems(), and CBLAST_DB_Dialog::x_FilterItems().

◆ OnLoadRIDs()

void CNetBLASTUIDataSource::OnLoadRIDs ( )

Definition at line 582 of file net_blast_ui_data_source.cpp.

References CAppDialogs::COpenDialog(), CNetBLASTUIDataSource::m_SrvLocator, and NET_BLAST_LOADER_LABEL.

Referenced by CNetBlastDSEvtHandler::OnLoadRIDs().

◆ OnLocalDBLoaderClick()

void CBLASTSearchOptionsPanel::OnLocalDBLoaderClick ( wxCommandEvent & event )

Definition at line 994 of file blast_search_options_panel.cpp.

References CBLASTSearchOptionsPanel::m_Params, and CBLASTParams::SetLocalDBLoader().

◆ OnMusclePathClick()

void CMuscleToolPanel::OnMusclePathClick ( wxCommandEvent & event )

Definition at line 235 of file muscle_tool_panel.cpp.

References _ASSERT, CMuscleToolPanel::ID_TEXTCTRL12, and wxT.

◆ OnNucRadioSelected()

void CBLASTSearchOptionsPanel::OnNucRadioSelected ( wxCommandEvent & event )

Definition at line 538 of file blast_search_options_panel.cpp.

References CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ OnOkClick()

void CBLAST_DB_Dialog::OnOkClick ( wxCommandEvent & event )

Definition at line 524 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::x_OnDatabaseSelected().

◆ OnOpenGraphicalView()

void CMultiAlignView::OnOpenGraphicalView ( CEvent * evt )

Definition at line 551 of file multi_align_view.cpp.

References COpenGraphicViewEvent::GetObject(), COpenGraphicViewEvent::GetParams(), IServiceLocator::GetServiceByType(), and CProjectViewBase::m_Workbench.

◆ OnProgramComboSelected()

void CBLASTSearchOptionsPanel::OnProgramComboSelected ( wxCommandEvent & event )

Definition at line 651 of file blast_search_options_panel.cpp.

References CBLASTParams::GetCurrProgram(), CBLASTParams::GetProgramByLabel(), CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProgramCombo, ToStdString(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

◆ OnProjectChanged() [1/8]

void CMPCrossAlignView::OnProjectChanged ( )

virtual

Reimplemented from CProjectViewBase.

◆ OnQuerySequenceSetSelected()

void CBLASTSearchOptionsPanel::OnQuerySequenceSetSelected ( wxCommandEvent & event )

Definition at line 642 of file blast_search_options_panel.cpp.

References CBLASTSearchOptionsPanel::m_CurrentQuerySet, ToStdString(), and CBLASTSearchOptionsPanel::x_FillQueryList().

◆ OnRepeatTypeSelected()

void CBLASTSearchParamsPanel::OnRepeatTypeSelected ( wxCommandEvent & event )

Definition at line 576 of file blast_search_params_panel.cpp.

References CBLASTSearchParamsPanel::m_Local, and CBLASTSearchParamsPanel::m_WMTaxIds.

◆ OnResetBtnClick()

void CBLAST_DB_Dialog::OnResetBtnClick ( wxCommandEvent & event )

Definition at line 308 of file blast_db_dialog.cpp.

References kEmptyStr, CBLAST_DB_Dialog::m_SearchCtrl, wxT, and CBLAST_DB_Dialog::x_FilterItems().

◆ OnResetClick()

void CNetBlastDMSearchFormPanel::OnResetClick ( wxCommandEvent & event )

Definition at line 207 of file net_blast_dm_search_form_panel.cpp.

References CNetBlastDMSearchFormPanel::m_SearchCtrl, and wxT.

◆ OnSearchTextUpdated()

void CBLAST_DB_Dialog::OnSearchTextUpdated ( wxCommandEvent & event )

Definition at line 299 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::m_SearchCtrl, query, ToStdString(), and CBLAST_DB_Dialog::x_FilterItems().

◆ OnSelectLocalDB()

void CBLASTSearchOptionsPanel::OnSelectLocalDB ( wxCommandEvent & event )

Definition at line 999 of file blast_search_options_panel.cpp.

References CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::m_LocalDBCtrl, CBLASTSearchOptionsPanel::m_Params, CLBLASTParamsPanel::SelectDatabase(), CBLASTParams::SetLocalNucDB(), CBLASTParams::SetLocalProtDB(), and text().

◆ OnSomethingEdited()

void CPhyTreeView::OnSomethingEdited ( CEvent * evt )

Definition at line 1592 of file phy_tree_view.cpp.

References CUser_object::AddField(), CUser_object_Base::CanGetType(), command, CObject_id_Base::e_not_set, eCmdFeaturesEdited, eCmdGrpExpandCollapse, eCmdLabelFormatChanged, eCmdNodeExpandCollapse, eCmdRenderingOptionsChanged, eCmdTreeLabelSet, CStopWatch::Elapsed(), ICommandProccessor::Execute(), CEvent::GetAttachment(), CPhyloTreeWidget::GetCurrRenderer(), CUser_field_Base::GetData(), CPhyloTreeWidget::GetDS(), CUser_object::GetField(), CEvent::GetID(), CConstRef< C, Locker >::GetPointer(), CPhyloTreeWidget::GetRotateLabels(), CPhyloTreeWidget::GetScheme(), CPhyloTreeDataSource::GetTree(), CPhyloTreeDataSource::GetTreeLabel(), CUser_object_Base::GetType(), CPhyloTreeWidget::GetUseDistances(), CPhyTreeView::GetWidget(), CUser_object::HasField(), CPhyloTreeWidget::HasScheme(), CUser_field_Base::C_Data::IsBool(), CUser_field_Base::C_Data::IsInt(), CUser_object_Base::IsSetType(), CUser_field_Base::C_Data::IsStr(), CPhyTreeView::m_BioTreeContainer, m_CreateProperyUndoCommand, m_CreateUndoCommand, CPhyTreeView::m_DataSource, CPhyTreeView::m_EditUpdate, m_ExecutePropertyCommand, m_ExecuteUndoCommand, CPhyTreeView::m_Scheme, NULL, CRef< C, Locker >::Reset(), CStopWatch::Restart(), CTreeLabel::SaveToUserObject(), CUser_field_Base::SetData(), CUser_object::SetField(), CPhyloTreeScheme::SetLabelFormat(), CObject_id_Base::SetStr(), CUser_object_Base::SetType(), CBioTreeContainer_Base::SetUser(), CStopWatch::Start(), TreeConvert2Container(), CObject_id_Base::Which(), and CProjectView::x_GetUndoManager().

◆ OnStandaloneClick()

void CBLASTSearchParamsPanel::OnStandaloneClick ( wxCommandEvent & event )

Definition at line 617 of file blast_search_params_panel.cpp.

References CBLASTSearchParamsPanel::x_UpdateMaskCtrls().

◆ OnSubjectLocalDBSelected()

void CBLASTSearchOptionsPanel::OnSubjectLocalDBSelected ( wxCommandEvent & event )

Definition at line 987 of file blast_search_options_panel.cpp.

References CBLASTParams::eLocalDB, CBLASTSearchOptionsPanel::m_Params, CBLASTParams::SetSubjectType(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ OnSubjectNCBIDBSelected()

void CBLASTSearchOptionsPanel::OnSubjectNCBIDBSelected ( wxCommandEvent & event )

Definition at line 980 of file blast_search_options_panel.cpp.

References CBLASTParams::eNCBIDB, CBLASTSearchOptionsPanel::m_Params, CBLASTParams::SetSubjectType(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ OnSubjectSequenceSetSelected()

void CBLASTSearchOptionsPanel::OnSubjectSequenceSetSelected ( wxCommandEvent & event )

Definition at line 750 of file blast_search_options_panel.cpp.

References CBLASTSearchOptionsPanel::m_CurrentSubjectSet, ToStdString(), and CBLASTSearchOptionsPanel::x_FillSubjectList().

◆ OnSubjectSequencesSelected()

void CBLASTSearchOptionsPanel::OnSubjectSequencesSelected ( wxCommandEvent & event )

Definition at line 973 of file blast_search_options_panel.cpp.

References CBLASTParams::eSequences, CBLASTSearchOptionsPanel::m_Params, CBLASTParams::SetSubjectType(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ OnSubmittedCheckClick()

void CNetBlastDMSearchFormPanel::OnSubmittedCheckClick ( wxCommandEvent & event )

Definition at line 219 of file net_blast_dm_search_form_panel.cpp.

References CNetBlastDMSearchFormPanel::RestartSearch().

◆ OnTimer()

void CBLASTSearchOptionsPanel::OnTimer ( wxTimerEvent & event )

protected

Definition at line 923 of file blast_search_options_panel.cpp.

References CBLASTSearchOptionsPanel::x_CheckDBLoaded().

◆ OnTreectrlItemActivated()

void CBLAST_DB_Dialog::OnTreectrlItemActivated ( wxTreeEvent & event )

Definition at line 518 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::x_OnDatabaseSelected().

◆ OnTreectrlItemCollapsed()

void CBLAST_DB_Dialog::OnTreectrlItemCollapsed ( wxTreeEvent & event )

Definition at line 491 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::x_UpdateCollapsedState().

◆ OnTreectrlItemExpanded()

void CBLAST_DB_Dialog::OnTreectrlItemExpanded ( wxTreeEvent & event )

Definition at line 497 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::x_UpdateCollapsedState().

◆ OnTreectrlSelChanged()

void CBLAST_DB_Dialog::OnTreectrlSelChanged ( wxTreeEvent & event )

Definition at line 503 of file blast_db_dialog.cpp.

References data, CBLAST_Dlg_Item::IsDatabase(), CBLASTDlgItemData::m_Item, CBLAST_DB_Dialog::m_OKBtn, and CBLAST_DB_Dialog::m_TreeCtrl.

◆ OnTryAgain()

void CBLASTSearchOptionsPanel::OnTryAgain ( wxCommandEvent & event )

protected

Definition at line 915 of file blast_search_options_panel.cpp.

References CBLASTDatabases::GetInstance(), CBLASTDatabases::Load(), CSysPath::ResolvePath(), wxT, and CBLASTSearchOptionsPanel::x_CheckDBLoaded().

◆ OnVisibleRangeChanged() [1/3]

void CCrossAlignView::OnVisibleRangeChanged	(	const CVisibleRange &	vrange,
		IVisibleRangeClient *	source
	)

virtual

Reimplemented from CProjectView.

Definition at line 330 of file cross_align_view.cpp.

References CGlRect< T >::Bottom(), CVisibleRange::Clamp(), CCrossAlnWidget::GetPort(), CGlPane::GetVisibleRect(), CGlRect< T >::Left(), CCrossAlignView::m_AlnWidget, CCrossAlignView::m_DataSource, CVisibleRange::Match(), compile_time_bits::range(), CGlRect< T >::Right(), CCrossAlnWidget::SetQueryVisibleRange(), CCrossAlnWidget::SetSubjectVisibleRange(), and CGlRect< T >::Top().

◆ OnVisibleRangeChanged() [2/3]

void CDotMatrixView::OnVisibleRangeChanged	(	const CVisibleRange &	vrange,
		IVisibleRangeClient *	source
	)

virtual

Reimplemented from CProjectView.

Definition at line 336 of file dot_matrix_view.cpp.

References CGlRect< T >::Bottom(), CVisibleRange::Clamp(), CHitMatrixWidget::GetPort(), CGlPane::GetVisibleRect(), CGlRect< T >::Left(), CDotMatrixView::m_AlnWidget, CDotMatrixView::m_DataSource, CVisibleRange::Match(), compile_time_bits::range(), CGlRect< T >::Right(), CHitMatrixWidget::SetQueryVisibleRange(), CHitMatrixWidget::SetSubjectVisibleRange(), and CGlRect< T >::Top().

◆ OnVisibleRangeChanged() [3/3]

void CMPCrossAlignView::OnVisibleRangeChanged	(	const CVisibleRange &	vrange,
		IVisibleRangeClient *	source
	)

virtual

Reimplemented from CProjectView.

Definition at line 385 of file mp_cross_align_view.cpp.

References CMPCrossAlignView::m_Views, NON_CONST_ITERATE, IVisibleRangeClient::OnVisibleRangeChanged(), and rapidjson::source.

◆ OnWidgetRangeChanged()

void CAlignSpanView::OnWidgetRangeChanged ( )

virtual

Reimplemented from CProjectView.

Definition at line 566 of file align_span_view.cpp.

References CAlignSpanView::x_UpdateStatusMessage().

◆ OnWidgetSelChanged()

void CAlignSpanView::OnWidgetSelChanged ( )

virtual

Reimplemented from CProjectView.

Definition at line 548 of file align_span_view.cpp.

References CProjectView::OnWidgetSelChanged(), and CAlignSpanView::x_UpdateStatusMessage().

◆ OnWindowmaskerTaxIdSelected()

void CBLASTSearchParamsPanel::OnWindowmaskerTaxIdSelected ( wxCommandEvent & event )

Definition at line 582 of file blast_search_params_panel.cpp.

References CBLASTSearchParamsPanel::m_Local, and CBLASTSearchParamsPanel::m_RepeatType.

◆ OnWMDownload()

void CBLASTSearchParamsPanel::OnWMDownload ( wxCommandEvent & event )

Definition at line 589 of file blast_search_params_panel.cpp.

References CWinMaskerFileStorage::GetInstance(), CWinMaskerFileStorage::ShowOptionsDlg(), and CBLASTSearchParamsPanel::x_InitTaxons().

◆ Open()

bool CNetBLASTUIDataSource::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 224 of file net_blast_ui_data_source.cpp.

References NStr::DoubleToString(), CStopWatch::Elapsed(), ERR_POST, CBLASTDatabases::GetInstance(), CExtensionRegistry::GetInstance(), Info(), kAppExpCmdExtPoint, kCmdExtPoint, CBLASTDatabases::Load(), CNetBLASTUIDataSource::m_Open, CSysPath::ResolvePath(), CStopWatch::Start(), sw, t, wxT, CNetBLASTUIDataSource::x_AutoStartMonitoring(), and CNetBLASTUIDataSource::x_LoadJobDescriptors().

◆ operator=() [1/12]

void CClustalOmegaToolParams::operator= ( const CClustalOmegaToolParams & data )

Definition at line 60 of file clustal_omega_tool_params.cpp.

References CClustalOmegaToolParams::Copy(), and data.

◆ operator=() [2/12]

void CClustalwToolParams::operator= ( const CClustalwToolParams & data )

Definition at line 53 of file clustalw_tool_params.cpp.

References CClustalwToolParams::Copy(), and data.

◆ operator=() [3/12]

void CFindOverlapParams::operator= ( const CFindOverlapParams & data )

Definition at line 52 of file find_overlap_params.cpp.

References CFindOverlapParams::Copy(), and data.

◆ operator=() [4/12]

void CKalignToolParams::operator= ( const CKalignToolParams & data )

Definition at line 56 of file kalign_tool_params.cpp.

References CKalignToolParams::Copy(), and data.

◆ operator=() [5/12]

void CMafftToolParams::operator= ( const CMafftToolParams & data )

Definition at line 56 of file mafft_tool_params.cpp.

References CMafftToolParams::Copy(), and data.

◆ operator=() [6/12]

void CMuscleToolParams::operator= ( const CMuscleToolParams & data )

Definition at line 56 of file muscle_tool_params.cpp.

References CMuscleToolParams::Copy(), and data.

◆ operator=() [7/12]

void CNeedlemanWunschToolParams::operator= ( const CNeedlemanWunschToolParams & data )

Definition at line 52 of file needlemanwunsch_tool_params.cpp.

References CNeedlemanWunschToolParams::Copy(), and data.

◆ operator=() [8/12]

CNetBlastJobDescriptor& CNetBlastJobDescriptor::operator= ( const CNetBlastJobDescriptor & )

protected

◆ operator=() [9/12]

void CNGAlignParams::operator= ( const CNGAlignParams & data )

Definition at line 59 of file ngalign_params.cpp.

References CNGAlignParams::Copy(), and data.

◆ operator=() [10/12]

void CSplignParams::operator= ( const CSplignParams & data )

Definition at line 52 of file splign_params.cpp.

References CSplignParams::Copy(), and data.

◆ operator=() [11/12]

void CTaxTreeToolParams::operator= ( const CTaxTreeToolParams & data )

Definition at line 52 of file taxtree_tool_params.cpp.

References CTaxTreeToolParams::Copy(), and data.

◆ operator=() [12/12]

void CTreeBuilderParams::operator= ( const CTreeBuilderParams & data )

Definition at line 52 of file tree_builder_params.cpp.

References CTreeBuilderParams::Copy(), and data.

◆ operator==() [1/11]

bool CClustalOmegaToolParams::operator== ( const CClustalOmegaToolParams & data ) const

Definition at line 65 of file clustal_omega_tool_params.cpp.

References data, CClustalOmegaToolParams::m_ClustalOmegaPath, CClustalOmegaToolParams::m_CommandLine, and CClustalOmegaToolParams::m_GenerateTree.

◆ operator==() [2/11]

bool CClustalwToolParams::operator== ( const CClustalwToolParams & data ) const

Definition at line 57 of file clustalw_tool_params.cpp.

References data, CClustalwToolParams::m_ClustalWPath, CClustalwToolParams::m_CommandLine, and CClustalwToolParams::m_GenerateTree.

◆ operator==() [3/11]

bool CFindOverlapParams::operator== ( const CFindOverlapParams & data ) const

Definition at line 56 of file find_overlap_params.cpp.

References data, CFindOverlapParams::m_BlastParams, CFindOverlapParams::m_FilterQty, and CFindOverlapParams::m_MaxSlop.

◆ operator==() [4/11]

bool CKalignToolParams::operator== ( const CKalignToolParams & data ) const

Definition at line 61 of file kalign_tool_params.cpp.

References data, CKalignToolParams::m_CommandLine, CKalignToolParams::m_KalignPath, and CKalignToolParams::m_QuietFlag.

◆ operator==() [5/11]

bool CMafftToolParams::operator== ( const CMafftToolParams & data ) const

Definition at line 61 of file mafft_tool_params.cpp.

References data, CMafftToolParams::m_AutoFlag, CMafftToolParams::m_CommandLine, CMafftToolParams::m_MafftPath, and CMafftToolParams::m_QuietFlag.

◆ operator==() [6/11]

bool CMuscleToolParams::operator== ( const CMuscleToolParams & data ) const

Definition at line 61 of file muscle_tool_params.cpp.

References data, CMuscleToolParams::m_CommandLine, CMuscleToolParams::m_GenerateTree, CMuscleToolParams::m_MusclePath, and CMuscleToolParams::m_ScoringMethod.

◆ operator==() [7/11]

bool CNeedlemanWunschToolParams::operator== ( const CNeedlemanWunschToolParams & data ) const

Definition at line 56 of file needlemanwunsch_tool_params.cpp.

References data, CNeedlemanWunschToolParams::m_BandSize, CNeedlemanWunschToolParams::m_FirstSeqFreeEnds, CNeedlemanWunschToolParams::m_GapExtendCost, CNeedlemanWunschToolParams::m_GapOpenCost, CNeedlemanWunschToolParams::m_MatchCost, CNeedlemanWunschToolParams::m_MismatchCost, and CNeedlemanWunschToolParams::m_SecondSeqFreeEnds.

◆ operator==() [8/11]

bool CNGAlignParams::operator== ( const CNGAlignParams & data ) const

Definition at line 64 of file ngalign_params.cpp.

References data, CNGAlignParams::m_AdvParams, CNGAlignParams::m_BestHit, CNGAlignParams::m_eValue, CNGAlignParams::m_FilterMode, CNGAlignParams::m_JobTitle, CNGAlignParams::m_WM_Dir, CNGAlignParams::m_WM_TaxId, and CNGAlignParams::m_WordSize.

◆ operator==() [9/11]

bool CSplignParams::operator== ( const CSplignParams & data ) const

Definition at line 56 of file splign_params.cpp.

References data, CSplignParams::m_cDNA_strand, CSplignParams::m_CompPenalty, CSplignParams::m_DiscType, CSplignParams::m_EndGapDetect, CSplignParams::m_MaxGenomicExtent, CSplignParams::m_MaxIntron, CSplignParams::m_MinCompIdentity, CSplignParams::m_MinExonIdentity, and CSplignParams::m_PolyADetect.

◆ operator==() [10/11]

bool CTaxTreeToolParams::operator== ( const CTaxTreeToolParams & data ) const

Definition at line 56 of file taxtree_tool_params.cpp.

◆ operator==() [11/11]

bool CTreeBuilderParams::operator== ( const CTreeBuilderParams & data ) const

Definition at line 56 of file tree_builder_params.cpp.

References data, CTreeBuilderParams::m_ConstructMethod, CTreeBuilderParams::m_DistanceMethod, and CTreeBuilderParams::m_LeafLabels.

◆ PostExecute()

bool CTextAlignObjectLoader::PostExecute ( )

virtual

Implements IExecuteUnit.

Definition at line 123 of file text_align_object_loader.cpp.

References wxT, and CReportLoaderErrors::x_ShowErrorsDlg().

◆ PreExecute()

bool CTextAlignObjectLoader::PreExecute ( )

virtual

Implements IExecuteUnit.

Definition at line 82 of file text_align_object_loader.cpp.

◆ PrintParams()

void CBLASTParams::PrintParams ( const string & log_title ) const

◆ ProgressCallback()

bool CCreateNeedlemanWunschJob::ProgressCallback	(	const string &	status,
		float	done
	)

References _ASSERT, CObjectIndex::Clear(), CPhyloTreeDataSource::GetTree(), CPhyTreeView::m_DataSource, CPhyTreeView::m_ObjectIndex, TreeDepthFirst(), and CProjectViewBase::x_GetScope().

Referenced by CChangePhyloPropertyCmd::Execute(), CPhyTreeView::OnBioTreeChanged(), and CChangePhyloPropertyCmd::Unexecute().

◆ RecognizeFormat() [1/4]

bool CPslLoadManager::RecognizeFormat ( CFormatGuess::EFormat fmt )

virtual

return true if the given file format is supported by this manager

Implements IFileFormatLoaderManager.

Definition at line 223 of file psl_load_manager.cpp.

References CFormatGuess::ePsl.

◆ RecognizeFormat() [2/4]

bool CTextAlignLoaderManager::RecognizeFormat ( CFormatGuess::EFormat fmt )

virtual

return true if the given file format is supported by this manager

Implements IFileFormatLoaderManager.

Definition at line 219 of file text_align_load_manager.cpp.

References CFormatGuess::eAlignment.

◆ RecognizeFormat() [3/4]

bool CPslLoadManager::RecognizeFormat ( const wxString & filename )

virtual

return true if the given file format is supported by this manager

Implements IFileFormatLoaderManager.

Definition at line 216 of file psl_load_manager.cpp.

References CFileExtensions::kPSL, and CFileExtensions::RecognizeExtension().

◆ RecognizeFormat() [4/4]

bool CTextAlignLoaderManager::RecognizeFormat ( const wxString & filename )

virtual

return true if the given file format is supported by this manager

Implements IFileFormatLoaderManager.

Definition at line 212 of file text_align_load_manager.cpp.

References CFileExtensions::kTxt, and CFileExtensions::RecognizeExtension().

◆ RegisterCommands() [1/5]

void CCrossAlignViewFactory::RegisterCommands	(	CUICommandRegistry &	,
		wxFileArtProvider &
	)

virtual

called by the framework to give Factory a chance to register commands used by view

Reimplemented from IViewFactory.

Definition at line 385 of file cross_align_view.cpp.

References CCrossAlnWidget::RegisterCommands().

◆ RegisterCommands() [2/5]

void CDotMatrixViewFactory::RegisterCommands	(	CUICommandRegistry &	,
		wxFileArtProvider &
	)

virtual

called by the framework to give Factory a chance to register commands used by view

Reimplemented from IViewFactory.

Definition at line 395 of file dot_matrix_view.cpp.

References CHitMatrixWidget::RegisterCommands().

◆ RegisterCommands() [3/5]

void CMPCrossAlignViewFactory::RegisterCommands	(	CUICommandRegistry &	,
		wxFileArtProvider &
	)

virtual

called by the framework to give Factory a chance to register commands used by view

Reimplemented from IViewFactory.

Definition at line 424 of file mp_cross_align_view.cpp.

◆ RegisterCommands() [4/5]

void CMultiAlignViewFactory::RegisterCommands	(	CUICommandRegistry &	,
		wxFileArtProvider &
	)

virtual

called by the framework to give Factory a chance to register commands used by view

Reimplemented from IViewFactory.

Definition at line 613 of file multi_align_view.cpp.

References CAlnMultiWidget::RegisterCommands(), and WidgetsData_RegisterCommands().

◆ RegisterCommands() [5/5]

void CPhyTreeViewFactory::RegisterCommands	(	CUICommandRegistry &	,
		wxFileArtProvider &
	)

Definition at line 595 of file blast_search_params_panel.cpp.

References CBLASTSearchParamsPanel::m_Params, CBLASTParams::ResetCurrParams(), and CBLASTSearchParamsPanel::TransferDataToWindow().

void CNGAlignPanel::RestoreDefaults ( )

virtual

override in derived classes

Restores the default options for the panel

Implements CAlgoToolManagerParamsPanel.

Definition at line 314 of file ngalign_panel.cpp.

◆ RestoreDefaults() [12/12]

void CTaxTreeToolPanel::RestoreDefaults ( )

virtual

override in derived classes

Restores the default options for the panel

Implements CAlgoToolManagerParamsPanel.

Definition at line 173 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::GetData(), and CTaxTreeToolParams::Init().

◆ Retrieve()

CRef< CSeq_align_set > CNetBlastJobDescriptor::Retrieve ( )

Definition at line 337 of file net_blast_job_descr.cpp.

References CNetBlastJobDescriptor::eCompleted, CNetBlastJobDescriptor::eRetrieved, eUnknown, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_State, NCBI_THROW, CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded(), and CNetBlastJobDescriptor::x_NotifyDataSource().

Referenced by CNetBlastLoadingJob::x_CreateProjectItems().

◆ Run() [1/2]

IAppJob::EJobState CNetBlastSubmittingJob::Run ( )

virtual

Function that does all the useful work, called by the Engine.

Run() shall be implemented so that it will allow for exiting once RequestCancel() is called.

Implements IAppJob.

Definition at line 86 of file blast_jobs.cpp.

References IAppJob::eCompleted, IAppJob::eFailed, Error(), CNetBlastSubmittingJob::GetDescr(), CException::GetMsg(), ITERATE, LOG_POST, CNetBlastSubmittingJob::m_Error, CNetBlastSubmittingJob::m_Errors, CNetBlastSubmittingJob::m_Mutex, CException::ReportAll(), CRef< C, Locker >::Reset(), CNetBlastSubmittingJob::x_ResetState(), and CNetBlastSubmittingJob::x_Run().

◆ Run() [2/2]

IAppJob::EJobState CNetBlastMonitoringJob::Run ( )

virtual

Function that does all the useful work, called by the Engine.

Run() shall be implemented so that it will allow for exiting once RequestCancel() is called.

Implements IAppJob.

Definition at line 285 of file blast_jobs.cpp.

References IAppJob::eFailed, Error(), CNetBlastMonitoringJob::GetDescr(), CException::GetMsg(), ITERATE, LOG_POST, CNetBlastMonitoringJob::m_Error, CNetBlastMonitoringJob::m_Errors, CNetBlastMonitoringJob::m_Mutex, CException::ReportAll(), CRef< C, Locker >::Reset(), CNetBlastMonitoringJob::x_ResetState(), and CNetBlastMonitoringJob::x_Run().

◆ s_AssignFeatureIds()

void CCreateGeneModelTask::s_AssignFeatureIds	(	objects::CSeq_annot &	annot,
		objects::CObject_id::TId &	max_id
	)

static

Definition at line 754 of file create_gene_model_tool_manager.cpp.

References EDIT_EACH_SEQFEAT_ON_SEQANNOT, CSeq_feat_Base::GetId(), CFeat_id_Base::IsLocal(), CSeq_feat_Base::IsSetId(), CSeq_feat_Base::ResetId(), and CSeq_feat_Base::SetId().

Referenced by CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats(), and CCreateGeneModelTask::x_AssignIDsAndUpdateGenes().

◆ s_BlastInterrupt()

Boolean CBLASTSeqToolJob::s_BlastInterrupt ( SBlastProgress * prog )

static

static callback for BLAST interruption this must match the API in CBl2Seq and BLAST

Definition at line 109 of file blast_seq_tool_job.cpp.

References FALSE, CJobCancelable::IsCanceled(), prog, and TRUE.

Referenced by CBLASTSeqToolJob::x_CreateProjectItems().

◆ s_CreateDBXref()

void SGeneCdsmRnaFeats::s_CreateDBXref	(	const objects::CSeq_feat &	from_feat,
		objects::CSeq_feat &	to_feat,
		const string &	dbname
	)

static

Definition at line 253 of file create_gene_model_tool_manager.cpp.

References CSeq_feat::AddDbxref(), dbname(), CSeq_feat::GetNamedDbxref(), NStr::IsBlank(), CSeq_feat_Base::IsSetDbxref(), str(), and tag.

Referenced by SGeneCdsmRnaFeats::CrossLinkTriple().

◆ s_CreateXRefLink()

void SGeneCdsmRnaFeats::s_CreateXRefLink	(	objects::CSeq_feat &	from_feat,
		objects::CSeq_feat &	to_feat
	)

virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 391 of file blast_search_options_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kTableTag, CBLASTSearchOptionsPanel::m_QueryListCtrl, CAlgoToolManagerParamsPanel::m_RegPath, CBLASTSearchOptionsPanel::m_SubjectListCtrl, CGuiRegistryUtil::MakeKey(), and CwxTableListCtrl::SaveTableSettings().

Referenced by CBLASTToolManager::DoTransition(), and CBLASTToolManager::SaveSettings().

◆ SaveSettings() [3/33]

virtual void CBLASTSearchParamsPanel::SaveSettings ( ) const

inlinevirtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 120 of file blast_search_params_panel.hpp.

◆ SaveSettings() [4/33]

void CBLASTToolManager::SaveSettings ( ) const

virtual

◆ SaveSettings() [5/33]

void SCleanupAlignmentsParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 73 of file cleanup_alignments_params_panel.cpp.

◆ SaveSettings() [6/33]

void CCleanupAlignmentsParamsPanel::SaveSettings ( ) const

virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 270 of file cleanup_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kTableTag, CCleanupAlignmentsParamsPanel::m_ObjectList, CCleanupAlignmentsParamsPanel::m_RegPath, CGuiRegistryUtil::MakeKey(), and CwxTableListCtrl::SaveTableSettings().

◆ SaveSettings() [7/33]

void CClustalOmegaToolParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 102 of file clustal_omega_tool_params.cpp.

References FnToStdString(), CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kClustalwPath, kCommandLine, kGenerateTree, CClustalOmegaToolParams::m_ClustalOmegaPath, CClustalOmegaToolParams::m_CommandLine, CClustalOmegaToolParams::m_GenerateTree, CClustalOmegaToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

void SGroupAlignmentsParams::SaveSettings ( ) const

virtual

◆ SaveSettings() [12/33]

void CGroupAlignmentsParamsPanel::SaveSettings ( ) const

virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 291 of file group_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kTableTag, CGroupAlignmentsParamsPanel::m_ObjectList, CGroupAlignmentsParamsPanel::m_RegPath, CGuiRegistryUtil::MakeKey(), and CwxTableListCtrl::SaveTableSettings().

◆ SaveSettings() [13/33]

void CKalignToolParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 98 of file kalign_tool_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kAlignPath, kCommandLine, kQuietMode, CKalignToolParams::m_CommandLine, CKalignToolParams::m_KalignPath, CKalignToolParams::m_QuietFlag, CKalignToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [14/33]

void CMafftToolParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 102 of file mafft_tool_params.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kAutoFlag, kCommandLine, kMafftPath, kQuietMode, CMafftToolParams::m_AutoFlag, CMafftToolParams::m_CommandLine, CMafftToolParams::m_MafftPath, CMafftToolParams::m_QuietFlag, CMafftToolParams::m_RegPath, CRegistryWriteView::Set(), CGuiRegistry::Set(), and ToStdString().

◆ SaveSettings() [15/33]

void SMergeAlignmentsParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 79 of file merge_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kDirectionTag, kFillUnalignedTag, kMergeAlgoTag, kMergeFlagsTag, SMergeAlignmentsParams::m_Direction, SMergeAlignmentsParams::m_FillUnaligned, SMergeAlignmentsParams::m_MergeAlgo, SMergeAlignmentsParams::m_MergeFlags, SMergeAlignmentsParams::m_RegPath, and CRegistryWriteView::Set().

◆ SaveSettings() [16/33]

void CMergeAlignmentsParamsPanel::SaveSettings ( ) const

virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 296 of file merge_alignments_params_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kTableTag, CMergeAlignmentsParamsPanel::m_ObjectListCtrl, CMergeAlignmentsParamsPanel::m_RegPath, CGuiRegistryUtil::MakeKey(), and CwxTableListCtrl::SaveTableSettings().

◆ SaveSettings() [17/33]

void CMultiAlignView::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 567 of file multi_align_view.cpp.

References CMultiAlignView::m_AlnWidget, CMultiAlignView::m_RegPath, and CAlnMultiWidget::SaveSettings().

◆ SaveSettings() [18/33]

void CMuscleToolParams::SaveSettings ( ) const

virtual

Implements IRegSettings.

Implements CAlgoToolManagerParamsPanel.

Definition at line 345 of file splign_panel.cpp.

References CSplignPanel::m_cDNAList, CSplignPanel::m_GenomicList, and CObjectListWidgetSel::SaveSettings().

◆ SaveSettings() [25/33]

void CSplignParams::SaveSettings ( ) const

void CNGAlignPanel::SaveSettings ( ) const

virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 283 of file ngalign_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kTable1Tag, kTable2Tag, CNGAlignPanel::m_QueryListCtrl, CAlgoToolManagerParamsPanel::m_RegPath, CNGAlignPanel::m_SubjectListCtrl, CGuiRegistryUtil::MakeKey(), and CwxTableListCtrl::SaveTableSettings().

Referenced by CNGAlignTool::DoTransition().

◆ SaveSettings() [31/33]

void CPslLoadManager::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 246 of file psl_load_manager.cpp.

References CPslLoadManager::m_Params, and CPslLoadParams::SaveSettings().

◆ SaveSettings() [32/33]

void CTaxTreeToolPanel::SaveSettings ( ) const

virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 163 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::m_SeqIds, and CObjectListWidgetSel::SaveSettings().

◆ SaveSettings() [33/33]

void CTextAlignLoaderManager::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 247 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::m_Params, and CTextAlignParams::SaveSettings().

◆ SCleanupAlignmentsParams()

SCleanupAlignmentsParams::SCleanupAlignmentsParams ( )

Definition at line 48 of file cleanup_alignments_params_panel.cpp.

References SCleanupAlignmentsParams::Init().

◆ SelectDatabases()

void CBLAST_DB_Dialog::SelectDatabases ( vector< string > & databases )

Definition at line 285 of file blast_db_dialog.cpp.

void CNetBLAST_DMSearchForm::SetDataSource ( CNetBLASTUIDataSource * dataSource )

Definition at line 309 of file net_blast_dm_search_tool.cpp.

References CEventHandler::AddListener(), CNetBLAST_DMSearchForm::m_NetBlastDS, CEventHandler::RemoveListener(), and CRef< C, Locker >::Reset().

◆ SetDbGeneticCode()

void CBLASTSearchParamsPanel::SetDbGeneticCode ( wxString value )

inline

Definition at line 142 of file blast_search_params_panel.hpp.

References CBLASTSearchParamsPanel::m_DbGeneticCode, and rapidjson::value.

◆ SetDBMap()

void CBLAST_DB_Dialog::SetDBMap ( const TDbMap & map )

Definition at line 279 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::m_DbMap.

Referenced by CBLASTSearchOptionsPanel::OnBrowseDatabases().

◆ SetDiscType()

void CSplignParams::SetDiscType ( int value )

inline

Definition at line 81 of file splign_params.hpp.

References CSplignParams::m_DiscType, and rapidjson::value.

◆ SetDistanceMethod()

void CTreeBuilderParams::SetDistanceMethod ( wxString value )

void CPslLoadManager::SetFilenames ( const vector< wxString > & filenames )

virtual

initilize the manager with the given filenames

Implements IFileFormatLoaderManager.

Definition at line 200 of file psl_load_manager.cpp.

References filenames, and CPslLoadManager::m_FileNames.

◆ SetFilenames() [2/2]

void CTextAlignLoaderManager::SetFilenames ( const vector< wxString > & filenames )

virtual

void CBLAST_Dlg_Item::SetId ( const wxTreeItemId & id )

inline

Definition at line 102 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_Id.

Referenced by CBLAST_DB_Dialog::x_BuildTreeItems().

◆ SetInput()

void CNetBLASTLoadOptionPanel::SetInput ( const string & input )

Definition at line 177 of file net_blast_load_option_panel.cpp.

References _ASSERT, CNetBLASTLoadOptionPanel::ID_TEXTCTRL1, and input().

Referenced by CNetBLASTUILoadManager::GetCurrentPanel().

◆ SetInputObjects()

string CBLASTToolManager::SetInputObjects ( const vector< TConstScopedObjects > & input )

virtual

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

the manager can save the pointer, it will remain valid until CleanUI() is called.

Implements IUIAlgoToolManager.

Definition at line 332 of file blast_tool_manager.cpp.

References ITERATE, and CBLASTToolManager::m_InputObjects.

◆ SetJobTitle() [1/2]

void CBLASTSearchParamsPanel::SetJobTitle ( wxString value )

inline

Definition at line 151 of file blast_search_params_panel.hpp.

References CBLASTSearchParamsPanel::m_JobTitle, and rapidjson::value.

◆ SetJobTitle() [2/2]

void CNGAlignParams::SetJobTitle ( wxString value )

inline

Definition at line 97 of file ngalign_params.hpp.

References CNGAlignParams::m_JobTitle, and rapidjson::value.

◆ SetKalignPath()

void CKalignToolParams::SetKalignPath ( wxString value )

inline

Definition at line 84 of file kalign_tool_params.hpp.

References CKalignToolParams::m_KalignPath, and rapidjson::value.

◆ SetLeafLabels()

void CTreeBuilderParams::SetLeafLabels ( wxString value )

inline

Definition at line 88 of file tree_builder_params.hpp.

References CTreeBuilderParams::m_LeafLabels, and rapidjson::value.

Referenced by CTreeBuilderPanel::TransferDataFromWindow().

◆ SetLoadingOptions() [1/2]

void CNetBlastMonitoringJob::SetLoadingOptions ( CSelectProjectOptions & options )

virtual

Definition at line 279 of file blast_jobs.cpp.

References CNetBlastMonitoringJob::m_LoadingOptions.

Referenced by CBlastSearchTask::SetLoadingOptions(), and CBlastSearchTask::x_InitMonitoringStage().

◆ SetLoadingOptions() [2/2]

void CBlastSearchTask::SetLoadingOptions ( CSelectProjectOptions & options )

virtual

define how the task results shall be handled

Definition at line 160 of file blast_search_task.cpp.

References CRef< C, Locker >::GetPointerOrNull(), CBlastSearchTask::m_CurrTask, CBlastSearchTask::m_LoadingOptions, CBlastSearchTask::m_MonitoringJob, CNetBlastMonitoringJob::SetLoadingOptions(), and CDataLoadingAppTask::SetOptions().

Referenced by CNetBLASTUILoadManager::GetTask(), and CNetBLASTUIDataSource::x_StartTask().

◆ SetLocalDBLoader()

void CBLASTParams::SetLocalDBLoader ( bool value )

inline

Definition at line 208 of file blast_search_params.hpp.

References rapidjson::value.

Referenced by CBLASTSearchOptionsPanel::OnLocalDBLoaderClick().

◆ SetLocalNucDB()

void CBLASTParams::SetLocalNucDB ( const string & value )

inline

Definition at line 199 of file blast_search_params.hpp.

References rapidjson::value.

Referenced by CBLASTSearchOptionsPanel::OnSelectLocalDB(), and CBLASTSearchOptionsPanel::TransferDataFromWindow().

◆ SetLocalProtDB()

void CBLASTParams::SetLocalProtDB ( const string & value )

void CSplignPanel::SetObjects	(	map< string, TConstScopedObjects > *	genomic,
		map< string, TConstScopedObjects > *	na
	)

Definition at line 295 of file splign_panel.cpp.

References CSplignPanel::m_cDNAList, CSplignPanel::m_GenomicList, and CObjectListWidgetSel::SetObjects().

Referenced by CSplignTool::x_CreateParamsPanelIfNeeded().

◆ SetObjects() [9/13]

void CMuscleToolPanel::SetObjects ( map< string, TConstScopedObjects > * objects )

Definition at line 182 of file muscle_tool_panel.cpp.

References CMuscleToolPanel::m_LocationSel, and CObjectListWidgetSel::SetObjects().

Referenced by CMuscleTool::x_CreateParamsPanelIfNeeded().

◆ SetObjects() [10/13]

void CTaxTreeToolPanel::SetObjects ( map< string, TConstScopedObjects > * objects )

Definition at line 118 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::m_SeqIds, and CObjectListWidgetSel::SetObjects().

Referenced by CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded().

◆ SetObjects() [11/13]

void CFindOverlapPanel::SetObjects ( TConstScopedObjects * objects )

inline

Definition at line 116 of file find_overlap_panel.hpp.

References CFindOverlapPanel::m_InputObjects.

Referenced by CFindOverlapTool::x_CreateParamsPanelIfNeeded().

◆ SetObjects() [12/13]

void CTreeBuilderPanel::SetObjects ( TConstScopedObjects * objects )

inline

Definition at line 119 of file tree_builder_panel.hpp.

References CTreeBuilderPanel::m_InputObjects.

Referenced by CTreeBuilderTool::x_CreateParamsPanelIfNeeded().

◆ SetObjects() [13/13]

void CNGAlignPanel::SetObjects ( TConstScopedObjects * objects )

Definition at line 215 of file ngalign_panel.cpp.

References CObjectListWidget::Init(), CNGAlignPanel::LoadSettings(), CNGAlignPanel::m_QueryListCtrl, CNGAlignPanel::m_SubjectListCtrl, CRef< C, Locker >::Reset(), s_CreateObjList(), and s_GetMinMaxRows().

Referenced by CNGAlignTool::x_CreateParamsPanelIfNeeded().

◆ SetParams() [1/5]

void CBLASTSearchParamsPanel::SetParams ( CBLASTParams * params )

Definition at line 368 of file blast_search_params_panel.cpp.

References CBLASTSearchParamsPanel::m_Params.

Referenced by CBLASTToolManager::x_CreateParamsPanelIfNeeded().

◆ SetParams() [2/5]

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

Definition at line 152 of file blast_search_options_panel.cpp.

References _ASSERT, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, and CBLASTSearchOptionsPanel::m_ProtObjects.

Referenced by CBLASTToolManager::x_CreateOptionsPanelIfNeeded().

◆ SetParams() [3/5]

void CCleanupAlignmentsParamsPanel::SetParams	(	SCleanupAlignmentsParams *	params,
		TConstScopedObjects *	objects
	)

Definition at line 295 of file cleanup_alignments_params_panel.cpp.

References CCleanupAlignmentsParamsPanel::m_InputObjects, and CCleanupAlignmentsParamsPanel::m_Params.

Referenced by CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ SetParams() [4/5]

void CGroupAlignmentsParamsPanel::SetParams	(	SGroupAlignmentsParams *	params,
		TConstScopedObjects *	objects
	)

Definition at line 316 of file group_alignments_params_panel.cpp.

References CGroupAlignmentsParamsPanel::m_InputObjects, and CGroupAlignmentsParamsPanel::m_Params.

Referenced by CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ SetParams() [5/5]

void CMergeAlignmentsParamsPanel::SetParams	(	SMergeAlignmentsParams *	params,
		TConstScopedObjects *	objects
	)

Definition at line 235 of file merge_alignments_params_panel.cpp.

References CMergeAlignmentsParamsPanel::m_InputObjects, and CMergeAlignmentsParamsPanel::m_Params.

Referenced by CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ SetParentWindow() [1/4]

void CBLASTToolManager::SetParentWindow ( wxWindow * parent )

virtual

Implements IUIToolManager.

Definition at line 94 of file blast_tool_manager.cpp.

References CBLASTToolManager::m_ParentWindow.

void CMafftToolParams::SetQuietFlag ( bool value )

inline

Definition at line 90 of file mafft_tool_params.hpp.

References CMafftToolParams::m_QuietFlag, and rapidjson::value.

◆ SetRegistryPath() [1/28]

void CBLASTToolManager::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 535 of file blast_tool_manager.cpp.

References CBLASTToolManager::m_RegPath.

◆ SetRegistryPath() [2/28]

void CCleanupAlignmentsParamsPanel::SetRegistryPath ( const string & reg_path )

virtual

CAlgoToolManagerParamsPanel.

Reimplemented from CAlgoToolManagerParamsPanel.

Definition at line 262 of file cleanup_alignments_params_panel.cpp.

References CCleanupAlignmentsParamsPanel::m_RegPath.

Referenced by CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ SetRegistryPath() [3/28]

virtual void CClustalOmegaToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 71 of file clustal_omega_tool_params.hpp.

References CClustalOmegaToolParams::m_RegPath.

◆ SetRegistryPath() [4/28]

virtual void CClustalwToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file clustalw_tool_params.hpp.

References CClustalwToolParams::m_RegPath.

◆ SetRegistryPath() [5/28]

virtual void CFindOverlapParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file find_overlap_params.hpp.

References CFindOverlapParams::m_RegPath.

◆ SetRegistryPath() [6/28]

void CGroupAlignmentsParamsPanel::SetRegistryPath ( const string & reg_path )

virtual

CAlgoToolManagerParamsPanel.

Reimplemented from CAlgoToolManagerParamsPanel.

Definition at line 283 of file group_alignments_params_panel.cpp.

References CGroupAlignmentsParamsPanel::m_RegPath.

Referenced by CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ SetRegistryPath() [7/28]

virtual void CKalignToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file kalign_tool_params.hpp.

References CKalignToolParams::m_RegPath.

◆ SetRegistryPath() [8/28]

virtual void CMafftToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file mafft_tool_params.hpp.

References CMafftToolParams::m_RegPath.

◆ SetRegistryPath() [9/28]

void CMergeAlignmentsParamsPanel::SetRegistryPath ( const string & reg_path )

virtual

CAlgoToolManagerParamsPanel.

Reimplemented from CAlgoToolManagerParamsPanel.

Definition at line 288 of file merge_alignments_params_panel.cpp.

References CMergeAlignmentsParamsPanel::m_RegPath.

Referenced by CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ SetRegistryPath() [10/28]

virtual void CMuscleToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file muscle_tool_params.hpp.

References CMuscleToolParams::m_RegPath.

◆ SetRegistryPath() [11/28]

virtual void CNeedlemanWunschToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 77 of file needlemanwunsch_tool_params.hpp.

References CNeedlemanWunschToolParams::m_RegPath.

◆ SetRegistryPath() [12/28]

void CNetBLASTUIDataSource::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 180 of file net_blast_ui_data_source.cpp.

References CNetBLASTUIDataSource::m_RegPath.

◆ SetRegistryPath() [13/28]

void CNetBLASTUILoadManager::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 210 of file net_blast_ui_load_manager.cpp.

References CNetBLASTUILoadManager::m_RegPath.

◆ SetRegistryPath() [14/28]

virtual void CNGAlignParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 73 of file ngalign_params.hpp.

References CNGAlignParams::m_RegPath.

◆ SetRegistryPath() [15/28]

void CSplignPanel::SetRegistryPath ( const string & reg_path )

virtual

CAlgoToolManagerParamsPanel.

Reimplemented from CAlgoToolManagerParamsPanel.

Definition at line 338 of file splign_panel.cpp.

References kCDNAList, kGenomicList, CSplignPanel::m_cDNAList, CSplignPanel::m_GenomicList, CSplignPanel::m_RegPath, and CObjectListWidgetSel::SetRegistryPath().

Referenced by CSplignTool::x_CreateParamsPanelIfNeeded().

◆ SetRegistryPath() [16/28]

virtual void CSplignParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file splign_params.hpp.

References CSplignParams::m_RegPath.

◆ SetRegistryPath() [17/28]

virtual void CTaxTreeToolParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 72 of file taxtree_tool_params.hpp.

References CTaxTreeToolParams::m_RegPath.

◆ SetRegistryPath() [18/28]

virtual void CTreeBuilderParams::SetRegistryPath ( const string & path )

inlinevirtual

IRegSettings.

Implements IRegSettings.

Definition at line 74 of file tree_builder_params.hpp.

References CTreeBuilderParams::m_RegPath.

◆ SetRegistryPath() [19/28]

void CMuscleToolPanel::SetRegistryPath ( const string & reg_path )

virtual

CAlgoToolManagerParamsPanel.

Reimplemented from CAlgoToolManagerParamsPanel.

Definition at line 219 of file muscle_tool_panel.cpp.

References kLocationSel, CMuscleToolPanel::m_LocationSel, CAlgoToolManagerParamsPanel::m_RegPath, and CObjectListWidgetSel::SetRegistryPath().

Referenced by CMuscleTool::x_CreateParamsPanelIfNeeded().

◆ SetRegistryPath() [20/28]

void CPslLoadManager::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 240 of file psl_load_manager.cpp.

References CPslLoadManager::m_Params, CPslLoadManager::m_RegPath, and CPslLoadParams::SetRegistryPath().

◆ SetRegistryPath() [21/28]

void CTaxTreeToolPanel::SetRegistryPath ( const string & reg_path )

virtual

CAlgoToolManagerParamsPanel.

Reimplemented from CAlgoToolManagerParamsPanel.

Definition at line 157 of file taxtree_tool_panel.cpp.

References kLocationSel, CAlgoToolManagerParamsPanel::m_RegPath, CTaxTreeToolPanel::m_SeqIds, and CObjectListWidgetSel::SetRegistryPath().

Referenced by CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded().

◆ SetRegistryPath() [22/28]

void CTextAlignLoaderManager::SetRegistryPath ( const string & path )

virtual

Implements IRegSettings.

Definition at line 241 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::m_Params, CTextAlignLoaderManager::m_RegPath, and CTextAlignParams::SetRegistryPath().

◆ SetRegistryPath() [23/28]

void CAlignSpanView::SetRegistryPath ( const string & reg_path )

virtual

Implements IRegSettings.

Definition at line 184 of file align_span_view.cpp.

References CAlignSpanView::m_RegPath.

void CNetBlastDMSearchFormPanel::SetRetrieved ( bool value )

inline

Definition at line 109 of file net_blast_dm_search_form_panel.hpp.

References CNetBlastDMSearchFormPanel::m_Retrieved, and rapidjson::value.

◆ SetRIDs()

void CNetBlastLoadingJob::SetRIDs	(	CNetBLASTUIDataSource &	ds,
		const vector< string > &	RIDs
	)

Definition at line 496 of file blast_jobs.cpp.

References CNetBLASTUIDataSource::CreateJobDescriptor(), CNetBLASTUIDataSource::FindJobDescriptor(), i, and CNetBlastLoadingJob::m_Descriptors.

Referenced by CNetBlastLoadingJob::CNetBlastLoadingJob().

◆ SetScoringMethod()

void CMuscleToolParams::SetScoringMethod ( int value )

inline

Definition at line 90 of file muscle_tool_params.hpp.

References CMuscleToolParams::m_ScoringMethod, and rapidjson::value.

◆ SetSearchValue()

void CNetBlastDMSearchFormPanel::SetSearchValue ( wxString value )

inline

Definition at line 115 of file net_blast_dm_search_form_panel.hpp.

References CNetBlastDMSearchFormPanel::m_SearchValue, and rapidjson::value.

◆ SetSecondSeqFreeEnds()

void CNeedlemanWunschToolParams::SetSecondSeqFreeEnds ( int value )

inline

Definition at line 104 of file needlemanwunsch_tool_params.hpp.

References CNeedlemanWunschToolParams::m_SecondSeqFreeEnds, and rapidjson::value.

◆ SetSelection()

void CMPCrossAlignView::SetSelection ( CSelectionEvent & evt )

virtual

handles selection broadcast received from Selection Service this function acts as a shell, it controlls state and catches exceptions.

all real work is performed by x_OnSetSelection() that shall be implemented in derived classes

Reimplemented from CProjectView.

Definition at line 325 of file mp_cross_align_view.cpp.

References CMPCrossAlignView::m_Views, and NON_CONST_ITERATE.

◆ SetSeq1()

SConstScopedObject& CFindOverlapParams::SetSeq1 ( )

inline

Definition at line 77 of file find_overlap_params.hpp.

References CFindOverlapParams::m_Seq1.

Referenced by CFindOverlapPanel::TransferDataFromWindow().

◆ SetSeq2()

SConstScopedObject& CFindOverlapParams::SetSeq2 ( )

inline

Definition at line 80 of file find_overlap_params.hpp.

References CFindOverlapParams::m_Seq2.

Referenced by CFindOverlapPanel::TransferDataFromWindow().

◆ SetServiceLocator() [1/6]

void CNetBLAST_DMSearchTool::SetServiceLocator ( IServiceLocator * locator )

virtual

Implements IServiceLocatorConsumer.

Definition at line 227 of file net_blast_dm_search_tool.cpp.

SConstScopedObject& CNGAlignParams::SetSubject ( )

inline

Definition at line 78 of file ngalign_params.hpp.

References CNGAlignParams::m_Subject.

Referenced by CNGAlignTool::x_CreateLoadingJob().

◆ SetSubject() [2/2]

SConstScopedObject& CNGAlignPanel::SetSubject ( void )

void CBLAST_Dlg_Item::SetVisible ( bool visible )

inline

Definition at line 89 of file blast_db_dialog.hpp.

References CBLAST_Dlg_Item::m_Visible.

Referenced by CBLAST_DB_Dialog::x_FilterItems().

void CBLASTSearchParamsPanel::SetWordSize ( long value )

inline

Definition at line 160 of file blast_search_params_panel.hpp.

References CBLASTSearchParamsPanel::m_WordSize, and rapidjson::value.

◆ SetWordSize() [2/2]

void CNGAlignParams::SetWordSize ( long value )

inline

Definition at line 88 of file ngalign_params.hpp.

References CNGAlignParams::m_WordSize, and rapidjson::value.

◆ SetWorkbench()

void CMPCrossAlignView::SetWorkbench ( IWorkbench * workbench )

virtual

IView implementation.

Reimplemented from CProjectView.

Definition at line 130 of file mp_cross_align_view.cpp.

References CProjectViewBase::SetWorkbench().

◆ SGeneCdsmRnaFeats()

SGeneCdsmRnaFeats::SGeneCdsmRnaFeats ( )

inline

Definition at line 102 of file create_gene_model_tool_manager.hpp.

◆ SGroupAlignmentsParams()

SGroupAlignmentsParams::SGroupAlignmentsParams ( )

Definition at line 62 of file group_alignments_params_panel.cpp.

References Init().

bool CMuscleToolPanel::ShowToolTips ( )

static

Definition at line 187 of file muscle_tool_panel.cpp.

Referenced by CMuscleToolPanel::CreateControls().

◆ ShowToolTips() [13/14]

bool CNGAlignPanel::ShowToolTips ( )

static

Definition at line 134 of file ngalign_panel.cpp.

◆ ShowToolTips() [14/14]

bool CTaxTreeToolPanel::ShowToolTips ( )

static

Definition at line 123 of file taxtree_tool_panel.cpp.

◆ SMergeAlignmentsParams()

SMergeAlignmentsParams::SMergeAlignmentsParams ( )

SMergeAlignmentsParams.

Definition at line 56 of file merge_alignments_params_panel.cpp.

References SMergeAlignmentsParams::Init().

◆ SProgParams() [1/2]

CBLASTParams::SProgParams::SProgParams ( )

Definition at line 77 of file blast_search_params.cpp.

◆ SProgParams() [2/2]

CBLASTParams::SProgParams::SProgParams	(	int	thresh,
		int	word,
		double	ev,
		bool	low_c,
		int	query_gen_code,
		int	db_gen_code
	)

Definition at line 91 of file blast_search_params.cpp.

◆ StandaloneRequested()

void CBLASTParams::StandaloneRequested ( bool req )

inline

Definition at line 160 of file blast_search_params.hpp.

Referenced by CBLASTSearchParamsPanel::TransferDataFromWindow().

◆ StartMonitoringTask()

void CNetBLASTUIDataSource::StartMonitoringTask ( TJobDescrVec & descriptors )

Definition at line 548 of file net_blast_ui_data_source.cpp.

References CNetBLASTUIDataSource::m_SrvLocator, and CNetBLASTUIDataSource::x_StartTask().

Referenced by CNetBlastDSEvtHandler::OnMonitor(), and CNetBLASTUIDataSource::x_AutoStartMonitoring().

◆ StartRetrievingTask()

void CNetBLASTUIDataSource::StartRetrievingTask ( TJobDescrVec & descriptors )

Definition at line 533 of file net_blast_ui_data_source.cpp.

References CNetBlastJobDescriptor::GetRID(), i, CNetBLASTUIDataSource::m_SrvLocator, and CNetBLASTUIDataSource::x_StartTask().

Referenced by CNetBlastDSEvtHandler::OnRetrieve().

◆ Submit()

void CNetBlastJobDescriptor::Submit ( objects::CBioseq_set & seq_set )

Definition at line 279 of file net_blast_job_descr.cpp.

References _ASSERT, CNetBlastJobDescriptor::eInitial, CNetBlastJobDescriptor::eSubmitted, eUnknown, CNetBlastJobDescriptor::m_Mutex, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_RID, CNetBlastJobDescriptor::m_State, CNetBlastJobDescriptor::m_SubmitTime, NCBI_THROW, and CNetBlastJobDescriptor::x_NotifyDataSource().

CArgs * CBLASTParams::ToArgs ( vector< string > & argv ) const

Definition at line 1041 of file blast_search_params.cpp.

References eBlastn, eBlastp, eBlastx, eDiscMegablast, eMegablast, EProgramToTaskName(), eTblastn, eTblastx, eUnknown, CBLASTParams::GetCurrProgram(), NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToArgVec().

◆ ToArgVec()

vector< string > & CBLASTParams::ToArgVec ( vector< string > & arg_vec ) const

Definition at line 952 of file blast_search_params.cpp.

Referenced by CBLASTParams::ToArgs(), CBLASTParams::ToArgVecBlastOptions(), and CBLASTParams::ToBlastOptions().

◆ ToArgVecBlastOptions()

CRef< blast::CBlastOptionsHandle > CBLASTParams::ToArgVecBlastOptions	(	vector< string > &	arg_vec,
		bool	local = `true`
	)		const

Definition at line 751 of file blast_search_params.cpp.

References CBlastOptionsFactory::Create(), eBlastn, eBlastp, eBlastx, eDiscMegablast, CBlastOptions::eLocal, eMegablast, EProgramToTaskName(), CBlastOptions::eRemote, eTblastn, eTblastx, eUnknown, CBLASTParams::GetCurrProgram(), kTask, local, NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToArgVec().

Referenced by CBLASTSeqToolJob::x_CreateProjectItems().

◆ ToBlastOptions()

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

Definition at line 820 of file blast_search_params.cpp.

References CBlastOptionsFactory::Create(), eBlastn, eBlastp, eBlastx, eDiscMegablast, CBlastOptions::eLocal, eMegablast, EProgramToTaskName(), CBlastOptions::eRemote, eTblastn, eTblastx, eUnknown, CBLASTParams::GetCurrProgram(), local, NCBI_THROW, CRef< C, Locker >::Reset(), and CBLASTParams::ToArgVec().

Referenced by CNetBlastJobDescriptor::Init(), and CBLASTToolManager::x_ValidateParams().

◆ ToString()

string CNetBLAST_DMSearchQuery::ToString ( ) const

virtual

Prepare a string representation of a query (for logging and debugging)

Implements IDMSearchQuery.

Definition at line 364 of file net_blast_dm_search_tool.cpp.

References CNetBLAST_DMSearchQuery::m_FilterStr.

◆ ToUserObject() [1/2]

CUser_object * CBLASTParams::ToUserObject ( ) const

Definition at line 503 of file blast_search_params.cpp.

References CUser_object::AddField(), CMRUList< T >::GetItems(), CBLASTParams::GetProgramLabel(), ITERATE, kAdvParamsTag, kBLASTParamsTag, kEntrezQueryTag, kJobTitleTag, kLocalDBLoader, kLocalNucDB, kLocalProtDB, kNucDBTag, kNucMRUDBsTag, kNucProgTag, kProtDBTag, kProtMRUDBsTag, kProtProgTag, kSubjectType, CBLASTParams::m_AdvancedParams, CBLASTParams::m_EntrezQuery, CBLASTParams::m_JobTitle, CBLASTParams::m_LocalDBLoader, CBLASTParams::m_LocalNucDB, CBLASTParams::m_LocalProtDB, CBLASTParams::m_NucDatabase, CBLASTParams::m_NucMRUDatabases, CBLASTParams::m_NucProgram, CBLASTParams::m_ProgToParams, CBLASTParams::m_ProtDatabase, CBLASTParams::m_ProtMRUDatabases, CBLASTParams::m_ProtProgram, CBLASTParams::m_SubjectType, CRef< C, Locker >::Release(), CUser_object_Base::SetType(), val, and CBLASTParams::x_ToUserObject().

Referenced by CBLASTToolManager::SaveSettings().

◆ ToUserObject() [2/2]

CUser_object * CNetBlastJobDescriptor::ToUserObject ( ) const

◆ TransferDataFromWindow() [1/11]

bool CBLASTSearchOptionsPanel::TransferDataFromWindow ( )

Definition at line 453 of file blast_search_options_panel.cpp.

Referenced by CBLASTToolManager::DoTransition().

◆ TransferDataFromWindow() [2/11]

bool CBLASTSearchParamsPanel::TransferDataFromWindow ( )

Definition at line 521 of file blast_search_params_panel.cpp.

Referenced by CBLASTToolManager::DoTransition().

◆ TransferDataFromWindow() [3/11]

Referenced by CBLASTToolManager::DoTransition(), and CBLASTSearchOptionsPanel::RestoreDefaults().

◆ TransferDataToWindow() [2/8]

bool CBLASTSearchParamsPanel::TransferDataToWindow ( )

Definition at line 413 of file blast_search_params_panel.cpp.

Referenced by CBLASTToolManager::DoTransition(), and CBLASTSearchParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [3/8]

bool CCleanupAlignmentsParamsPanel::TransferDataToWindow ( )

Definition at line 303 of file cleanup_alignments_params_panel.cpp.

Referenced by CCleanupAlignmentsParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [4/8]

bool CFindOverlapPanel::TransferDataToWindow ( )

virtual

Definition at line 184 of file find_overlap_panel.cpp.

References CFindOverlapPanel::m_InputObjects, CFindOverlapPanel::m_Seq1List, CFindOverlapPanel::m_Seq2List, and CObjectListWidget::SetObjects().

◆ TransferDataToWindow() [5/8]

bool CGroupAlignmentsParamsPanel::TransferDataToWindow ( )

Definition at line 324 of file group_alignments_params_panel.cpp.

Referenced by CGroupAlignmentsParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [6/8]

bool CMergeAlignmentsParamsPanel::TransferDataToWindow ( )

Definition at line 243 of file merge_alignments_params_panel.cpp.

Referenced by CMergeAlignmentsParamsPanel::RestoreDefaults().

◆ TransferDataToWindow() [7/8]

bool CNetBlastDMSearchFormPanel::TransferDataToWindow ( )

Definition at line 233 of file net_blast_dm_search_form_panel.cpp.

References CNetBlastDMSearchFormPanel::m_BlockEvents.

Referenced by CNetBLAST_DMSearchForm::Update().

◆ TransferDataToWindow() [8/8]

bool CTreeBuilderPanel::TransferDataToWindow ( )

virtual

Definition at line 199 of file tree_builder_panel.cpp.

References CTreeBuilderPanel::m_InputObjects, CTreeBuilderPanel::m_Seq1List, CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CTreeBuilderPanel::RestoreDefaults().

◆ Update()

void CNetBLAST_DMSearchForm::Update ( void )

virtual

Implements IDMSearchForm.

Definition at line 269 of file net_blast_dm_search_tool.cpp.

References _ASSERT, CNetBLAST_DMSearchForm::m_Panel, and CNetBlastDMSearchFormPanel::TransferDataToWindow().

◆ UpdateContexts()

void CNetBLAST_DMSearchForm::UpdateContexts ( )

void CBLASTParams::x_AddProgramParams	(	blast::EProgram	program,
		int	thresh,
		int	word,
		int	ev
	)

protected

◆ x_AddTreeProjectItem()

void CMSAToolJob::x_AddTreeProjectItem	(	const string &	title,
		const string &	comment
	)

protectedvirtual

◆ x_AdjustToAlgoSelector()

void CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector ( )

private

Switch params panel according to current algo-selector.

Definition at line 227 of file cleanup_alignments_params_panel.cpp.

References CCleanupAlignmentsParamsPanel::m_AlgoSelector, and CCleanupAlignmentsParamsPanel::m_ParamsPanel.

Referenced by CCleanupAlignmentsParamsPanel::OnComboboxSelected(), and CCleanupAlignmentsParamsPanel::TransferDataToWindow().

◆ x_AreSelfAlignmentsOnly()

bool CCleanupAlignmentsToolManager::x_AreSelfAlignmentsOnly ( ) const

protected

Definition at line 151 of file cleanup_alignments_tool_manager.cpp.

References CSeq_align::CheckNumRows(), CSeq_id_Handle::GetHandle(), CSeq_align::GetSeq_id(), set< Key, Compare >::insert(), ITERATE, CCleanupAlignmentsToolManager::m_Alignments, and set< Key, Compare >::size().

Referenced by CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ x_ArgsToBlastOptions()

void CBLASTParams::x_ArgsToBlastOptions	(	const string &	cmd_line,
		blast::CBlastOptions &	opts
	)		const

protected

Definition at line 1083 of file blast_search_params.cpp.

References eUnknown, NCBI_THROW, s_NextToken(), string, NStr::StringToDouble(), NStr::StringToInt(), and val.

◆ x_AssignIDsAndCrossLinkFeats()

void CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats	(	objects::CSeq_annot &	annot,
		const objects::CSeq_id_Handle &	idh,
		objects::CObject_id::TId	max_id
	)

private

Definition at line 742 of file create_gene_model_tool_manager.cpp.

References SGeneCdsmRnaFeats::CrossLinkTriple(), CCreateGeneModelTask::m_GeneModelMap, NON_CONST_ITERATE, CCreateGeneModelTask::s_AssignFeatureIds(), CCreateGeneModelTask::s_FeaturesHaveIDs(), and CCreateGeneModelTask::s_FeaturesHaveXrefs().

Referenced by CCreateGeneModelTask::x_GetCommand().

◆ x_AssignIDsAndUpdateGenes()

CRef< CCmdComposite > CCreateGeneModelTask::x_AssignIDsAndUpdateGenes	(	objects::CSeq_annot &	annot,
		const objects::CSeq_id_Handle &	idh,
		objects::CSeq_entry_Handle	seh
	)

private

Definition at line 798 of file create_gene_model_tool_manager.cpp.

Referenced by CCreateGeneModelTask::x_GetCommand().

◆ x_AutoStartMonitoring()

void CNetBLASTUIDataSource::x_AutoStartMonitoring ( )

protected

Definition at line 604 of file net_blast_ui_data_source.cpp.

References CNetBlastJobDescriptor::eSubmitted, i, Info(), LOG_POST, CNetBLASTUIDataSource::m_JobDescrMutex, CNetBLASTUIDataSource::m_JobDescrs, n, and CNetBLASTUIDataSource::StartMonitoringTask().

Referenced by CNetBLASTUIDataSource::Open().

◆ x_BuildTreeItems()

void CBLAST_DB_Dialog::x_BuildTreeItems ( CBLAST_Dlg_Item & item )

protected

Definition at line 377 of file blast_db_dialog.cpp.

References data, CBLAST_Dlg_Item::GetChildItems(), CBLAST_Dlg_Item::GetId(), CBLAST_Dlg_Item::GetLabel(), CBLAST_Dlg_Item::GetParent(), CBLAST_Dlg_Item::IsExpanded(), CBLAST_Dlg_Item::IsVisible(), label, CBLAST_DB_Dialog::m_TreeCtrl, NON_CONST_ITERATE, and CBLAST_Dlg_Item::SetId().

Referenced by CBLAST_DB_Dialog::x_CreateTreeItems().

CRef< CSearchJobBase > CNetBLAST_DMSearchTool::x_CreateJob ( IDMSearchQuery & query )

protectedvirtual

implementing CSearchToolBase pure virtual function

Implements CSearchToolBase.

Definition at line 186 of file net_blast_dm_search_tool.cpp.

References _ASSERT, query, CRef< C, Locker >::Reset(), and CNetBLAST_DMSearchTool::x_GetDataSource().

◆ x_CreateLoadingJob() [1/17]

CDataLoadingAppJob * CCleanupAlignmentsToolManager::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 191 of file cleanup_alignments_tool_manager.cpp.

References CCleanupAlignmentsToolManager::m_Params.

◆ x_CreateLoadingJob() [2/17]

CDataLoadingAppJob * CClustalOmegaTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 125 of file clustal_omega_tool.cpp.

References CClustalOmegaToolPanel::GetData(), CClustalOmegaTool::m_Panel, and CClustalOmegaTool::m_Params.

◆ x_CreateLoadingJob() [3/17]

CDataLoadingAppJob * CClustalwTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 125 of file clustalw_tool.cpp.

References CClustalwToolPanel::GetData(), CClustalwTool::m_Panel, and CClustalwTool::m_Params.

CDataLoadingAppJob * CKalignTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 124 of file kalign_tool.cpp.

References CKalignToolPanel::GetData(), CKalignTool::m_Panel, and CKalignTool::m_Params.

Referenced by CKalignTool::QuickLaunch().

◆ x_CreateLoadingJob() [8/17]

CDataLoadingAppJob * CMafftTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 124 of file mafft_tool.cpp.

References CMafftToolPanel::GetData(), CMafftTool::m_Panel, and CMafftTool::m_Params.

Referenced by CMafftTool::QuickLaunch().

◆ x_CreateLoadingJob() [9/17]

CDataLoadingAppJob * CMergeAlignmentsToolManager::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 163 of file merge_alignments_tool_manager.cpp.

References CMergeAlignmentsToolManager::m_Params.

◆ x_CreateLoadingJob() [10/17]

CDataLoadingAppJob * CMuscleTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 124 of file muscle_tool.cpp.

References CMuscleToolPanel::GetData(), CMuscleTool::m_Panel, and CMuscleTool::m_Params.

Referenced by CMuscleTool::QuickLaunch().

◆ x_CreateLoadingJob() [11/17]

CDataLoadingAppJob * CNGAlignTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 288 of file ngalign_tool.cpp.

References CNGAlignBLASTPanel::GetData(), CNGAlignPanel::GetQueries(), CNGAlignPanel::GetSubject(), CNGAlignTool::m_BLASTPanel, CNGAlignTool::m_Panel, CNGAlignTool::m_Params, CNGAlignParams::SetQueries(), and CNGAlignParams::SetSubject().

◆ x_CreateLoadingJob() [12/17]

CDataLoadingAppJob * CProSplignTool::x_CreateLoadingJob ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 169 of file prosplign_tool.cpp.

References _ASSERT, copy(), CDebugDumpable::DebugDumpText(), CProSplignPanel::GetData(), CProSplignPanel::GetNucleotideSeqs(), CProSplignPanel::GetProteinSeq(), CProSplignTool::m_NAObjects, CProSplignTool::m_Panel, CProSplignTool::m_Params, CProSplignTool::m_ProteinObjects, and NON_CONST_ITERATE.

◆ x_CreateLoadingJob() [13/17]

CDataLoadingAppJob * CSplignTool::x_CreateLoadingJob ( )

void CDotMatrixView::x_CreateMenuBarMenu ( )

protectedvirtual

initializes m_MenuBarMenu; override in derived classes

Reimplemented from CProjectViewBase.

Definition at line 94 of file dot_matrix_view.cpp.

References CUICommandRegistry::AppendMenuItem(), eCmdChooseSeq, eCmdColorByScore, IWorkbench::GetUICommandRegistry(), CProjectViewBase::m_MenuBarMenu, CProjectViewBase::m_Workbench, wxID_ANY, and wxT.

void CBLASTToolManager::x_CreateOptionsPanelIfNeeded ( )

protectedvirtual

bool CNGAlignTool::x_CreateParamsPanelIfNeeded ( )

bool CCreateNeedlemanWunschToolManager::x_CreateParamsPanelIfNeeded ( )

protectedvirtual

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

Implements CAlgoToolManagerBase.

Definition at line 109 of file create_needleman_wunsch_tool_manager.cpp.

References CAlignNeedlemanWunschPanel::Create(), CAlignNeedlemanWunschPanel::LoadSettings(), CCreateNeedlemanWunschToolManager::m_Objects, CCreateNeedlemanWunschToolManager::m_Panel, CCreateNeedlemanWunschToolManager::m_Params, CAlgoToolManagerBase::m_ParentWindow, CAlgoToolManagerBase::m_RegPath, NULL, CAlignNeedlemanWunschPanel::SetData(), CAlignNeedlemanWunschPanel::SetObjects(), CAlignNeedlemanWunschPanel::SetRegistryPath(), and CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects().

◆ x_CreateProjectItems() [1/12]

void CNetBlastLoadingJob::x_CreateProjectItems ( )

protectedvirtual

iterates on the given RIDs and creates Project Items or accumulates error

Implements CDataLoadingAppJob.

Definition at line 524 of file blast_jobs.cpp.

◆ x_CreateProjectItems() [2/12]

void CBLASTSeqToolJob::x_CreateProjectItems ( )

protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 141 of file blast_seq_tool_job.cpp.

References CMappingRanges::AddConversion(), CDataLoadingAppJob::AddProjectItem(), CLBLASTObjectLoader::CreateLoader(), CDebugDumpable::DebugDumpText(), CSeq_id_Base::e_Local, CTime::eCurrent, CLabel::eDefault, CBLASTParams::eLocalDB, eNa_strand_plus, CExec::eNoWait, EProgramToTaskName(), ERR_POST, Error(), CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CBLASTParams::eSequences, eSerial_AsnText, FindCompartments(), CSeq_annot_Base::C_Data::GetAlign(), CScope::GetBioseqHandle(), CBLASTParams::GetCurrParams(), CBLASTParams::GetCurrProgram(), CSeq_annot_Base::GetData(), CIOException::GetErrCodeString(), CProcess::CExitInfo::GetExitCode(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CLabel::GetLabel(), GetLength(), CBLASTParams::GetLocalDBLoader(), CBLASTParams::GetLocalNucDB(), CBLASTParams::GetLocalProtDB(), CException::GetMsg(), CBlastOptionsHandle::GetOptions(), CRef< C, Locker >::GetPointer(), CExec::CResult::GetProcessHandle(), CBLASTParams::GetSeqLocs(), GetStart(), CSysPath::GetStdPath(), GetStrand(), CBLASTParams::GetSubjectType(), CBLASTParams::GetSubjSeqLocs(), CDirEntry::GetTmpName(), CBLASTParams::GetWmDir(), i, Info(), NStr::IntToString(), CSeq_annot::IsAlign(), CJobCancelable::IsCanceled(), CBLASTParams::IsCompartmentsRequested(), CBLASTParams::IsNucInput(), CBioseq_Handle::IsNucleotide(), CRef< C, Locker >::IsNull(), CBLASTParams::IsStandaloneRequested(), CBLASTParams::IsSubjNucInput(), CSeq_loc_Base::IsWhole(), ITERATE, kArgDb, kArgOutput, kArgQuery, kArgSubject, kInfiniteTimeoutMs, kInvalidProcHandle, label, LOG_POST, CBLASTParams::SProgParams::m_MaskLowercase, CBLASTParams::SProgParams::m_MaskRepeats, CBLASTSeqToolJob::m_Params, CBLASTSeqToolJob::m_ProcHandle, CBLASTParams::SProgParams::m_WM_TaxId, CSeq_loc_Mapper_Base::Map(), MSerial_AsnText, NON_CONST_ITERATE, nuc, NULL, CObjectOStream::Open(), CDirEntry::Remove(), CBl2Seq::Run(), CBLASTSeqToolJob::s_BlastInterrupt(), SSeqLoc::scope, SSeqLoc::seqloc, CSeq_align_set_Base::Set(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CBl2Seq::SetInterruptCallback(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSeq_annot::SetNameDesc(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CSeq_annot::SetTitleDesc(), si, CExec::SpawnV(), CBLASTParams::ToArgVecBlastOptions(), ToWxString(), CProcess::Wait(), Warning(), WindowMaskerPathGet(), WindowMaskerPathInit(), CFastaOstream::Write(), wxT, CAppJob::x_SetStatusText(), and x_ToBlastVec().

◆ x_CreateProjectItems() [3/12]

void CCleanupAlignmentsJob::x_CreateProjectItems ( )

protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 230 of file cleanup_alignments_tool_manager.cpp.

void CDebugMacroToolJob::x_CreateProjectItems ( )

protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 57 of file debug_macro_tool_job.cpp.

◆ x_CreateProjectItems() [11/12]

void CCreateNeedlemanWunschJob::x_CreateProjectItems ( )

protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 200 of file create_needleman_wunsch_tool_manager.cpp.

◆ x_CreateProjectItems() [12/12]

void CBLASTSeqToolJob::x_CreateProjectItems ( vector< CRef< objects::CSeq_align_set > > & aligns )

protected

◆ x_CreateProjectItemsFromBlastResult()

void CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult	(	objects::CSeq_align_set &	results,
		CRef< blast::CRemoteBlast >	RemoteBlast
	)

protected

Definition at line 573 of file blast_jobs.cpp.

References CGBProjectHelper::AddProjectItemsFromRID(), CObjectManager::GetInstance(), CNetBlastLoadingJob::m_Scope, and CRef< C, Locker >::Reset().

Referenced by CNetBlastLoadingJob::x_CreateProjectItems().

◆ x_CreateRemoteBlastIfNeeded()

void CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded ( )

protected

Definition at line 430 of file net_blast_job_descr.cpp.

References _ASSERT, CNetBlastJobDescriptor::m_RemoteBlast, CNetBlastJobDescriptor::m_RID, and CRef< C, Locker >::Reset().

Referenced by CNetBlastJobDescriptor::Check(), CNetBlastJobDescriptor::GetRemoteBlast(), and CNetBlastJobDescriptor::Retrieve().

◆ x_CreateTreeItems()

void CBLAST_DB_Dialog::x_CreateTreeItems ( )

protected

Definition at line 418 of file blast_db_dialog.cpp.

References CBLAST_DB_Dialog::m_Root, CBLAST_DB_Dialog::m_TreeCtrl, and CBLAST_DB_Dialog::x_BuildTreeItems().

Referenced by CBLAST_DB_Dialog::x_FilterItems().

◆ x_DoSearch()

IAppJob::EJobState CNetBLAST_DMSearchJob::x_DoSearch ( )

protectedvirtual

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

Implements CSearchJobBase.

Definition at line 387 of file net_blast_dm_search_tool.cpp.

References CObjectList::AddRow(), IAppJob::eCompleted, NStr::FindNoCase(), CNetBLASTUIDataSource::GetJobDescriptors(), GetNetBlastJobDescription(), CNetBlastJobDescriptor::GetState(), i, CJobCancelable::IsCanceled(), CSearchJobBase::m_AccList, CNetBLAST_DMSearchQuery::m_FilterStr, CNetBLAST_DMSearchJob::m_NetBlastDS, CNetBLAST_DMSearchJob::m_Query, CNetBLAST_DMSearchQuery::m_States, n, NULL, and skNumColumns.

◆ x_FillQueryList()

void CBLASTSearchOptionsPanel::x_FillQueryList ( )

protected

Definition at line 611 of file blast_search_options_panel.cpp.

References ctll::empty(), i, CBLASTParams::IsNucInput(), CBLASTSearchOptionsPanel::m_CurrentQuerySet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_QueryListCtrl, CBLASTSearchOptionsPanel::m_SubjectListCtrl, s_UseSets(), CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CBLASTSearchOptionsPanel::OnQuerySequenceSetSelected(), and CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ x_FillSubjectList()

void CBLASTSearchOptionsPanel::x_FillSubjectList ( )

protected

Definition at line 719 of file blast_search_options_panel.cpp.

References ctll::empty(), i, CBLASTParams::IsSubjNucInput(), CBLASTSearchOptionsPanel::m_CurrentSubjectSet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_SubjectListCtrl, s_UseSets(), CwxTableListCtrl::SelectAll(), and CObjectListWidget::SetObjects().

Referenced by CBLASTSearchOptionsPanel::OnSubjectSequenceSetSelected(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

◆ x_FilterItems()

void CBLAST_DB_Dialog::x_FilterItems ( const string & query )

protected

◆ x_FromUserObject()

void CBLASTParams::x_FromUserObject	(	const objects::CUser_object &	user_obj,
		blast::EProgram	prg,
		SProgParams &	params
	)

staticprotected

reads SProgParams fields from CUser_object

Definition at line 651 of file blast_search_params.cpp.

Referenced by CBLASTParams::FromUserObject().

◆ x_GetCommand()

CRef< CCmdComposite > CCreateGeneModelTask::x_GetCommand ( )

private

Definition at line 337 of file create_gene_model_tool_manager.cpp.

Referenced by CCreateGeneModelTask::x_Run().

◆ x_GetCommandLine() [1/6]

wxString CClustalOmegaToolJob::x_GetCommandLine	(	const wxString &	input,
		const wxString &	output,
		bool	is_nucleotide
	)

protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 51 of file clustal_omega_tool_job.cpp.

References eUnknown, CClustalOmegaToolParams::GetClustalOmegaExecutable(), CClustalOmegaToolParams::GetCommandLine(), CClustalOmegaToolParams::GetGenerateTree(), input(), CClustalOmegaToolJob::m_Params, CMSAToolJob::m_TmpTreeOut, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [2/6]

wxString CClustalwToolJob::x_GetCommandLine	(	const wxString &	input,
		const wxString &	output,
		bool	is_nucleotide
	)

protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 51 of file clustalw_tool_job.cpp.

References eUnknown, CClustalwToolParams::GetClustalWExecutable(), CClustalwToolParams::GetCommandLine(), CClustalwToolParams::GetGenerateTree(), input(), CClustalwToolJob::m_Params, CMSAToolJob::m_TmpTreeOut, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [3/6]

wxString CKalignToolJob::x_GetCommandLine	(	const wxString &	input,
		const wxString &	output,
		bool	is_nucleotide
	)

protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 50 of file kalign_tool_job.cpp.

References eUnknown, CKalignToolParams::GetCommandLine(), CKalignToolParams::GetKalignExecutable(), CKalignToolParams::GetQuietFlag(), input(), CKalignToolJob::m_Params, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [4/6]

wxString CMafftToolJob::x_GetCommandLine	(	const wxString &	input,
		const wxString &	output,
		bool	is_nucleotide
	)

protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 50 of file mafft_tool_job.cpp.

References eUnknown, CMafftToolParams::GetAutoFlag(), CMafftToolParams::GetCommandLine(), CMafftToolParams::GetMafftExecutable(), CMafftToolParams::GetQuietFlag(), input(), CMafftToolJob::m_Params, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [5/6]

wxString CMuscleToolJob::x_GetCommandLine	(	const wxString &	input,
		const wxString &	output,
		bool	is_nucleotide
	)

protectedvirtual

Returns the command line, that will be used to execute the third-party tool.

Implements CMSAToolJob.

Definition at line 57 of file muscle_tool_job.cpp.

References eUnknown, CMuscleToolParams::GetCommandLine(), CMuscleToolParams::GetGenerateTree(), CMuscleToolParams::GetMuscleExecutable(), CMuscleToolParams::GetScoringMethod(), input(), CMuscleToolJob::m_Params, CMSAToolJob::m_TmpTreeOut, NCBI_THROW, output, and wxT.

◆ x_GetCommandLine() [6/6]

virtual wxString CMSAToolJob::x_GetCommandLine	(	const wxString &	input,
		const wxString &	output,
		bool	is_nucleotide
	)

protectedpure virtual

Returns the command line, that will be used to execute the third-party tool.

Implemented in CMuscleToolJob, CMafftToolJob, CKalignToolJob, CClustalwToolJob, and CClustalOmegaToolJob.

Referenced by CMSAToolJob::BeforeRun().

◆ x_GetCurrentPage()

wxPanel * CNGAlignTool::x_GetCurrentPage ( )

protected

Definition at line 216 of file ngalign_tool.cpp.

References CNGAlignTool::m_BLASTPanel, CNGAlignTool::m_CurrentPage, CNGAlignTool::m_Panel, and NULL.

Referenced by CNGAlignTool::DoTransition(), CNGAlignTool::GetCurrentPanel(), and CNGAlignTool::x_LoadPage().

◆ x_GetCurrentSubTask()

CIRef< IAppTask > CBlastSearchTask::x_GetCurrentSubTask ( )

protectedvirtual

returns a references to the current subtask

Implements CCompositeAppTask.

Definition at line 196 of file blast_search_task.cpp.

References CBlastSearchTask::m_CurrTask.

◆ x_GetDataSource()

CNetBLASTUIDataSource * CNetBLAST_DMSearchTool::x_GetDataSource ( )

protected

Definition at line 201 of file net_blast_dm_search_tool.cpp.

References _ASSERT, IServiceLocator::GetServiceByType(), and CNetBLAST_DMSearchTool::m_SrvLocator.

Referenced by CNetBLAST_DMSearchTool::CreateSearchForm(), and CNetBLAST_DMSearchTool::x_CreateJob().

◆ x_GetNewOLTModel()

CObjectListTableModel * CNetBLAST_DMSearchJob::x_GetNewOLTModel ( ) const

protectedvirtual

factory method creating new column handler for CObjectListWidget

factory method creating new model for CObjectListWidget

Reimplemented from CSearchJobBase.

Definition at line 433 of file net_blast_dm_search_tool.cpp.

◆ x_GetObjects() [1/6]

virtual TConstScopedObjects& CClustalOmegaToolJob::x_GetObjects ( )

inlineprotectedvirtual

Returns the sequences that will be aligned.

Implements CMSAToolJob.

Definition at line 61 of file clustal_omega_tool_job.hpp.

◆ x_GetOrigObject() [6/7]

const CObject * CMultiAlignView::x_GetOrigObject ( ) const

protectedvirtual

Reimplemented from CProjectViewBase.

Definition at line 583 of file multi_align_view.cpp.

References CConstRef< C, Locker >::GetPointer(), CMultiAlignView::m_OrigAlign, and CMultiAlignView::m_OrigAnnot.

CPslParamsPanel * CPslLoadManager::x_GetParamsPanel ( )

protected

Definition at line 119 of file psl_load_manager.cpp.

References CPslLoadManager::m_Params, CPslLoadManager::m_ParamsPanel, CPslLoadManager::m_ParentWindow, NULL, CPslParamsPanel::SetData(), and CPslParamsPanel::TransferDataToWindow().

Referenced by CPslLoadManager::GetCurrentPanel(), and CPslLoadManager::CPage::GetPanel().

◆ x_GetParamsPanel() [19/19]

CTextAlignParamsPanel * CTextAlignLoaderManager::x_GetParamsPanel ( )

protected

Definition at line 117 of file text_align_load_manager.cpp.

References CTextAlignLoaderManager::m_Params, CTextAlignLoaderManager::m_ParamsPanel, CTextAlignLoaderManager::m_ParentWindow, NULL, CTextAlignParamsPanel::SetData(), and CTextAlignParamsPanel::TransferDataToWindow().

Referenced by CTextAlignLoaderManager::GetCurrentPanel(), and CTextAlignLoaderManager::CPage::GetPanel().

◆ x_GetRowSeqLoc()

void CMultiAlignView::x_GetRowSeqLoc	(	CAlnVec::TNumrow	row,
		CSelectionEvent::TRangeColl &	loc
	)		const

Returns the directory where to execute the msa tool.

Reimplemented from CMSAToolJob.

Definition at line 91 of file mafft_tool_job.cpp.

References CMafftToolParams::GetMafftExecutable(), and CMafftToolJob::m_Params.

◆ x_GetWorkingDirectory() [2/2]

virtual wxString CMSAToolJob::x_GetWorkingDirectory ( ) const

inlineprotectedvirtual

void CCreateGeneModelTask::x_GroupGenes	(	const objects::CSeq_id_Handle &	idh,
		CRef< objects::CSeq_feat >	gene
	)

private

Definition at line 727 of file create_gene_model_tool_manager.cpp.

References SGeneCdsmRnaFeats::gene, CCreateGeneModelTask::m_GeneModelMap, NON_CONST_ITERATE, and CCreateGeneModelTask::s_GetGeneID().

Referenced by CCreateGeneModelTask::x_Group_By_GeneID().

◆ x_HideShowInputs()

void CBLASTSearchParamsPanel::x_HideShowInputs ( )

protected

Definition at line 375 of file blast_search_params_panel.cpp.

Referenced by CBLASTSearchParamsPanel::TransferDataToWindow().

◆ x_InitGeneticCodesCombo()

void CBLASTSearchParamsPanel::x_InitGeneticCodesCombo ( )

protected

Definition at line 325 of file blast_search_params_panel.cpp.

References arr, CBLASTParams::GetGeneticCodeLabels(), CBLASTSearchParamsPanel::m_DbGenCodeCombo, CBLASTSearchParamsPanel::m_QueryGenCodeCombo, and ToArrayString().

Referenced by CBLASTSearchParamsPanel::CreateControls().

◆ x_InitMenuResources()

void CAlignSpanView::x_InitMenuResources ( )

protected

Definition at line 104 of file align_span_view.cpp.

Referenced by CAlignSpanView::x_CreateMenuBarMenu().

◆ x_InitMonitoringStage()

void CBlastSearchTask::x_InitMonitoringStage ( TDescriptors & descriptors )

protected

preapres App Job for monitoring stage of the task

Definition at line 134 of file blast_search_task.cpp.

References CBlastSearchTask::eMonitor, i, CBlastSearchTask::m_CurrTask, CAppTask::m_Descr, CBlastSearchTask::m_LoadingOptions, CBlastSearchTask::m_MonitoringJob, CBlastSearchTask::m_NetBlastDS, CBlastSearchTask::m_SrvLocator, CBlastSearchTask::m_Stage, CBlastSearchTask::m_ToolName, CRef< C, Locker >::Reset(), and CNetBlastMonitoringJob::SetLoadingOptions().

Referenced by CBlastSearchTask::Init_Monitoring(), and CBlastSearchTask::x_NextSubTask().

◆ x_InitProjectParams() [1/3]

void CBLASTToolManager::x_InitProjectParams ( )

protected

Definition at line 304 of file blast_tool_manager.cpp.

References IServiceLocator::GetServiceByType(), SProjectSelectorParams::m_CreateFolder, SProjectSelectorParams::m_FolderName, CBLASTToolManager::m_InputObjects, CBLASTToolManager::m_ProjectParams, CBLASTToolManager::m_SrvLocator, NON_CONST_ITERATE, and SProjectSelectorParams::SelectProjectByObjects().

Referenced by CBLASTToolManager::DoTransition().

◆ x_InitProjectParams() [2/3]

void CGroupAlignmentsToolManager::x_InitProjectParams ( )

protectedvirtual

init m_ProjectParams, in particular can select target project based on the tool input

Reimplemented from CAlgoToolManagerBase.

Definition at line 108 of file group_alignments_tool_manager.cpp.

References IServiceLocator::GetServiceByType(), SGroupAlignmentsParams::m_Alignments, CGroupAlignmentsToolManager::m_Params, CAlgoToolManagerBase::m_ProjectParams, CAlgoToolManagerBase::m_SrvLocator, and SProjectSelectorParams::SelectProjectByObjects().

◆ x_InitProjectParams() [3/3]

void CMergeAlignmentsToolManager::x_InitProjectParams ( )

protectedvirtual

init m_ProjectParams, in particular can select target project based on the tool input

Reimplemented from CAlgoToolManagerBase.

Definition at line 170 of file merge_alignments_tool_manager.cpp.

References IServiceLocator::GetServiceByType(), SMergeAlignmentsParams::m_Alignments, CMergeAlignmentsToolManager::m_Params, CAlgoToolManagerBase::m_ProjectParams, CAlgoToolManagerBase::m_SrvLocator, and SProjectSelectorParams::SelectProjectByObjects().

◆ x_InitTaxons()

void CBLASTSearchParamsPanel::x_InitTaxons ( )

protected

Definition at line 475 of file blast_search_params_panel.cpp.

References CTaxIdHelper::FillControl(), CBLASTParams::GetCurrParams(), CTaxIdHelper::GetInstance(), CBLASTSearchParamsPanel::m_Local, CBLASTSearchParamsPanel::m_Params, CBLASTSearchParamsPanel::m_RepeatType, CBLASTParams::SProgParams::m_WM_TaxId, CBLASTSearchParamsPanel::m_WMTaxIds, and CBLASTSearchParamsPanel::x_ShowWM().

Referenced by CBLASTSearchParamsPanel::OnWMDownload(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ x_InitWidget() [1/3]

void CAlignSpanView::x_InitWidget ( )

protected

bool CBLASTToolManager::x_IsNucInput ( ) const

protectedvirtual

defines whether Nucleotide or Protein options shall be selected by default

Definition at line 523 of file blast_tool_manager.cpp.

References map_checker< Container >::empty(), false, CBLASTToolManager::m_NucObjects, CBLASTToolManager::m_ProtObjects, and CBLASTToolManager::m_UseNucForMixInput.

Referenced by CBLASTToolManager::QuickLaunch(), and CBLASTToolManager::x_CreateOptionsPanelIfNeeded().

◆ x_LoadJobDescriptors()

void CNetBLASTUIDataSource::x_LoadJobDescriptors ( )

protected

Definition at line 492 of file net_blast_ui_data_source.cpp.

References CNetBLASTUIDataSource::CNetBlastJobDescriptor, CNetBlastJobDescriptor::eInvalidState, Error(), CUser_field_Base::GetData(), CUser_object::GetField(), CException::GetMsg(), CUser_field_Base::C_Data::GetObjects(), i, Info(), kJobDescrPath, kJobsTag, LOG_POST, CNetBLASTUIDataSource::m_JobDescrs, MSerial_AsnText, and CSysPath::ResolvePath().

Referenced by CNetBLASTUIDataSource::Open().

◆ x_LoadPage()

bool CNGAlignTool::x_LoadPage ( )

protected

Definition at line 198 of file ngalign_tool.cpp.

References _ASSERT, CNGAlignTool::m_CurrentPage, NcbiErrorBox(), CNGAlignTool::x_CreateBALSTPanelIfNeeded(), CNGAlignTool::x_CreateParamsPanelIfNeeded(), and CNGAlignTool::x_GetCurrentPage().

Referenced by CNGAlignTool::x_GoFirstPage(), CNGAlignTool::x_GoLastPage(), CNGAlignTool::x_GoNextPage(), and CNGAlignTool::x_GoPrevPage().

◆ x_LoadSettings()

void CNetBLAST_DMSearchForm::x_LoadSettings ( const CRegistryReadView & view )

protectedvirtual

Implements CSearchFormBase.

Definition at line 278 of file net_blast_dm_search_tool.cpp.

◆ x_MergeObjects()

bool CMultiAlignView::x_MergeObjects ( TConstScopedObjects & objects )

protectedvirtual

Definition at line 690 of file multi_align_view.cpp.

References data, NON_CONST_ITERATE, NULL, and CSeq_annot_Base::SetData().

Referenced by CMultiAlignView::InitView().

◆ x_NextSubTask()

CIRef< IAppTask > CBlastSearchTask::x_NextSubTask ( )

protectedvirtual

prepares the next subtask (makes it current), this function is used for iterating subtasks.

Implements CCompositeAppTask.

Definition at line 202 of file blast_search_task.cpp.

References _ASSERT, CBlastSearchTask::eFinished, CBlastSearchTask::eMonitor, CBlastSearchTask::eRetrieve, CBlastSearchTask::eSubmit, CNetBlastSubmittingJob::GetDescriptors(), CBlastSearchTask::m_CurrTask, CBlastSearchTask::m_MonitoringJob, CBlastSearchTask::m_Stage, CBlastSearchTask::m_SubmittingJob, CRef< C, Locker >::Reset(), and CBlastSearchTask::x_InitMonitoringStage().

Definition at line 538 of file align_span_view.cpp.

References CSelectionEvent::HasObjectSelection(), and CAlignSpanView::x_UpdateStatusMessage().

void CMPCrossAlignView::x_OnSetSelection ( CSelectionEvent & evt )

protectedvirtual

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 363 of file mp_cross_align_view.cpp.

◆ x_OnSetSelection() [6/7]

void CMultiAlignView::x_OnSetSelection ( CSelectionEvent & evt )

protectedvirtual

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 418 of file multi_align_view.cpp.

◆ x_OnSetSelection() [7/7]

void CPhyTreeView::x_OnSetSelection ( CSelectionEvent & evt )

protectedvirtual

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

objects::CScope * CDotMatrixView::x_PreAttachToProject ( TConstScopedObjects & objects )

protectedvirtual

Reimplemented from CProjectView.

Definition at line 159 of file dot_matrix_view.cpp.

References ExtractSeqAligns(), CDotMatrixView::m_Aligns, NON_CONST_ITERATE, and NULL.

void CNetBlastSubmittingJob::x_Run ( void )

protected

this fucntions performs real work

Definition at line 130 of file blast_jobs.cpp.

References _ASSERT, CLabel::eDefault, CLabel::GetLabel(), CException::GetMsg(), i, Info(), LOG_POST, CNetBlastSubmittingJob::m_Descriptors, CNetBlastSubmittingJob::m_Mutex, CNetBlastSubmittingJob::m_SeqLocs, SeqLocToBioseq(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), str(), string, CException::what(), and CNetBlastSubmittingJob::x_AddError().

Referenced by CNetBlastSubmittingJob::Run().

◆ x_Run() [2/3]

IAppJob::EJobState CNetBlastMonitoringJob::x_Run ( void )

protected

this functions performs real work every call to this function does pools each job once, then functions exits if some of jobs are still pending it returns eRunning state, so that it can be executed one more time

Definition at line 335 of file blast_jobs.cpp.

References CNetBLASTUIDataSource::DeleteJobDescriptors(), done, IAppJob::eCanceled, CNetBlastJobDescriptor::eCompleted, IAppJob::eCompleted, CNetBlastJobDescriptor::eExpired, CNetBlastJobDescriptor::eFailed, CNetBlastJobDescriptor::eRetrieved, IAppJob::eRunning, i, CJobCancelable::IsCanceled(), CNetBlastMonitoringJob::m_Descriptors, CNetBlastMonitoringJob::m_Errors, CNetBlastMonitoringJob::m_Mutex, CNetBlastMonitoringJob::m_NetBlastDS, t, and CNetBlastMonitoringJob::x_StartRetrivingTask().

Referenced by CNetBlastMonitoringJob::Run().

◆ x_Run() [3/3]

IAppTask::ETaskState CCreateGeneModelTask::x_Run ( void )

protectedvirtual

override this function in derived classes

Reimplemented from CAppTask.

Definition at line 280 of file create_gene_model_tool_manager.cpp.

References _ASSERT, CSelectProjectOptions::AddItemsToWorkspace(), cmd, data, IAppTask::eCanceled, IAppTask::eCompleted, IAppTask::eFailed, ICommandProccessor::Execute(), CGBDocument::GetUndoManager(), CCreateGeneModelTask::m_Items, SCreateGeneModelParams::m_MergeResults, CCreateGeneModelTask::m_Options, CCreateGeneModelTask::m_Params, CCreateGeneModelTask::m_Scope, CCreateGeneModelTask::m_Service, CPrefetchSeqDescr::PrefetchSeqDescr(), and CCreateGeneModelTask::x_GetCommand().

◆ x_RunCurrentSubTask()

IAppTask::ETaskState CBlastSearchTask::x_RunCurrentSubTask ( )

protectedvirtual

runs the current subtask; one may override this function in order to perform special pre-execution or post-execution actions

Reimplemented from CCompositeAppTask.

Definition at line 242 of file blast_search_task.cpp.

References IAppTask::eCompleted, CBlastSearchTask::eRetrieve, CBlastSearchTask::eSubmit, CNetBlastSubmittingJob::GetErrors(), CNetBlastLoadingJob::GetErrors(), CBlastSearchTask::m_LoadingJob, CBlastSearchTask::m_Stage, CBlastSearchTask::m_SubmittingJob, CBlastSearchTask::x_ReportErrors(), and CCompositeAppTask::x_RunCurrentSubTask().

◆ x_SaveJobDescriptors()

void CNetBLASTUIDataSource::x_SaveJobDescriptors ( )

protected

Definition at line 454 of file net_blast_ui_data_source.cpp.

References CUser_object::AddField(), Error(), CException::GetMsg(), i, Info(), CNetBlastJobDescriptor::IsDeleted(), kJobDescrPath, kJobsTag, LOG_POST, CNetBLASTUIDataSource::m_JobDescrs, MSerial_AsnText, CSysPath::ResolvePath(), CUser_object_Base::SetType(), and CNetBlastJobDescriptor::ToUserObject().

Referenced by CNetBLASTUIDataSource::Close().

◆ x_SaveSettings()

void CNetBLAST_DMSearchForm::x_SaveSettings ( CRegistryWriteView view ) const

protectedvirtual

Implements CSearchFormBase.

Definition at line 284 of file net_blast_dm_search_tool.cpp.

◆ x_SelectCompatibleInputObjects() [1/18]

void CBLASTToolManager::x_SelectCompatibleInputObjects ( )

protectedvirtual

◆ x_SelectCompatibleInputObjects() [2/18]

void CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects ( )

protected

select only Seq-aligns

Definition at line 135 of file cleanup_alignments_tool_manager.cpp.

References ITERATE, SCleanupAlignmentsParams::m_Alignments, CCleanupAlignmentsToolManager::m_Alignments, CAlgoToolManagerBase::m_InputObjects, CCleanupAlignmentsToolManager::m_Params, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [3/18]

void CClustalOmegaTool::x_SelectCompatibleInputObjects ( )

protected

Definition at line 103 of file clustal_omega_tool.cpp.

References CClustalOmegaTool::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CClustalOmegaTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [4/18]

void CClustalwTool::x_SelectCompatibleInputObjects ( )

protected

Definition at line 103 of file clustalw_tool.cpp.

References CClustalwTool::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CClustalwTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [5/18]

void CCreateGeneModelToolManager::x_SelectCompatibleInputObjects ( )

protected

Definition at line 134 of file create_gene_model_tool_manager.cpp.

References ITERATE, SCreateGeneModelParams::m_Alignments, CCreateGeneModelToolManager::m_Alignments, CAlgoToolManagerBase::m_InputObjects, CCreateGeneModelToolManager::m_Params, CAlgoToolManagerBase::x_ConvertInputObjects(), and CCreateGeneModelToolManager::x_RemoveDuplicates().

Referenced by CCreateGeneModelToolManager::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [6/18]

void CFindOverlapTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

select only Seq-ids

Definition at line 130 of file find_overlap_tool.cpp.

References CRef< C, Locker >::IsNull(), CFindOverlapTool::m_SeqIds, NON_CONST_ITERATE, NULL, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CFindOverlapTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [7/18]

void CGroupAlignmentsToolManager::x_SelectCompatibleInputObjects ( )

protected

select only Seq-aligns

Definition at line 130 of file group_alignments_tool_manager.cpp.

References ITERATE, SGroupAlignmentsParams::m_Alignments, CGroupAlignmentsToolManager::m_Alignments, CAlgoToolManagerBase::m_InputObjects, CGroupAlignmentsToolManager::m_Params, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CGroupAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [8/18]

void CKalignTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

Definition at line 102 of file kalign_tool.cpp.

References CKalignTool::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CKalignTool::QuickLaunch(), and CKalignTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [9/18]

void CMafftTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

Definition at line 102 of file mafft_tool.cpp.

References CMafftTool::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CMafftTool::QuickLaunch(), and CMafftTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [10/18]

void CMergeAlignmentsToolManager::x_SelectCompatibleInputObjects ( )

protected

select only Seq-aligns

Definition at line 134 of file merge_alignments_tool_manager.cpp.

References ITERATE, SMergeAlignmentsParams::m_Alignments, CMergeAlignmentsToolManager::m_Alignments, CAlgoToolManagerBase::m_InputObjects, CMergeAlignmentsToolManager::m_Params, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CMergeAlignmentsToolManager::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [11/18]

void CMuscleTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

Definition at line 102 of file muscle_tool.cpp.

References CMuscleTool::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CMuscleTool::QuickLaunch(), and CMuscleTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [12/18]

void CNGAlignTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

Definition at line 264 of file ngalign_tool.cpp.

References CRef< C, Locker >::IsNull(), CNGAlignTool::m_SeqIds, NON_CONST_ITERATE, NULL, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CNGAlignTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [13/18]

void CProSplignTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

Definition at line 198 of file prosplign_tool.cpp.

References map_checker< Container >::clear(), copy(), CSeq_loc::GetId(), CBioseq_Handle::IsAa(), CSeq_loc_Base::IsInt(), CBioseq_Handle::IsNa(), CSeq_loc_Base::IsWhole(), CProSplignTool::m_NAObjects, CProSplignTool::m_ProteinObjects, NON_CONST_ITERATE, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CProSplignTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [14/18]

void CSplignTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

◆ x_SelectCompatibleInputObjects() [15/18]

void CCommonTaxTreeTool::x_SelectCompatibleInputObjects ( )

protected

Definition at line 103 of file taxtree_tool.cpp.

References CCommonTaxTreeTool::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [16/18]

void CTreeBuilderTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

select only Seq-ids

Definition at line 145 of file tree_builder_tool.cpp.

References CTreeBuilderTool::m_SeqIds, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CTreeBuilderTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [17/18]

void CAdvancedCleanupTool::x_SelectCompatibleInputObjects ( )

protectedvirtual

Definition at line 98 of file advanced_cleanup_tool.cpp.

References ITERATE, CAdvancedCleanupTool::m_Alignments, CAlgoToolManagerBase::m_InputObjects, CAdvancedCleanupParams::m_Objects, CAdvancedCleanupTool::m_Params, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CAdvancedCleanupTool::x_CreateParamsPanelIfNeeded().

◆ x_SelectCompatibleInputObjects() [18/18]

void CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects ( )

protected

select only Seq-aligns

Definition at line 129 of file create_needleman_wunsch_tool_manager.cpp.

References CCreateNeedlemanWunschToolManager::m_Objects, and CAlgoToolManagerBase::x_ConvertInputObjects().

Referenced by CCreateNeedlemanWunschToolManager::x_CreateParamsPanelIfNeeded().

◆ x_SetStatusText() [1/2]

void CNetBlastSubmittingJob::x_SetStatusText ( const string & text )

protected

Definition at line 196 of file blast_jobs.cpp.

References CNetBlastSubmittingJob::m_Mutex, CNetBlastSubmittingJob::m_Status, and text().

◆ x_SetStatusText() [2/2]

protectedvirtual

void CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet ( )

protected

Definition at line 580 of file blast_search_options_panel.cpp.

References i, CBLASTParams::IsNucInput(), kSelectedSequences, CBLASTSearchOptionsPanel::m_CurrentQuerySet, CBLASTSearchOptionsPanel::m_NucObjects, CBLASTSearchOptionsPanel::m_Params, CBLASTSearchOptionsPanel::m_ProtObjects, CBLASTSearchOptionsPanel::m_QuerySeqSetCombo, CBLASTSearchOptionsPanel::m_QuerySeqSetStatic, s_UseSets(), ToStdString(), and ToWxString().

Referenced by CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

Definition at line 120 of file cleanup_alignments_tool_manager.cpp.

References CUIObject::GetLabel(), SCleanupAlignmentsParams::m_Alignments, CAlgoToolManagerBase::m_Descriptor, CCleanupAlignmentsToolManager::m_Params, and NcbiErrorBox().

◆ x_ValidateParams() [3/18]

bool CClustalOmegaTool::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 98 of file clustal_omega_tool.cpp.

◆ x_ValidateParams() [4/18]

bool CClustalwTool::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 98 of file clustalw_tool.cpp.

◆ x_ValidateParams() [5/18]

bool CCreateGeneModelToolManager::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 120 of file create_gene_model_tool_manager.cpp.

References CUIObject::GetLabel(), SCreateGeneModelParams::m_Alignments, CAlgoToolManagerBase::m_Descriptor, CCreateGeneModelToolManager::m_Params, and NcbiErrorBox().

◆ x_ValidateParams() [6/18]

bool CFindOverlapTool::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 124 of file find_overlap_tool.cpp.

◆ x_ValidateParams() [7/18]

bool CGroupAlignmentsToolManager::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 115 of file group_alignments_tool_manager.cpp.

References CUIObject::GetLabel(), SGroupAlignmentsParams::m_Alignments, CAlgoToolManagerBase::m_Descriptor, CGroupAlignmentsToolManager::m_Params, and NcbiErrorBox().

◆ x_ValidateParams() [8/18]

bool CKalignTool::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 97 of file kalign_tool.cpp.

◆ x_ValidateParams() [9/18]

bool CMafftTool::x_ValidateParams ( )

protectedvirtual

validates user input in Parameters panel, report errors if any

validate parameters after Params page override this function in derived classes

Reimplemented from CAlgoToolManagerBase.

Definition at line 97 of file mafft_tool.cpp.

◆ x_ValidateParams() [10/18]

bool CMergeAlignmentsToolManager::x_ValidateParams ( )

CBLASTSearchOptionsPanel::~CBLASTSearchOptionsPanel ( )

Definition at line 139 of file blast_search_options_panel.cpp.

◆ ~CBLASTSearchParamsPanel()

CBLASTSearchParamsPanel::~CBLASTSearchParamsPanel ( )

Definition at line 120 of file blast_search_params_panel.cpp.

◆ ~CBlastSearchTask()

CBlastSearchTask::~CBlastSearchTask ( )

virtual

Definition at line 58 of file blast_search_task.cpp.

◆ ~CCleanupAlignmentsParamsPanel()

CCleanupAlignmentsParamsPanel::~CCleanupAlignmentsParamsPanel ( )

Definition at line 123 of file cleanup_alignments_params_panel.cpp.

◆ ~CClustalOmegaToolParams()

CClustalOmegaToolParams::~CClustalOmegaToolParams ( )

Definition at line 56 of file clustal_omega_tool_params.cpp.

◆ ~CClustalwToolParams()

CClustalwToolParams::~CClustalwToolParams ( )

Definition at line 50 of file clustalw_tool_params.cpp.

◆ ~CCreateGeneModelTask()

CCreateGeneModelTask::~CCreateGeneModelTask ( )

virtual

Definition at line 276 of file create_gene_model_tool_manager.cpp.

◆ ~CFindOverlapPanel()

CFindOverlapPanel::~CFindOverlapPanel ( )

Definition at line 91 of file find_overlap_panel.cpp.

◆ ~CFindOverlapParams()

CFindOverlapParams::~CFindOverlapParams ( )

Definition at line 49 of file find_overlap_params.cpp.

◆ ~CGroupAlignmentsParamsPanel()

CGroupAlignmentsParamsPanel::~CGroupAlignmentsParamsPanel ( )

Definition at line 169 of file group_alignments_params_panel.cpp.

◆ ~CKalignToolParams()

CKalignToolParams::~CKalignToolParams ( )

◆ ~CNetBLASTLoadOptionPanel()

CNetBLASTLoadOptionPanel::~CNetBLASTLoadOptionPanel ( )

Definition at line 86 of file net_blast_load_option_panel.cpp.

◆ ~CNetBLASTUIDataSource()

CNetBLASTUIDataSource::~CNetBLASTUIDataSource ( )

virtual

Definition at line 153 of file net_blast_ui_data_source.cpp.

References _ASSERT, and CNetBLASTUIDataSource::m_Open.

◆ ~CNGAlignPanel()

CNGAlignPanel::~CNGAlignPanel ( )

Definition at line 95 of file ngalign_panel.cpp.

◆ ~CNGAlignParams()

CNGAlignParams::~CNGAlignParams ( )

Definition at line 55 of file ngalign_params.cpp.

◆ ~CPhyTreeView()

CPhyTreeView::~CPhyTreeView ( )

Definition at line 738 of file phy_tree_view.cpp.

References CPhyTreeView::DestroyViewWindow(), CAttribMenuInstance::GetInstance(), and CAttribMenu::RemoveMenuR().

◆ ~CSplignPanel()

CSplignPanel::~CSplignPanel ( )

Definition at line 187 of file splign_panel.cpp.

◆ ~CSplignParams()

CSplignParams::~CSplignParams ( )

Definition at line 49 of file splign_params.cpp.

◆ ~CTaxTreeToolPanel()

CTaxTreeToolPanel::~CTaxTreeToolPanel ( )

Definition at line 88 of file taxtree_tool_panel.cpp.

◆ ~CTaxTreeToolParams()

CTaxTreeToolParams::~CTaxTreeToolParams ( )

Definition at line 49 of file taxtree_tool_params.cpp.

◆ ~CTreeBuilderPanel()

CTreeBuilderPanel::~CTreeBuilderPanel ( )

Definition at line 100 of file tree_builder_panel.cpp.

◆ ~CTreeBuilderParams()

CTreeBuilderParams::~CTreeBuilderParams ( )

Definition at line 49 of file tree_builder_params.cpp.

◆ ~SGeneCdsmRnaFeats()

SGeneCdsmRnaFeats::~SGeneCdsmRnaFeats ( )

inline

Definition at line 103 of file create_gene_model_tool_manager.hpp.

Variable Documentation

◆ cds

CRef<objects::CSeq_feat> SGeneCdsmRnaFeats::cds

Definition at line 114 of file create_gene_model_tool_manager.hpp.

Referenced by SGeneCdsmRnaFeats::CrossLinkTriple(), SGeneCdsmRnaFeats::GetID(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CCreateGeneModelTask::x_StoreGeneratedFeats(), and CCreateGeneModelTask::x_UpdateGeneOnSequence().

◆ gene

CRef<objects::CSeq_feat> SGeneCdsmRnaFeats::gene

Definition at line 113 of file create_gene_model_tool_manager.hpp.

Referenced by SGeneCdsmRnaFeats::CrossLinkTriple(), SGeneCdsmRnaFeats::GetID(), CCreateGeneModelTask::x_GroupGenes(), CCreateGeneModelTask::x_StoreGeneratedFeats(), and CCreateGeneModelTask::x_UpdateGeneOnSequence().

◆ m_AdvancedParams

string CBLASTParams::m_AdvancedParams

protected

Definition at line 248 of file blast_search_params.hpp.

Referenced by CBLASTParams::FromUserObject(), CBLASTParams::GetAdvancedParams(), and CBLASTParams::ToUserObject().

◆ m_AdvParams [1/2]

wxString CBLASTSearchParamsPanel::m_AdvParams

protected

Definition at line 187 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::GetAdvParams(), CBLASTSearchParamsPanel::SetAdvParams(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_AdvParams [2/2]

wxString CNGAlignParams::m_AdvParams

private

Definition at line 119 of file ngalign_params.hpp.

Referenced by CNGAlignParams::Copy(), CNGAlignParams::GetAdvParams(), CNGAlignParams::LoadSettings(), CNGAlignParams::LogDump(), CNGAlignParams::operator==(), CNGAlignParams::SaveSettings(), and CNGAlignParams::SetAdvParams().

◆ m_Algo

EAlgorithm SCleanupAlignmentsParams::m_Algo

Definition at line 110 of file cleanup_alignments_params_panel.hpp.

Referenced by SCleanupAlignmentsParams::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsParamsPanel::TransferDataToWindow(), and CCleanupAlignmentsJob::x_CreateProjectItems().

◆ m_AlgoSelector

wxComboBox* CCleanupAlignmentsParamsPanel::m_AlgoSelector

Definition at line 173 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsParamsPanel::TransferDataToWindow(), and CCleanupAlignmentsParamsPanel::x_AdjustToAlgoSelector().

◆ m_Alignments [1/8]

TConstScopedObjects SCleanupAlignmentsParams::m_Alignments

Definition at line 103 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsJob::x_CreateProjectItems(), CCleanupAlignmentsToolManager::x_SelectCompatibleInputObjects(), and CCleanupAlignmentsToolManager::x_ValidateParams().

◆ m_Alignments [2/8]

TConstScopedObjects CCleanupAlignmentsToolManager::m_Alignments

TConstScopedObjects CAdvancedCleanupTool::m_Alignments

private

Definition at line 82 of file advanced_cleanup_tool.hpp.

Referenced by CAdvancedCleanupTool::x_CreateParamsPanelIfNeeded(), and CAdvancedCleanupTool::x_SelectCompatibleInputObjects().

◆ m_Aligns [1/2]

TAlignVector CAnnotCompareView::m_Aligns

private

Definition at line 107 of file annot_compare_view.hpp.

Referenced by CAnnotCompareView::x_PreAttachToProject().

◆ m_Aligns [2/2]

TAlignVector CDotMatrixView::m_Aligns

private

Definition at line 116 of file dot_matrix_view.hpp.

Referenced by CDotMatrixView::x_GetOrigObject(), CDotMatrixView::x_InitWidget(), and CDotMatrixView::x_PreAttachToProject().

◆ m_AlnMgr_FillUnaligned [1/2]

bool SCleanupAlignmentsParams::m_AlnMgr_FillUnaligned

Definition at line 124 of file cleanup_alignments_params_panel.hpp.

Referenced by SCleanupAlignmentsParams::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsParamsPanel::TransferDataToWindow(), and CCleanupAlignmentsJob::x_CreateProjectItems().

◆ m_AlnMgr_FillUnaligned [2/2]

wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_FillUnaligned

Definition at line 180 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), and CCleanupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_AlnMgr_PreserveRows [1/2]

bool SCleanupAlignmentsParams::m_AlnMgr_PreserveRows

Definition at line 121 of file cleanup_alignments_params_panel.hpp.

Referenced by SCleanupAlignmentsParams::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsParamsPanel::TransferDataToWindow(), CCleanupAlignmentsToolManager::x_CreateParamsPanelIfNeeded(), and CCleanupAlignmentsJob::x_CreateProjectItems().

◆ m_AlnMgr_PreserveRows [2/2]

wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_PreserveRows

Definition at line 179 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), and CCleanupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_AlnMgr_Sort [1/2]

bool SCleanupAlignmentsParams::m_AlnMgr_Sort

Definition at line 123 of file cleanup_alignments_params_panel.hpp.

Referenced by SCleanupAlignmentsParams::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsParamsPanel::TransferDataToWindow(), and CCleanupAlignmentsJob::x_CreateProjectItems().

◆ m_AlnMgr_Sort [2/2]

wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_Sort

Definition at line 178 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), and CCleanupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_AlnMgr_Transloc [1/2]

bool SCleanupAlignmentsParams::m_AlnMgr_Transloc

Definition at line 122 of file cleanup_alignments_params_panel.hpp.

Referenced by SCleanupAlignmentsParams::Init(), and CCleanupAlignmentsParamsPanel::TransferDataFromWindow().

◆ m_AlnMgr_Transloc [2/2]

wxCheckBox* CCleanupAlignmentsParamsPanel::m_AlnMgr_Transloc

Definition at line 177 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), and CCleanupAlignmentsParamsPanel::TransferDataFromWindow().

◆ m_AlnWidget [1/4]

CAlnSpanWidget* CAlignSpanView::m_AlnWidget

private

Definition at line 148 of file align_span_view.hpp.

Referenced by CAlignSpanView::CreateViewWindow(), CAlignSpanView::DestroyViewWindow(), CAlignSpanView::GetSelection(), CAlignSpanView::GetVisibleRanges(), CAlignSpanView::LoadSettings(), CAlignSpanView::SaveSettings(), CAlignSpanView::x_InitWidget(), CAlignSpanView::x_Update(), and CAlignSpanView::x_UpdateStatusMessage().

◆ m_AlnWidget [2/4]

CCrossAlnWidget* CCrossAlignView::m_AlnWidget

private

Definition at line 113 of file cross_align_view.hpp.

Referenced by CCrossAlignView::CreateViewWindow(), CCrossAlignView::DestroyViewWindow(), CCrossAlignView::GetSelection(), CCrossAlignView::GetVisibleRanges(), CCrossAlignView::GetWindow(), CCrossAlignView::OnVisibleRangeChanged(), CCrossAlignView::x_OnSetSelection(), and CCrossAlignView::x_PostAttachToProject().

◆ m_AlnWidget [3/4]

CHitMatrixWidget* CDotMatrixView::m_AlnWidget

private

Definition at line 120 of file dot_matrix_view.hpp.

Referenced by CDotMatrixView::CreateViewWindow(), CDotMatrixView::DestroyViewWindow(), CDotMatrixView::GetSelection(), CDotMatrixView::GetVisibleRanges(), CDotMatrixView::GetWindow(), CDotMatrixView::OnVisibleRangeChanged(), CDotMatrixView::x_InitWidget(), and CDotMatrixView::x_OnSetSelection().

◆ m_AlnWidget [4/4]

CAlnMultiWidget* CMultiAlignView::m_AlnWidget

protected

Definition at line 150 of file multi_align_view.hpp.

Referenced by CMultiAlignView::CreateViewWindow(), CMultiAlignView::DestroyViewWindow(), CMultiAlignView::GetSelection(), CMultiAlignView::GetWindow(), CMultiAlignView::LoadSettings(), CMultiAlignView::OnDSChanged(), CMultiAlignView::OnProjectChanged(), CMultiAlignView::SaveSettings(), CMultiAlignView::SetRegistryPath(), CMultiAlignView::x_GetSeqRangeSelection(), and CMultiAlignView::x_OnSetSelection().

◆ m_BLASTPanel

CNGAlignBLASTPanel* CNGAlignTool::m_BLASTPanel

protected

Definition at line 105 of file ngalign_tool.hpp.

Referenced by CNGAlignTool::CleanUI(), CNGAlignTool::InitUI(), CNGAlignTool::x_CreateBALSTPanelIfNeeded(), CNGAlignTool::x_CreateLoadingJob(), and CNGAlignTool::x_GetCurrentPage().

◆ m_BlastParams

wxString CFindOverlapParams::m_BlastParams

private

Definition at line 96 of file find_overlap_params.hpp.

Referenced by CFindOverlapParams::Copy(), CFindOverlapParams::GetBlastParams(), CFindOverlapParams::Init(), CFindOverlapParams::LoadSettings(), CFindOverlapParams::operator==(), CFindOverlapParams::SaveSettings(), and CFindOverlapParams::SetBlastParams().

◆ m_BlockEvents

bool CNetBlastDMSearchFormPanel::m_BlockEvents

protected

Definition at line 138 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated(), and CNetBlastDMSearchFormPanel::TransferDataToWindow().

◆ m_BrowseDBBtn

wxBitmapButton* CBLASTSearchOptionsPanel::m_BrowseDBBtn

Definition at line 160 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_CheckDBLoaded().

◆ m_Btc

CRef<objects::CBioTreeContainer> CPhyloTreeJob::m_Btc

private

Definition at line 192 of file phy_tree_view.hpp.

Referenced by CPhyloTreeJob::CPhyloTreeJob(), and CPhyloTreeJob::x_CreateProjectItems().

◆ m_Builder

◆ m_ClustalWPath

wxString CClustalwToolParams::m_ClustalWPath

private

Definition at line 95 of file clustalw_tool_params.hpp.

Referenced by CClustalwToolParams::Copy(), CClustalwToolParams::GetClustalWExecutable(), CClustalwToolParams::GetClustalWPath(), CClustalwToolParams::LoadSettings(), CClustalwToolParams::operator==(), CClustalwToolParams::SaveSettings(), and CClustalwToolParams::SetClustalWPath().

◆ m_CmdLine

wxString CMSAToolJob::m_CmdLine

protected

Definition at line 97 of file msa_tool_job.hpp.

Referenced by CMSAToolJob::BeforeRun(), and CMSAToolJob::x_CreateProjectItems().

◆ m_Command

ECommand CBlastSearchTask::m_Command

wxCheckBox* CBLASTSearchParamsPanel::m_CompartCheck

Definition at line 184 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_Completed

bool CNetBlastDMSearchFormPanel::m_Completed

protected

Definition at line 132 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::CreateControls(), CNetBlastDMSearchFormPanel::GetCompleted(), CNetBlastDMSearchFormPanel::Init(), and CNetBlastDMSearchFormPanel::SetCompleted().

◆ m_CompPenalty

double CSplignParams::m_CompPenalty

private

Definition at line 110 of file splign_params.hpp.

Referenced by CSplignParams::Copy(), CSplignParams::DebugDump(), CSplignParams::GetCompPenalty(), CSplignParams::Init(), CSplignParams::LoadSettings(), CSplignParams::operator==(), CSplignParams::SaveSettings(), and CSplignParams::SetCompPenalty().

◆ m_ConstructMethod

wxString CTreeBuilderParams::m_ConstructMethod

private

Definition at line 94 of file tree_builder_params.hpp.

Referenced by CTreeBuilderParams::Copy(), CTreeBuilderParams::GetConstructMethod(), CTreeBuilderParams::LoadSettings(), CTreeBuilderParams::operator==(), CTreeBuilderParams::SaveSettings(), and CTreeBuilderParams::SetConstructMethod().

◆ m_Cont

CRef<objects::CBioTreeContainer> CPhyTreeView::m_Cont

mutableprivate

Definition at line 129 of file phy_tree_view.hpp.

Referenced by CPhyTreeView::GetSelection().

CFindOverlapParams CFindOverlapPanel::m_data

Definition at line 123 of file find_overlap_panel.hpp.

Referenced by CFindOverlapPanel::GetData(), CFindOverlapPanel::SetData(), and CFindOverlapPanel::TransferDataFromWindow().

◆ m_data [2/5]

CSplignParams CSplignPanel::m_data

private

Definition at line 158 of file splign_panel.hpp.

Referenced by CSplignPanel::GetData(), and CSplignPanel::SetData().

◆ m_data [3/5]

CTreeBuilderParams CTreeBuilderPanel::m_data

Definition at line 125 of file tree_builder_panel.hpp.

Referenced by CTreeBuilderPanel::GetData(), CTreeBuilderPanel::SetData(), and CTreeBuilderPanel::TransferDataFromWindow().

◆ m_data [4/5]

CMuscleToolParams CMuscleToolPanel::m_data

Definition at line 129 of file muscle_tool_panel.hpp.

Referenced by CMuscleToolPanel::GetData(), and CMuscleToolPanel::SetData().

◆ m_data [5/5]

CTaxTreeToolParams CTaxTreeToolPanel::m_data

Definition at line 127 of file taxtree_tool_panel.hpp.

Referenced by CTaxTreeToolPanel::GetData(), and CTaxTreeToolPanel::SetData().

◆ m_DatabaseCombo

wxComboBox* CBLASTSearchOptionsPanel::m_DatabaseCombo

Definition at line 159 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::OnBrowseDatabases(), CBLASTSearchOptionsPanel::OnDatabaseComboSelected(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), and CBLASTSearchOptionsPanel::x_UpdateDBCombo().

◆ m_DataSource [1/8]

CRef<IAlnMultiDataSource> CAlignSpanView::m_DataSource

private

Definition at line 143 of file align_span_view.hpp.

Referenced by CAlignSpanView::x_InitWidget().

◆ m_DataSource [2/8]

CNetBLASTUIDataSource* CBLASTSearchOptionsPanel::m_DataSource

protected

Definition at line 228 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::Setup().

◆ m_DataSource [3/8]

CIRef<ICrossAlnDataSource> CCrossAlignView::m_DataSource

private

Definition at line 111 of file cross_align_view.hpp.

Referenced by CCrossAlignView::GetSelection(), CCrossAlignView::GetVisibleRanges(), CCrossAlignView::OnVisibleRangeChanged(), CCrossAlignView::x_OnSetSelection(), and CCrossAlignView::x_PostAttachToProject().

◆ m_DataSource [4/8]

CIRef<IHitMatrixDataSource> CDotMatrixView::m_DataSource

private

Definition at line 118 of file dot_matrix_view.hpp.

Referenced by CDotMatrixView::GetSelection(), CDotMatrixView::GetVisibleRanges(), CDotMatrixView::OnVisibleRangeChanged(), CDotMatrixView::x_InitWidget(), and CDotMatrixView::x_OnSetSelection().

◆ m_DataSource [5/8]

CIRef<ICrossAlnDataSource> CMPCrossAlignView::m_DataSource

private

Definition at line 118 of file mp_cross_align_view.hpp.

◆ m_DataSource [6/8]

CIRef<IAlnMultiDataSource> CMultiAlignView::m_DataSource

protected

Definition at line 148 of file multi_align_view.hpp.

Referenced by CMultiAlignView::GetSelection(), CMultiAlignView::OnProjectChanged(), CMultiAlignView::x_GetRowSeqLoc(), CMultiAlignView::x_GetSeqRangeSelection(), CMultiAlignView::x_OnSetSelection(), and CMultiAlignView::x_RebuildObjectIndex().

◆ m_DataSource [7/8]

CRef<CNetBLASTUIDataSource> CNetBLASTUILoadManager::m_DataSource

protected

Definition at line 103 of file net_blast_ui_load_manager.hpp.

Referenced by CNetBLASTUILoadManager::GetTask().

◆ m_DataSource [8/8]

CRef<CPhyloTreeDataSource> CPhyTreeView::m_DataSource

private

Definition at line 138 of file phy_tree_view.hpp.

Referenced by CPhyTreeView::CreateViewWindow(), CPhyTreeView::GetSelection(), CPhyTreeView::OnBioTreeChanged(), CPhyTreeView::OnCreateSelectedSubtree(), CPhyTreeView::OnExportTree(), CPhyTreeView::OnProjectChanged(), CPhyTreeView::OnSomethingEdited(), CPhyTreeView::RebuildObjectIndex(), and CPhyTreeView::x_OnSetSelection().

◆ m_DbGenCodeCombo

wxComboBox* CBLASTSearchParamsPanel::m_DbGenCodeCombo

Definition at line 176 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_InitGeneticCodesCombo().

◆ m_DbGenCodeLabel

wxStaticText* CBLASTSearchParamsPanel::m_DbGenCodeLabel

Definition at line 175 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), and CBLASTSearchParamsPanel::x_HideShowInputs().

◆ m_DbGeneticCode [1/2]

int CBLASTParams::SProgParams::m_DbGeneticCode

Definition at line 93 of file blast_search_params.hpp.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTParams::x_FromUserObject(), and CBLASTParams::x_ToUserObject().

◆ m_DbGeneticCode [2/2]

wxString CBLASTSearchParamsPanel::m_DbGeneticCode

protected

Definition at line 188 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::GetDbGeneticCode(), CBLASTSearchParamsPanel::SetDbGeneticCode(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_DbItems

TItemDeque CBLAST_DB_Dialog::m_DbItems

protected

Definition at line 212 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::OnInitDialog(), CBLAST_DB_Dialog::x_CreateItems(), and CBLAST_DB_Dialog::x_FilterItems().

◆ m_DBLoadState

int CBLASTSearchOptionsPanel::m_DBLoadState

protected

Definition at line 238 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::x_CheckDBLoaded(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_DbMap

const TDbMap* CBLAST_DB_Dialog::m_DbMap

protected

Definition at line 206 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::Init(), CBLAST_DB_Dialog::SetDBMap(), and CBLAST_DB_Dialog::x_CreateItems().

◆ m_DBSizer

wxBoxSizer* CBLASTSearchOptionsPanel::m_DBSizer

Definition at line 158 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_CheckDBLoaded().

◆ m_Deleted

bool CNetBlastJobDescriptor::m_Deleted

protected

Definition at line 131 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::IsDeleted(), and CNetBlastJobDescriptor::MarkDeleted().

◆ m_Descr [1/6]

string CNetBlastSubmittingJob::m_Descr

◆ m_Descriptor [2/2]

CUIObject CNetBLASTUILoadManager::m_Descriptor

protected

Definition at line 108 of file net_blast_ui_load_manager.hpp.

Referenced by CNetBLASTUILoadManager::CNetBLASTUILoadManager(), CNetBLASTUILoadManager::GetDescriptor(), and CNetBLASTUILoadManager::GetTask().

◆ m_Descriptors [1/3]

vector< CRef<CNetBlastJobDescriptor> > CNetBlastSubmittingJob::m_Descriptors

protected

Definition at line 101 of file blast_jobs.hpp.

Referenced by CNetBlastSubmittingJob::CNetBlastSubmittingJob(), CNetBlastSubmittingJob::GetDescriptors(), CNetBlastSubmittingJob::GetErrors(), and CNetBlastSubmittingJob::x_Run().

◆ m_Descriptors [2/3]

TDescriptors CNetBlastMonitoringJob::m_Descriptors

protected

Definition at line 160 of file blast_jobs.hpp.

Referenced by CNetBlastMonitoringJob::x_Run().

◆ m_Descriptors [3/3]

TDescriptors CNetBlastLoadingJob::m_Descriptors

protected

Definition at line 189 of file blast_jobs.hpp.

Referenced by CNetBlastLoadingJob::SetRIDs(), and CNetBlastLoadingJob::x_CreateProjectItems().

string CBLASTParams::m_EntrezQuery

string CNetBlastJobDescriptor::m_Errors

protected

Definition at line 128 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::Check(), CNetBlastJobDescriptor::FromUserObject(), CNetBlastJobDescriptor::GetErrors(), and CNetBlastJobDescriptor::ToUserObject().

vector<wxString> CTextAlignLoaderManager::m_FileNames

protected

Definition at line 154 of file text_align_load_manager.hpp.

Referenced by CTextAlignLoaderManager::GetExecuteUnit(), CTextAlignLoaderManager::GetFilenames(), and CTextAlignLoaderManager::SetFilenames().

◆ m_FillUnaligned [1/2]

bool SMergeAlignmentsParams::m_FillUnaligned

Definition at line 98 of file merge_alignments_params_panel.hpp.

Referenced by SMergeAlignmentsParams::Init(), SMergeAlignmentsParams::LoadSettings(), SMergeAlignmentsParams::SaveSettings(), CMergeAlignmentsParamsPanel::TransferDataFromWindow(), CMergeAlignmentsParamsPanel::TransferDataToWindow(), and CMergeAlignmentsJob::x_CreateProjectItems().

◆ m_FillUnaligned [2/2]

wxCheckBox* CMergeAlignmentsParamsPanel::m_FillUnaligned

Definition at line 148 of file merge_alignments_params_panel.hpp.

Referenced by CMergeAlignmentsParamsPanel::CreateControls(), CMergeAlignmentsParamsPanel::Init(), CMergeAlignmentsParamsPanel::TransferDataFromWindow(), and CMergeAlignmentsParamsPanel::TransferDataToWindow().

TGeneModelMap CCreateGeneModelTask::m_GeneModelMap

private

Definition at line 174 of file create_gene_model_tool_manager.hpp.

Referenced by CCreateGeneModelTask::x_AssignIDsAndCrossLinkFeats(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CCreateGeneModelTask::x_GetCommand(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), and CCreateGeneModelTask::x_GroupGenes().

◆ m_GeneralSizer

wxFlexGridSizer* CBLASTSearchParamsPanel::m_GeneralSizer

Definition at line 170 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), and CBLASTSearchParamsPanel::Init().

◆ m_GenerateTree [1/3]

bool CClustalOmegaToolParams::m_GenerateTree

private

Definition at line 96 of file clustal_omega_tool_params.hpp.

Referenced by CClustalOmegaToolParams::Copy(), CClustalOmegaToolParams::GetGenerateTree(), CClustalOmegaToolParams::Init(), CClustalOmegaToolParams::LoadSettings(), CClustalOmegaToolParams::operator==(), CClustalOmegaToolParams::SaveSettings(), and CClustalOmegaToolParams::SetGenerateTree().

◆ m_GenerateTree [2/3]

bool CClustalwToolParams::m_GenerateTree

private

Definition at line 97 of file clustalw_tool_params.hpp.

Referenced by CClustalwToolParams::Copy(), CClustalwToolParams::GetGenerateTree(), CClustalwToolParams::Init(), CClustalwToolParams::LoadSettings(), CClustalwToolParams::operator==(), CClustalwToolParams::SaveSettings(), and CClustalwToolParams::SetGenerateTree().

◆ m_GenerateTree [3/3]

bool CMuscleToolParams::m_GenerateTree

private

Definition at line 99 of file muscle_tool_params.hpp.

Referenced by CMuscleToolParams::Copy(), CMuscleToolParams::GetGenerateTree(), CMuscleToolParams::Init(), CMuscleToolParams::LoadSettings(), CMuscleToolParams::operator==(), CMuscleToolParams::SaveSettings(), and CMuscleToolParams::SetGenerateTree().

◆ m_GenomicList

CObjectListWidgetSel* CSplignPanel::m_GenomicList

Definition at line 153 of file splign_panel.hpp.

Referenced by CSplignPanel::CreateControls(), CSplignPanel::Init(), CSplignPanel::LoadSettings(), CSplignPanel::SaveSettings(), CSplignPanel::SetObjects(), CSplignPanel::SetRegistryPath(), and CSplignPanel::TransferDataFromWindow().

◆ m_GenomicListAccValidator

CMolTypeValidator CSplignPanel::m_GenomicListAccValidator

private

Definition at line 178 of file splign_panel.hpp.

Referenced by CSplignPanel::CreateControls().

◆ m_GenomicObjects

TObjects CSplignTool::m_GenomicObjects

protected

Definition at line 87 of file splign_tool.hpp.

Referenced by CSplignTool::QuickLaunch(), CSplignTool::x_CreateLoadingJob(), CSplignTool::x_CreateParamsPanelIfNeeded(), and CSplignTool::x_SelectCompatibleInputObjects().

◆ m_GenomicSeq

SConstScopedObject CSplignPanel::m_GenomicSeq

private

Definition at line 156 of file splign_panel.hpp.

Referenced by CSplignPanel::GetGenomicSeq(), CSplignPanel::SetGenomicSeq(), and CSplignPanel::TransferDataFromWindow().

◆ m_GroupByEST [1/2]

bool SGroupAlignmentsParams::m_GroupByEST

Definition at line 104 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByEST [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByEST

Definition at line 159 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByGenBank [1/2]

bool SGroupAlignmentsParams::m_GroupByGenBank

Definition at line 105 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByGenBank [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByGenBank

Definition at line 161 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), and CGroupAlignmentsParamsPanel::Init().

◆ m_GroupByHTGS [1/2]

bool SGroupAlignmentsParams::m_GroupByHTGS

Definition at line 107 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByHTGS [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByHTGS

Definition at line 163 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByLikeTaxId [1/2]

bool SGroupAlignmentsParams::m_GroupByLikeTaxId

Definition at line 101 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByLikeTaxId [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByLikeTaxId

Definition at line 157 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByPatent [1/2]

bool SGroupAlignmentsParams::m_GroupByPatent

Definition at line 108 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByPatent [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByPatent

Definition at line 164 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByPredictedRefSeq [1/2]

bool SGroupAlignmentsParams::m_GroupByPredictedRefSeq

Definition at line 103 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByPredictedRefSeq [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByPredictedRefSeq

Definition at line 160 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByRefSeq [1/2]

bool SGroupAlignmentsParams::m_GroupByRefSeq

Definition at line 102 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByRefSeq [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByRefSeq

Definition at line 158 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupBySeqId [1/2]

bool SGroupAlignmentsParams::m_GroupBySeqId

Definition at line 98 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupBySeqId [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupBySeqId

Definition at line 154 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByStrand [1/2]

bool SGroupAlignmentsParams::m_GroupByStrand

Definition at line 99 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByStrand [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByStrand

Definition at line 155 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByTaxId [1/2]

bool SGroupAlignmentsParams::m_GroupByTaxId

Definition at line 100 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByTaxId [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByTaxId

Definition at line 156 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_GroupByWGS [1/2]

bool SGroupAlignmentsParams::m_GroupByWGS

Definition at line 106 of file group_alignments_params_panel.hpp.

Referenced by SGroupAlignmentsParams::Init(), SGroupAlignmentsParams::LoadSettings(), SGroupAlignmentsParams::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), CGroupAlignmentsParamsPanel::TransferDataToWindow(), and CGroupAlignmentsJob::x_CreateProjectItems().

◆ m_GroupByWGS [2/2]

wxCheckBox* CGroupAlignmentsParamsPanel::m_GroupByWGS

Definition at line 162 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_HitFilter_MinIdentity [1/2]

float SCleanupAlignmentsParams::m_HitFilter_MinIdentity

Definition at line 116 of file cleanup_alignments_params_panel.hpp.

Referenced by SCleanupAlignmentsParams::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), CCleanupAlignmentsParamsPanel::TransferDataToWindow(), and CCleanupAlignmentsJob::x_CreateProjectItems().

◆ m_HitFilter_MinIdentity [2/2]

wxTextCtrl* CCleanupAlignmentsParamsPanel::m_HitFilter_MinIdentity

Definition at line 175 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), and CCleanupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_HitFilter_MinLength [1/2]

int SCleanupAlignmentsParams::m_HitFilter_MinLength

Definition at line 115 of file cleanup_alignments_params_panel.hpp.

TConstScopedObjects* CFindOverlapPanel::m_InputObjects

Definition at line 134 of file find_overlap_panel.hpp.

Referenced by CFindOverlapPanel::SetObjects(), and CFindOverlapPanel::TransferDataToWindow().

◆ m_InputObjects [4/8]

TConstScopedObjects* CGroupAlignmentsParamsPanel::m_InputObjects

protected

Definition at line 189 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::SetParams(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_InputObjects [5/8]

TConstScopedObjects* CMergeAlignmentsParamsPanel::m_InputObjects

protected

Definition at line 169 of file merge_alignments_params_panel.hpp.

Referenced by CMergeAlignmentsParamsPanel::SetParams(), and CMergeAlignmentsParamsPanel::TransferDataToWindow().

◆ m_InputObjects [6/8]

TConstScopedObjects* CTreeBuilderPanel::m_InputObjects

Definition at line 137 of file tree_builder_panel.hpp.

Referenced by CTreeBuilderPanel::SetObjects(), and CTreeBuilderPanel::TransferDataToWindow().

◆ m_InputObjects [7/8]

TConstScopedObjects* CMuscleToolPanel::m_InputObjects

string CBLASTParams::SProgInfo::m_Label

Definition at line 76 of file blast_search_params.hpp.

◆ m_LabelLength

size_t CBLAST_Dlg_Item::m_LabelLength

protected

Definition at line 106 of file blast_db_dialog.hpp.

Referenced by CBLAST_Dlg_Item::CBLAST_Dlg_Item(), and CBLAST_Dlg_Item::GetLabel().

◆ m_LabelPos

size_t CBLAST_Dlg_Item::m_LabelPos

protected

Definition at line 105 of file blast_db_dialog.hpp.

Referenced by CBLAST_Dlg_Item::CBLAST_Dlg_Item(), and CBLAST_Dlg_Item::GetLabel().

wxTextCtrl* CBLASTSearchOptionsPanel::m_LocalDBCtrl

Definition at line 163 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::OnSelectLocalDB(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSearchOptionsPanel::x_UpdateSubjects().

◆ m_LocalDBLoader

bool CBLASTParams::m_LocalDBLoader

protected

Definition at line 258 of file blast_search_params.hpp.

Referenced by CBLASTParams::FromUserObject(), and CBLASTParams::ToUserObject().

◆ m_LocalDBLoaderCtrl

wxCheckBox* CBLASTSearchOptionsPanel::m_LocalDBLoaderCtrl

Definition at line 164 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_LocalDBSizer

wxBoxSizer* CBLASTSearchOptionsPanel::m_LocalDBSizer

Definition at line 162 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_LocalNucDB

string CBLASTParams::m_LocalNucDB

protected

Definition at line 254 of file blast_search_params.hpp.

Referenced by CBLASTParams::FromUserObject(), and CBLASTParams::ToUserObject().

◆ m_LocalProtDB

string CBLASTParams::m_LocalProtDB

protected

Definition at line 255 of file blast_search_params.hpp.

Referenced by CBLASTParams::FromUserObject(), and CBLASTParams::ToUserObject().

◆ m_LocalSeqsSizer

wxBoxSizer* CBLASTSearchOptionsPanel::m_LocalSeqsSizer

Definition at line 155 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_LocalSizer

wxStaticBoxSizer* CBLASTSearchOptionsPanel::m_LocalSizer

Definition at line 149 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_LocalWinMaskDirPath

string CBLASTToolManager::m_LocalWinMaskDirPath

protected

Definition at line 141 of file blast_tool_manager.hpp.

Referenced by CBLASTToolManager::LoadSettings().

◆ m_LocationSel

CObjectListWidgetSel* CMuscleToolPanel::m_LocationSel

Definition at line 128 of file muscle_tool_panel.hpp.

Referenced by CMuscleToolPanel::CreateControls(), CMuscleToolPanel::Init(), CMuscleToolPanel::LoadSettings(), CMuscleToolPanel::SaveSettings(), CMuscleToolPanel::SetObjects(), CMuscleToolPanel::SetRegistryPath(), and CMuscleToolPanel::TransferDataFromWindow().

◆ m_MafftPath

wxString CMafftToolParams::m_MafftPath

private

Definition at line 100 of file mafft_tool_params.hpp.

Referenced by CMafftToolParams::Copy(), CMafftToolParams::GetMafftExecutable(), CMafftToolParams::GetMafftPath(), CMafftToolParams::LoadSettings(), CMafftToolParams::operator==(), CMafftToolParams::SaveSettings(), and CMafftToolParams::SetMafftPath().

◆ m_MainSplitter

wxSplitterWindow* CMPCrossAlignView::m_MainSplitter

private

Definition at line 120 of file mp_cross_align_view.hpp.

Referenced by CMPCrossAlignView::CreateViewWindow(), CMPCrossAlignView::DestroyViewWindow(), CMPCrossAlignView::GetMainObject(), CMPCrossAlignView::GetWindow(), and CMPCrossAlignView::InitView().

◆ m_Manager [1/2]

CPslLoadManager& CPslLoadManager::CPage::m_Manager

Definition at line 137 of file psl_load_manager.hpp.

Referenced by CPslLoadManager::CPage::GetPanel().

◆ m_Manager [2/2]

CTextAlignLoaderManager& CTextAlignLoaderManager::CPage::m_Manager

Definition at line 139 of file text_align_load_manager.hpp.

Referenced by CTextAlignLoaderManager::CPage::GetPanel().

◆ m_MaskLCRegions

bool CBLASTSearchParamsPanel::m_MaskLCRegions

protected

Definition at line 192 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_MaskLowercase

bool CBLASTParams::SProgParams::m_MaskLowercase

mask Lowercase features

Definition at line 94 of file blast_search_params.hpp.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTParams::x_FromUserObject(), and CBLASTParams::x_ToUserObject().

◆ m_MaskRepeats [1/2]

bool CBLASTParams::SProgParams::m_MaskRepeats

mask Repeat features

Definition at line 95 of file blast_search_params.hpp.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), CBLASTParams::x_FromUserObject(), and CBLASTParams::x_ToUserObject().

◆ m_MaskRepeats [2/2]

bool CBLASTSearchParamsPanel::m_MaskRepeats

protected

Definition at line 193 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_MatchCost

int CNeedlemanWunschToolParams::m_MatchCost

private

Definition at line 114 of file needlemanwunsch_tool_params.hpp.

Referenced by CNeedlemanWunschToolParams::Copy(), CNeedlemanWunschToolParams::GetMatchCost(), CNeedlemanWunschToolParams::Init(), CNeedlemanWunschToolParams::LoadSettings(), CNeedlemanWunschToolParams::operator==(), CNeedlemanWunschToolParams::SaveSettings(), and CNeedlemanWunschToolParams::SetMatchCost().

◆ m_MaxGenomicExtent

long CSplignParams::m_MaxGenomicExtent

private

Definition at line 113 of file splign_params.hpp.

Referenced by CSplignParams::Copy(), CSplignParams::DebugDump(), CSplignParams::GetMaxGenomicExtent(), CSplignParams::Init(), CSplignParams::LoadSettings(), CSplignParams::operator==(), CSplignParams::SaveSettings(), and CSplignParams::SetMaxGenomicExtent().

◆ m_MaxIntron

long CSplignParams::m_MaxIntron

private

Definition at line 114 of file splign_params.hpp.

Referenced by CSplignParams::Copy(), CSplignParams::DebugDump(), CSplignParams::GetMaxIntron(), CSplignParams::Init(), CSplignParams::LoadSettings(), CSplignParams::operator==(), CSplignParams::SaveSettings(), and CSplignParams::SetMaxIntron().

◆ m_MaxSlop

wxString CFindOverlapParams::m_MaxSlop

private

Definition at line 98 of file find_overlap_params.hpp.

Referenced by CFindOverlapParams::Copy(), CFindOverlapParams::GetMaxSlop(), CFindOverlapParams::Init(), CFindOverlapParams::LoadSettings(), CFindOverlapParams::operator==(), CFindOverlapParams::SaveSettings(), and CFindOverlapParams::SetMaxSlop().

◆ m_MergeAlgo

int SMergeAlignmentsParams::m_MergeAlgo

Definition at line 96 of file merge_alignments_params_panel.hpp.

Referenced by SMergeAlignmentsParams::Init(), SMergeAlignmentsParams::LoadSettings(), SMergeAlignmentsParams::SaveSettings(), CMergeAlignmentsParamsPanel::TransferDataFromWindow(), CMergeAlignmentsParamsPanel::TransferDataToWindow(), and CMergeAlignmentsJob::x_CreateProjectItems().

◆ m_MergeFlags

int SMergeAlignmentsParams::m_MergeFlags

Definition at line 97 of file merge_alignments_params_panel.hpp.

Referenced by SMergeAlignmentsParams::Init(), SMergeAlignmentsParams::LoadSettings(), SMergeAlignmentsParams::SaveSettings(), CMergeAlignmentsParamsPanel::TransferDataFromWindow(), CMergeAlignmentsParamsPanel::TransferDataToWindow(), and CMergeAlignmentsJob::x_CreateProjectItems().

◆ m_MergeQuerySeqOnly

wxCheckBox* CMergeAlignmentsParamsPanel::m_MergeQuerySeqOnly

Definition at line 144 of file merge_alignments_params_panel.hpp.

Referenced by CMergeAlignmentsParamsPanel::CreateControls(), CMergeAlignmentsParamsPanel::Init(), CMergeAlignmentsParamsPanel::TransferDataFromWindow(), and CMergeAlignmentsParamsPanel::TransferDataToWindow().

◆ m_MinCompIdentity

double CSplignParams::m_MinCompIdentity

private

Definition at line 115 of file splign_params.hpp.

Referenced by CSplignParams::Copy(), CSplignParams::DebugDump(), CSplignParams::GetMinCompIdentity(), CSplignParams::Init(), CSplignParams::LoadSettings(), CSplignParams::operator==(), CSplignParams::SaveSettings(), and CSplignParams::SetMinCompIdentity().

◆ m_MinExonIdentity

double CSplignParams::m_MinExonIdentity

private

Definition at line 116 of file splign_params.hpp.

Referenced by CSplignParams::Copy(), CSplignParams::DebugDump(), CSplignParams::GetMinExonIdentity(), CSplignParams::Init(), CSplignParams::LoadSettings(), CSplignParams::operator==(), CSplignParams::SaveSettings(), and CSplignParams::SetMinExonIdentity().

◆ m_MismatchCost

int CNeedlemanWunschToolParams::m_MismatchCost

CFastMutex CNetBlastSubmittingJob::m_Mutex

protected

Definition at line 94 of file blast_jobs.hpp.

Referenced by CNetBlastSubmittingJob::GetProgress(), CNetBlastSubmittingJob::Run(), CNetBlastSubmittingJob::x_AddError(), CNetBlastSubmittingJob::x_ResetState(), CNetBlastSubmittingJob::x_Run(), and CNetBlastSubmittingJob::x_SetStatusText().

◆ m_Mutex [2/3]

CFastMutex CNetBlastMonitoringJob::m_Mutex

protected

Definition at line 147 of file blast_jobs.hpp.

Referenced by CNetBlastMonitoringJob::CNetBlastMonitoringJob(), CNetBlastMonitoringJob::GetProgress(), CNetBlastMonitoringJob::Run(), CNetBlastMonitoringJob::x_ResetState(), CNetBlastMonitoringJob::x_Run(), and CNetBlastMonitoringJob::x_SetStatusText().

◆ m_Mutex [3/3]

CMutex CNetBlastJobDescriptor::m_Mutex

mutableprotected

Definition at line 118 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::Check(), CNetBlastJobDescriptor::GetDescription(), CNetBlastJobDescriptor::GetErrors(), CNetBlastJobDescriptor::GetJobTitle(), CNetBlastJobDescriptor::GetRemoteBlast(), CNetBlastJobDescriptor::GetRID(), CNetBlastJobDescriptor::GetSubmitTime(), CNetBlastJobDescriptor::Init(), CNetBlastJobDescriptor::MarkDeleted(), CNetBlastJobDescriptor::Release(), CNetBlastJobDescriptor::Retrieve(), and CNetBlastJobDescriptor::Submit().

◆ m_NAObjects [1/2]

TObjects CProSplignTool::m_NAObjects

protected

Definition at line 84 of file prosplign_tool.hpp.

Referenced by CProSplignTool::x_CreateLoadingJob(), CProSplignTool::x_CreateParamsPanelIfNeeded(), and CProSplignTool::x_SelectCompatibleInputObjects().

◆ m_NAObjects [2/2]

TObjects CSplignTool::m_NAObjects

protected

Definition at line 88 of file splign_tool.hpp.

Referenced by CSplignTool::QuickLaunch(), CSplignTool::x_CreateLoadingJob(), CSplignTool::x_CreateParamsPanelIfNeeded(), and CSplignTool::x_SelectCompatibleInputObjects().

◆ m_NCBIDBSizer

wxFlexGridSizer* CBLASTSearchOptionsPanel::m_NCBIDBSizer

Definition at line 157 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_NeedsDbGenCode

bool CBLASTParams::SProgInfo::m_NeedsDbGenCode

Definition at line 81 of file blast_search_params.hpp.

◆ m_NeedsQueryGenCode

bool CBLASTParams::SProgInfo::m_NeedsQueryGenCode

string CBLASTParams::m_NucDatabase

protected

Definition at line 233 of file blast_search_params.hpp.

Referenced by CBLASTParams::FromUserObject(), CBLASTParams::GetDatabase(), and CBLASTParams::ToUserObject().

◆ m_NucDB

bool CBLASTParams::SProgInfo::m_NucDB

wxRadioButton* CBLASTSearchOptionsPanel::m_NucRadio

Definition at line 143 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_Numrow

IAlnExplorer::TNumrow CSelRowHandle::m_Numrow

protected

Definition at line 194 of file multi_align_view.hpp.

Referenced by CSelRowHandle::GetNumrow().

◆ m_Object

SConstScopedObject CTreeBuilderParams::m_Object

private

Definition at line 99 of file tree_builder_params.hpp.

Referenced by CTreeBuilderParams::Copy(), CTreeBuilderParams::GetObject(), and CTreeBuilderParams::SetObject().

◆ m_ObjectIndex

CObjectIndex CPhyTreeView::m_ObjectIndex

private

Definition at line 141 of file phy_tree_view.hpp.

Referenced by CPhyTreeView::OnProjectChanged(), CPhyTreeView::RebuildObjectIndex(), and CPhyTreeView::x_OnSetSelection().

◆ m_ObjectList [1/2]

CObjectListWidget* CCleanupAlignmentsParamsPanel::m_ObjectList

Definition at line 172 of file cleanup_alignments_params_panel.hpp.

Referenced by CCleanupAlignmentsParamsPanel::CreateControls(), CCleanupAlignmentsParamsPanel::Init(), CCleanupAlignmentsParamsPanel::LoadSettings(), CCleanupAlignmentsParamsPanel::SaveSettings(), CCleanupAlignmentsParamsPanel::TransferDataFromWindow(), and CCleanupAlignmentsParamsPanel::TransferDataToWindow().

◆ m_ObjectList [2/2]

CObjectListWidget* CGroupAlignmentsParamsPanel::m_ObjectList

Definition at line 153 of file group_alignments_params_panel.hpp.

Referenced by CGroupAlignmentsParamsPanel::CreateControls(), CGroupAlignmentsParamsPanel::Init(), CGroupAlignmentsParamsPanel::LoadSettings(), CGroupAlignmentsParamsPanel::SaveSettings(), CGroupAlignmentsParamsPanel::TransferDataFromWindow(), and CGroupAlignmentsParamsPanel::TransferDataToWindow().

TObjects CCommonTaxTreeTool::m_Objects

protected

Definition at line 85 of file taxtree_tool.hpp.

Referenced by CCommonTaxTreeTool::x_CreateParamsPanelIfNeeded(), and CCommonTaxTreeTool::x_SelectCompatibleInputObjects().

◆ m_Objects [13/15]

TConstScopedObjects CTaxTreeToolParams::m_Objects

Definition at line 86 of file taxtree_tool_params.hpp.

Referenced by CTaxTreeToolParams::Copy(), CTaxTreeToolParams::GetObjects(), and CTaxTreeToolParams::SetObjects().

◆ m_Objects [14/15]

TObjects CTextAlignObjectLoader::m_Objects

private

Definition at line 86 of file text_align_object_loader.hpp.

Referenced by CTextAlignObjectLoader::Execute(), and CTextAlignObjectLoader::GetObjects().

◆ m_Objects [15/15]

TConstScopedObjects CCreateNeedlemanWunschToolManager::m_Objects

protected

Definition at line 85 of file create_needleman_wunsch_tool_manager.hpp.

Referenced by CCreateNeedlemanWunschToolManager::x_CreateParamsPanelIfNeeded(), and CCreateNeedlemanWunschToolManager::x_SelectCompatibleInputObjects().

◆ m_ObjIndex

CObjectIndex CMultiAlignView::m_ObjIndex

protected

Definition at line 152 of file multi_align_view.hpp.

Referenced by CMultiAlignView::OnProjectChanged(), CMultiAlignView::x_OnSetSelection(), and CMultiAlignView::x_RebuildObjectIndex().

◆ m_OKBtn

wxButton* CBLAST_DB_Dialog::m_OKBtn

Definition at line 172 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::CreateControls(), CBLAST_DB_Dialog::Init(), and CBLAST_DB_Dialog::OnTreectrlSelChanged().

◆ m_Open

bool CNetBLASTUIDataSource::m_Open

protected

Definition at line 199 of file net_blast_ui_data_source.hpp.

Referenced by CNetBLASTUIDataSource::Close(), CNetBLASTUIDataSource::IsOpen(), CNetBLASTUIDataSource::Open(), and CNetBLASTUIDataSource::~CNetBLASTUIDataSource().

◆ m_OptionPanel

CNetBLASTLoadOptionPanel* CNetBLASTUILoadManager::m_OptionPanel

protected

Definition at line 114 of file net_blast_ui_load_manager.hpp.

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

◆ m_Options

CSelectProjectOptions CCreateGeneModelTask::m_Options

private

Definition at line 172 of file create_gene_model_tool_manager.hpp.

Referenced by CCreateGeneModelTask::x_Run().

CConstRef<objects::CSeq_align> CMultiAlignView::m_OrigAlign

protected

Definition at line 147 of file multi_align_view.hpp.

Referenced by CMultiAlignView::OnProjectChanged(), CMultiAlignView::x_GetOrigObject(), and CMultiAlignView::x_GetValidInputData().

◆ m_OrigAnnot [1/4]

CConstRef<CSeq_annot> CAlignSpanView::m_OrigAnnot

private

original data object passed to the view

Definition at line 136 of file align_span_view.hpp.

Referenced by CAlignSpanView::x_GetOrigObject(), CAlignSpanView::x_InitWidget(), and CAlignSpanView::x_PreAttachToProject().

◆ m_OrigAnnot [2/4]

CConstRef<CSeq_annot> CCrossAlignView::m_OrigAnnot

private

original data object passed to the view

Definition at line 108 of file cross_align_view.hpp.

Referenced by CCrossAlignView::x_GetOrigObject(), CCrossAlignView::x_PostAttachToProject(), and CCrossAlignView::x_PreAttachToProject().

◆ m_OrigAnnot [3/4]

CConstRef<CSeq_annot> CMPCrossAlignView::m_OrigAnnot

private

original data object passed to the view

Definition at line 116 of file mp_cross_align_view.hpp.

Referenced by CMPCrossAlignView::InitView(), and CMPCrossAlignView::x_GetOrigObject().

◆ m_OrigAnnot [4/4]

CConstRef<objects::CSeq_annot> CMultiAlignView::m_OrigAnnot

protected

Definition at line 84 of file tree_builder_tool.hpp.

Referenced by CTreeBuilderTool::x_CreateLoadingJob(), CTreeBuilderTool::x_CreateParamsPanelIfNeeded(), and CTreeBuilderTool::x_GetParamsAsRegSetting().

protected

Definition at line 108 of file blast_db_dialog.hpp.

Referenced by CBLAST_Dlg_Item::GetLabel(), and CBLAST_Dlg_Item::GetPath().

◆ m_pConstruct

wxChoice* CTreeBuilderPanel::m_pConstruct

Definition at line 139 of file tree_builder_panel.hpp.

Referenced by CTreeBuilderPanel::CreateControls(), and CTreeBuilderPanel::TransferDataFromWindow().

◆ m_pDistance

wxChoice* CTreeBuilderPanel::m_pDistance

Definition at line 138 of file tree_builder_panel.hpp.

Referenced by CTreeBuilderPanel::CreateControls(), and CTreeBuilderPanel::TransferDataFromWindow().

◆ m_PId

long CMSAToolJob::m_PId

protected

Definition at line 88 of file msa_tool_job.hpp.

Referenced by CMSAToolJob::BeforeRun(), and CMSAToolJob::x_CreateProjectItems().

◆ m_pLabels

wxChoice* CTreeBuilderPanel::m_pLabels

Definition at line 140 of file tree_builder_panel.hpp.

Referenced by CTreeBuilderPanel::CreateControls(), and CTreeBuilderPanel::TransferDataFromWindow().

◆ m_PolyADetect

bool CSplignParams::m_PolyADetect

private

Definition at line 117 of file splign_params.hpp.

Referenced by CSplignParams::Copy(), CSplignParams::DebugDump(), CSplignParams::GetPolyADetect(), CSplignParams::Init(), CSplignParams::LoadSettings(), CSplignParams::operator==(), CSplignParams::SaveSettings(), and CSplignParams::SetPolyADetect().

◆ m_ProcHandle

TProcessHandle CBLASTSeqToolJob::m_ProcHandle

private

Definition at line 72 of file blast_seq_tool_job.hpp.

Referenced by CBLASTSeqToolJob::RequestCancel(), and CBLASTSeqToolJob::x_CreateProjectItems().

◆ m_Program

blast::EProgram CBLASTParams::SProgInfo::m_Program

Definition at line 75 of file blast_search_params.hpp.

◆ m_ProgramCombo

wxComboBox* CBLASTSearchOptionsPanel::m_ProgramCombo

Definition at line 148 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::OnProgramComboSelected(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSearchOptionsPanel::x_OnInputTypeChanged().

◆ m_ProgToParams

TProgramParamsMap CBLASTParams::m_ProgToParams

protected

Common parameters.

Definition at line 246 of file blast_search_params.hpp.

Referenced by CBLASTParams::CBLASTParams(), CBLASTParams::FromUserObject(), CBLASTParams::GetCurrParams(), CBLASTParams::ResetCurrParams(), and CBLASTParams::ToUserObject().

wxRadioButton* CBLASTSearchOptionsPanel::m_ProtRadio

Definition at line 144 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_Queries [1/2]

TConstScopedObjects CNGAlignParams::m_Queries

private

Definition at line 127 of file ngalign_params.hpp.

Referenced by CNGAlignParams::Copy(), CNGAlignParams::GetQueries(), CNGAlignParams::LogDump(), and CNGAlignParams::SetQueries().

◆ m_Queries [2/2]

TConstScopedObjects CNGAlignPanel::m_Queries

Definition at line 133 of file ngalign_panel.hpp.

Referenced by CNGAlignPanel::GetQueries(), and CNGAlignPanel::SetQueries().

◆ m_Query

CRef<CNetBLAST_DMSearchQuery> CNetBLAST_DMSearchJob::m_Query

protected

Definition at line 192 of file net_blast_dm_search_tool.hpp.

Referenced by CNetBLAST_DMSearchJob::x_DoSearch(), and CNetBLAST_DMSearchJob::x_ValidateParams().

◆ m_QueryCombo

wxComboBox* CBLASTSearchOptionsPanel::m_QueryCombo

Definition at line 161 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_QueryGenCodeCombo

wxComboBox* CBLASTSearchParamsPanel::m_QueryGenCodeCombo

Definition at line 174 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_InitGeneticCodesCombo().

◆ m_QueryGenCodeLabel

wxStaticText* CBLASTSearchParamsPanel::m_QueryGenCodeLabel

Definition at line 173 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), and CBLASTSearchParamsPanel::x_HideShowInputs().

◆ m_QueryGeneticCode [1/2]

int CBLASTParams::SProgParams::m_QueryGeneticCode

Definition at line 92 of file blast_search_params.hpp.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTParams::x_FromUserObject(), and CBLASTParams::x_ToUserObject().

◆ m_QueryGeneticCode [2/2]

wxString CBLASTSearchParamsPanel::m_QueryGeneticCode

protected

Definition at line 194 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::GetGeneticCode(), CBLASTSearchParamsPanel::SetGeneticCode(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_QueryListCtrl [1/2]

CObjectListWidget* CBLASTSearchOptionsPanel::m_QueryListCtrl

Definition at line 147 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::LoadSettings(), CBLASTSearchOptionsPanel::SaveSettings(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), and CBLASTSearchOptionsPanel::x_FillQueryList().

◆ m_QueryListCtrl [2/2]

CObjectListWidget* CNGAlignPanel::m_QueryListCtrl

Definition at line 123 of file ngalign_panel.hpp.

Referenced by CNGAlignPanel::CreateControls(), CNGAlignPanel::Init(), CNGAlignPanel::LoadSettings(), CNGAlignPanel::SaveSettings(), CNGAlignPanel::SetObjects(), and CNGAlignPanel::TransferDataFromWindow().

◆ m_QuerySeqSetCombo

wxChoice* CBLASTSearchOptionsPanel::m_QuerySeqSetCombo

Definition at line 146 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::x_UpdateQuerySeqSet().

string SCleanupAlignmentsParams::m_RegPath

Definition at line 102 of file cleanup_alignments_params_panel.hpp.

◆ m_RegPath [4/25]

string CCleanupAlignmentsParamsPanel::m_RegPath

private

Definition at line 203 of file cleanup_alignments_params_panel.hpp.

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

◆ m_RegPath [5/25]

string CClustalOmegaToolParams::m_RegPath

private

Definition at line 99 of file clustal_omega_tool_params.hpp.

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

◆ m_RegPath [6/25]

string CClustalwToolParams::m_RegPath

private

Definition at line 100 of file clustalw_tool_params.hpp.

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

◆ m_RegPath [7/25]

string CFindOverlapParams::m_RegPath

private

Definition at line 101 of file find_overlap_params.hpp.

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

◆ m_RegPath [8/25]

string SGroupAlignmentsParams::m_RegPath

Definition at line 95 of file group_alignments_params_panel.hpp.

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

◆ m_RegPath [9/25]

string CGroupAlignmentsParamsPanel::m_RegPath

protected

Definition at line 193 of file group_alignments_params_panel.hpp.

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

◆ m_RegPath [10/25]

string CKalignToolParams::m_RegPath

private

Definition at line 100 of file kalign_tool_params.hpp.

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

◆ m_RegPath [11/25]

string CMafftToolParams::m_RegPath

private

Definition at line 104 of file mafft_tool_params.hpp.

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

string CTaxTreeToolParams::m_RegPath

Definition at line 85 of file taxtree_tool_params.hpp.

Referenced by CTaxTreeToolParams::SetRegistryPath().

◆ m_RegPath [23/25]

string CTreeBuilderParams::m_RegPath

private

Definition at line 98 of file tree_builder_params.hpp.

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

◆ m_RegPath [24/25]

string CPslLoadManager::m_RegPath

protected

Definition at line 148 of file psl_load_manager.hpp.

Referenced by CPslLoadManager::SetRegistryPath().

◆ m_RegPath [25/25]

string CTextAlignLoaderManager::m_RegPath

protected

Definition at line 150 of file text_align_load_manager.hpp.

Referenced by CTextAlignLoaderManager::SetRegistryPath().

◆ m_RemoteBlast

CRef<blast::CRemoteBlast> CNetBlastJobDescriptor::m_RemoteBlast

protected

a proxy to Net BLAST that is used for updating Job state

Definition at line 134 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::Check(), CNetBlastJobDescriptor::GetRemoteBlast(), CNetBlastJobDescriptor::Init(), CNetBlastJobDescriptor::Release(), CNetBlastJobDescriptor::Retrieve(), CNetBlastJobDescriptor::Submit(), and CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded().

◆ m_RepeatLib

string CBLASTParams::SProgParams::m_RepeatLib

Definition at line 96 of file blast_search_params.hpp.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_RepeatsCheck

wxCheckBox* CBLASTSearchParamsPanel::m_RepeatsCheck

Definition at line 179 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_UpdateMaskCtrls().

◆ m_RepeatType

wxChoice* CBLASTSearchParamsPanel::m_RepeatType

Definition at line 177 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::OnWindowmaskerTaxIdSelected(), CBLASTSearchParamsPanel::TaxonsLoaded(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_InitTaxons().

◆ m_ResetBtn

wxButton* CNetBlastDMSearchFormPanel::m_ResetBtn

Definition at line 126 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::CreateControls(), and CNetBlastDMSearchFormPanel::Init().

◆ m_Retrieved

bool CNetBlastDMSearchFormPanel::m_Retrieved

protected

Definition at line 135 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::CreateControls(), CNetBlastDMSearchFormPanel::GetRetrieved(), CNetBlastDMSearchFormPanel::Init(), and CNetBlastDMSearchFormPanel::SetRetrieved().

◆ m_RID

string CNetBlastJobDescriptor::m_RID

protected

Job attributes.

Definition at line 125 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::FromUserObject(), CNetBlastJobDescriptor::GetRID(), CNetBlastJobDescriptor::Init(), CNetBlastJobDescriptor::Submit(), CNetBlastJobDescriptor::ToUserObject(), and CNetBlastJobDescriptor::x_CreateRemoteBlastIfNeeded().

◆ m_Root

CRef<CBLAST_Dlg_Item> CBLAST_DB_Dialog::m_Root

protected

Definition at line 208 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::x_CreateItems(), CBLAST_DB_Dialog::x_CreateTreeItems(), and CBLAST_DB_Dialog::x_FilterItems().

◆ m_SavedInput

string CNetBLASTUILoadManager::m_SavedInput

mutableprotected

Definition at line 112 of file net_blast_ui_load_manager.hpp.

Referenced by CNetBLASTUILoadManager::CleanUI(), CNetBLASTUILoadManager::GetCurrentPanel(), and CNetBLASTUILoadManager::SaveSettings().

◆ m_Scheme

CRef<CPhyloTreeScheme> CPhyTreeView::m_Scheme

private

Definition at line 139 of file phy_tree_view.hpp.

Referenced by CPhyTreeView::GetScheme(), CPhyTreeView::OnBioTreeChanged(), CPhyTreeView::OnProjectChanged(), and CPhyTreeView::OnSomethingEdited().

◆ m_Scope [1/4]

CRef<CScope> CAlignSpanView::m_Scope

private

Definition at line 151 of file align_span_view.hpp.

◆ m_Scope [2/4]

CScope* CNetBlastLoadingJob::m_Scope

protected

Definition at line 192 of file blast_jobs.hpp.

Referenced by CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult().

◆ m_Scope [3/4]

CRef<objects::CScope> CCreateGeneModelTask::m_Scope

private

Definition at line 177 of file create_gene_model_tool_manager.hpp.

Referenced by CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CCreateGeneModelTask::x_GetCommand(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), and CCreateGeneModelTask::x_Run().

◆ m_Scope [4/4]

CRef<objects::CScope> CTextAlignObjectLoader::m_Scope

private

Definition at line 88 of file text_align_object_loader.hpp.

Referenced by CTextAlignObjectLoader::Init(), and CTextAlignObjectLoader::LoadFromStream().

◆ m_ScoringMethod

int CMuscleToolParams::m_ScoringMethod

private

Definition at line 101 of file muscle_tool_params.hpp.

Referenced by CMuscleToolParams::Copy(), CMuscleToolParams::GetScoringMethod(), CMuscleToolParams::Init(), CMuscleToolParams::LoadSettings(), CMuscleToolParams::operator==(), CMuscleToolParams::SaveSettings(), and CMuscleToolParams::SetScoringMethod().

◆ m_ScoringMethods

vector<string> CMultiAlignView::m_ScoringMethods

private

Definition at line 137 of file multi_align_view.hpp.

◆ m_SearchCtrl [1/2]

wxTextCtrl* CBLAST_DB_Dialog::m_SearchCtrl

Definition at line 169 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::CreateControls(), CBLAST_DB_Dialog::Init(), CBLAST_DB_Dialog::OnResetBtnClick(), and CBLAST_DB_Dialog::OnSearchTextUpdated().

◆ m_SearchCtrl [2/2]

wxTextCtrl* CNetBlastDMSearchFormPanel::m_SearchCtrl

Definition at line 125 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::CreateControls(), CNetBlastDMSearchFormPanel::Init(), CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated(), and CNetBlastDMSearchFormPanel::OnResetClick().

◆ m_SearchValue

wxString CNetBlastDMSearchFormPanel::m_SearchValue

protected

Definition at line 137 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::CreateControls(), CNetBlastDMSearchFormPanel::GetSearchValue(), CNetBlastDMSearchFormPanel::OnFilterInputTextUpdated(), and CNetBlastDMSearchFormPanel::SetSearchValue().

◆ m_SecondSeqFreeEnds

int CNeedlemanWunschToolParams::m_SecondSeqFreeEnds

private

Definition at line 116 of file needlemanwunsch_tool_params.hpp.

Referenced by CNeedlemanWunschToolParams::Copy(), CNeedlemanWunschToolParams::GetSecondSeqFreeEnds(), CNeedlemanWunschToolParams::Init(), CNeedlemanWunschToolParams::LoadSettings(), CNeedlemanWunschToolParams::operator==(), CNeedlemanWunschToolParams::SaveSettings(), and CNeedlemanWunschToolParams::SetSecondSeqFreeEnds().

◆ m_SelDatabase

ECommand CBlastSearchTask::m_Stage

wxStaticText* CBLAST_DB_Dialog::m_StatusText

Definition at line 170 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::CreateControls(), CBLAST_DB_Dialog::Init(), and CBLAST_DB_Dialog::x_UpdateFilterStatusText().

◆ m_StyleCatalog

CRowStyleCatalog CMultiAlignView::m_StyleCatalog

protected

Definition at line 135 of file multi_align_view.hpp.

Referenced by CMultiAlignView::CreateViewWindow().

◆ m_Subject [1/2]

SConstScopedObject CNGAlignParams::m_Subject

private

Definition at line 126 of file ngalign_params.hpp.

Referenced by CNGAlignParams::Copy(), CNGAlignParams::GetSubject(), CNGAlignParams::LogDump(), and CNGAlignParams::SetSubject().

◆ m_Subject [2/2]

SConstScopedObject CNGAlignPanel::m_Subject

Definition at line 132 of file ngalign_panel.hpp.

Referenced by CNGAlignPanel::GetSubject(), and CNGAlignPanel::SetSubject().

◆ m_SubjectListCtrl [1/2]

CObjectListWidget* CBLASTSearchOptionsPanel::m_SubjectListCtrl

Definition at line 156 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::LoadSettings(), CBLASTSearchOptionsPanel::SaveSettings(), CBLASTSearchOptionsPanel::TransferDataFromWindow(), CBLASTSearchOptionsPanel::x_FillQueryList(), and CBLASTSearchOptionsPanel::x_FillSubjectList().

◆ m_SubjectListCtrl [2/2]

CObjectListWidget* CNGAlignPanel::m_SubjectListCtrl

Definition at line 124 of file ngalign_panel.hpp.

Referenced by CNGAlignPanel::CreateControls(), CNGAlignPanel::Init(), CNGAlignPanel::LoadSettings(), CNGAlignPanel::SaveSettings(), CNGAlignPanel::SetObjects(), and CNGAlignPanel::TransferDataFromWindow().

◆ m_SubjectSeqSetCombo

wxChoice* CBLASTSearchOptionsPanel::m_SubjectSeqSetCombo

Definition at line 154 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_SubjectSeqSetStatic

wxStaticText* CBLASTSearchOptionsPanel::m_SubjectSeqSetStatic

Definition at line 153 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::x_UpdateSubjectSeqSet(), and CBLASTSearchOptionsPanel::x_UpdateSubjectType().

◆ m_SubjectType

ESubjectType CBLASTParams::m_SubjectType

protected

Definition at line 257 of file blast_search_params.hpp.

Referenced by CBLASTParams::FromUserObject(), and CBLASTParams::ToUserObject().

◆ m_SubjectTypeLDBCtrl

wxRadioButton* CBLASTSearchOptionsPanel::m_SubjectTypeLDBCtrl

Definition at line 152 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_SubjectTypeNCBICtrl

wxRadioButton* CBLASTSearchOptionsPanel::m_SubjectTypeNCBICtrl

Definition at line 151 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_SubjectTypeSeqsCtrl

wxRadioButton* CBLASTSearchOptionsPanel::m_SubjectTypeSeqsCtrl

Definition at line 150 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::CreateControls(), CBLASTSearchOptionsPanel::Init(), and CBLASTSearchOptionsPanel::TransferDataToWindow().

◆ m_SubjSeqLocs

TConstScopedObjects CBLASTParams::m_SubjSeqLocs

protected

Params applying only to BLAST Sequences.

Definition at line 243 of file blast_search_params.hpp.

Referenced by CBLASTParams::GetSubjSeqLocs().

◆ m_Submitted

bool CNetBlastDMSearchFormPanel::m_Submitted

protected

Definition at line 133 of file net_blast_dm_search_form_panel.hpp.

Referenced by CNetBlastDMSearchFormPanel::CreateControls(), CNetBlastDMSearchFormPanel::GetSubmitted(), CNetBlastDMSearchFormPanel::Init(), and CNetBlastDMSearchFormPanel::SetSubmitted().

◆ m_SubmitTime

time_t CNetBlastJobDescriptor::m_SubmitTime

protected

Definition at line 129 of file net_blast_job_descr.hpp.

Referenced by CNetBlastJobDescriptor::CNetBlastJobDescriptor(), CNetBlastJobDescriptor::FromUserObject(), CNetBlastJobDescriptor::GetSubmitTime(), CNetBlastJobDescriptor::Submit(), and CNetBlastJobDescriptor::ToUserObject().

◆ m_SubmittingJob

CRef<CNetBlastSubmittingJob> CBlastSearchTask::m_SubmittingJob

Referenced by CNetBlastMonitoringJob::CNetBlastMonitoringJob(), and CNetBlastMonitoringJob::x_StartRetrivingTask().

◆ m_ToolName [2/4]

string CBLASTSearchOptionsPanel::m_ToolName

protected

Definition at line 229 of file blast_search_options_panel.hpp.

Referenced by CBLASTSearchOptionsPanel::Init(), CBLASTSearchOptionsPanel::OnBrowseDatabases(), and CBLASTSearchOptionsPanel::Setup().

◆ m_ToolName [3/4]

string CBlastSearchTask::m_ToolName

protected

name of the tool that launched the task; used in UI

Definition at line 109 of file blast_search_task.hpp.

Referenced by CBlastSearchTask::Init_Monitoring(), CBlastSearchTask::Init_RetrieveRID(), CBlastSearchTask::Init_SubmitSearch(), CBlastSearchTask::x_InitMonitoringStage(), and CBlastSearchTask::x_ReportErrors().

◆ m_ToolName [4/4]

wxString CMSAToolJob::m_ToolName

protected

Definition at line 98 of file msa_tool_job.hpp.

Referenced by CMSAToolJob::BeforeRun(), and CMSAToolJob::x_CreateProjectItems().

◆ m_TreeCtrl

wxTreeCtrl* CBLAST_DB_Dialog::m_TreeCtrl

Definition at line 171 of file blast_db_dialog.hpp.

Referenced by CBLAST_DB_Dialog::CreateControls(), CBLAST_DB_Dialog::Init(), CBLAST_DB_Dialog::OnInitDialog(), CBLAST_DB_Dialog::OnTreectrlSelChanged(), CBLAST_DB_Dialog::x_BuildTreeItems(), CBLAST_DB_Dialog::x_CreateTreeItems(), CBLAST_DB_Dialog::x_FilterItems(), CBLAST_DB_Dialog::x_GetSelectedDBItem(), and CBLAST_DB_Dialog::x_UpdateCollapsedState().

◆ m_TruncateOverlap

wxCheckBox* CMergeAlignmentsParamsPanel::m_TruncateOverlap

Definition at line 146 of file merge_alignments_params_panel.hpp.

Referenced by CMergeAlignmentsParamsPanel::CreateControls(), CMergeAlignmentsParamsPanel::Init(), CMergeAlignmentsParamsPanel::TransferDataFromWindow(), and CMergeAlignmentsParamsPanel::TransferDataToWindow().

◆ m_Type

CRef<CNetBLASTUIDataSourceType> CNetBLASTUIDataSource::m_Type

mutableprotected

Definition at line 194 of file net_blast_ui_data_source.hpp.

Referenced by CNetBLASTUIDataSource::GetType().

◆ m_TypeDescr [1/3]

CProjectViewTypeDescriptor CAlignSpanView::m_TypeDescr

staticprivate

Definition at line 156 of file align_span_view.hpp.

Referenced by CAlignSpanViewFactory::GetProjectViewTypeDescriptor(), and CAlignSpanView::GetTypeDescriptor().

◆ m_TypeDescr [2/3]

CProjectViewTypeDescriptor CDotMatrixView::m_TypeDescr

staticprivate

Definition at line 122 of file dot_matrix_view.hpp.

Referenced by CDotMatrixViewFactory::GetProjectViewTypeDescriptor(), and CDotMatrixView::GetTypeDescriptor().

◆ m_TypeDescr [3/3]

CProjectViewTypeDescriptor CMPCrossAlignView::m_TypeDescr

staticprivate

Definition at line 123 of file mp_cross_align_view.hpp.

◆ m_UseDustFilter

bool CBLASTParams::SProgInfo::m_UseDustFilter

Definition at line 82 of file blast_search_params.hpp.

◆ m_UseNucForMixInput

bool CBLASTToolManager::m_UseNucForMixInput

mutableprotected

Definition at line 149 of file blast_tool_manager.hpp.

Referenced by CBLASTToolManager::LoadSettings(), CBLASTToolManager::QuickLaunch(), CBLASTToolManager::SaveSettings(), and CBLASTToolManager::x_IsNucInput().

◆ m_ViewManager [1/2]

CRef<COpenViewManager> CDotMatrixViewFactory::m_ViewManager

private

Definition at line 157 of file dot_matrix_view.hpp.

Referenced by CDotMatrixViewFactory::GetOpenViewManager().

◆ m_ViewManager [2/2]

CRef<COpenViewManager> CMultiAlignViewFactory::m_ViewManager

private

Definition at line 184 of file multi_align_view.hpp.

Referenced by CMultiAlignViewFactory::CMultiAlignViewFactory(), and CMultiAlignViewFactory::GetOpenViewManager().

◆ m_Views

TViews CMPCrossAlignView::m_Views

private

Definition at line 121 of file mp_cross_align_view.hpp.

Referenced by CMPCrossAlignView::BroadcastVisibleRange(), CMPCrossAlignView::DestroyView(), CMPCrossAlignView::GetSelection(), CMPCrossAlignView::InitView(), CMPCrossAlignView::OnVisibleRangeChanged(), and CMPCrossAlignView::SetSelection().

◆ m_Visible

bool CBLAST_Dlg_Item::m_Visible

protected

Definition at line 111 of file blast_db_dialog.hpp.

Referenced by CBLAST_Dlg_Item::IsVisible(), and CBLAST_Dlg_Item::SetVisible().

◆ m_WaitPeriodIndex

int CNetBlastMonitoringJob::m_WaitPeriodIndex

protected

Definition at line 158 of file blast_jobs.hpp.

Referenced by CNetBlastMonitoringJob::GetWaitPeriod().

◆ m_WM_Dir [1/2]

string CBLASTParams::m_WM_Dir

protected

path to WM statistics databases

Definition at line 252 of file blast_search_params.hpp.

◆ m_WM_Dir [2/2]

string CNGAlignParams::m_WM_Dir

private

Definition at line 121 of file ngalign_params.hpp.

Referenced by CNGAlignParams::Copy(), CNGAlignParams::GetWMDir(), CNGAlignParams::operator==(), and CNGAlignParams::SetWMDir().

◆ m_WM_TaxId [1/2]

int CBLASTParams::SProgParams::m_WM_TaxId

winmask tax id

Definition at line 97 of file blast_search_params.hpp.

Referenced by CBLASTSearchParamsPanel::TaxonsLoaded(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSeqToolJob::x_CreateProjectItems(), and CBLASTSearchParamsPanel::x_InitTaxons().

◆ m_WM_TaxId [2/2]

int CNGAlignParams::m_WM_TaxId

private

Definition at line 120 of file ngalign_params.hpp.

Referenced by CNGAlignParams::Copy(), CNGAlignParams::GetWMTaxId(), CNGAlignParams::Init(), CNGAlignParams::LoadSettings(), CNGAlignParams::LogDump(), CNGAlignParams::operator==(), CNGAlignParams::SaveSettings(), and CNGAlignParams::SetWMTaxId().

◆ m_WMDownload

wxButton* CBLASTSearchParamsPanel::m_WMDownload

Definition at line 183 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_ShowWM().

◆ m_WMStatic

wxStaticText* CBLASTSearchParamsPanel::m_WMStatic

Definition at line 181 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), and CBLASTSearchParamsPanel::x_ShowWM().

◆ m_WMStaticBoxSizer

wxStaticBoxSizer* CBLASTSearchParamsPanel::m_WMStaticBoxSizer

Definition at line 180 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::x_HideShowInputs(), and CBLASTSearchParamsPanel::x_ShowWM().

◆ m_WMTaxIds

wxChoice* CBLASTSearchParamsPanel::m_WMTaxIds

Definition at line 182 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::Init(), CBLASTSearchParamsPanel::OnRepeatTypeSelected(), CBLASTSearchParamsPanel::TaxonsLoaded(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::x_InitTaxons(), and CBLASTSearchParamsPanel::x_ShowWM().

◆ m_WordSize [1/3]

int CBLASTParams::SProgParams::m_WordSize

Definition at line 89 of file blast_search_params.hpp.

Referenced by CBLASTParams::PrintParams(), CBLASTParams::ToArgVec(), CBLASTSearchParamsPanel::TransferDataFromWindow(), CBLASTSearchParamsPanel::TransferDataToWindow(), CBLASTParams::x_FromUserObject(), and CBLASTParams::x_ToUserObject().

◆ m_WordSize [2/3]

long CBLASTSearchParamsPanel::m_WordSize

protected

Definition at line 196 of file blast_search_params_panel.hpp.

Referenced by CBLASTSearchParamsPanel::CreateControls(), CBLASTSearchParamsPanel::GetWordSize(), CBLASTSearchParamsPanel::SetWordSize(), CBLASTSearchParamsPanel::TransferDataFromWindow(), and CBLASTSearchParamsPanel::TransferDataToWindow().

◆ m_WordSize [3/3]

long CNGAlignParams::m_WordSize

private

Definition at line 116 of file ngalign_params.hpp.

Referenced by CNGAlignParams::Copy(), CNGAlignParams::GetWordSize(), CNGAlignParams::Init(), CNGAlignParams::LoadSettings(), CNGAlignParams::LogDump(), CNGAlignParams::operator==(), CNGAlignParams::SaveSettings(), and CNGAlignParams::SetWordSize().

◆ mf_FindComparts

bool CBLASTParams::mf_FindComparts

protected

Definition at line 250 of file blast_search_params.hpp.

◆ mf_Standalone

bool CBLASTParams::mf_Standalone

protected

Definition at line 251 of file blast_search_params.hpp.

◆ mRNA

CRef<objects::CSeq_feat> SGeneCdsmRnaFeats::mRNA

Definition at line 115 of file create_gene_model_tool_manager.hpp.

Referenced by SGeneCdsmRnaFeats::CrossLinkTriple(), SGeneCdsmRnaFeats::GetID(), CCreateGeneModelTask::x_StoreGeneratedFeats(), and CCreateGeneModelTask::x_UpdateGeneOnSequence().

◆ sGeneDbName

const string CCreateGeneModelTask::sGeneDbName

static

CCreateGeneModelTask.

Definition at line 149 of file create_gene_model_tool_manager.hpp.

Referenced by SGeneCdsmRnaFeats::CrossLinkTriple(), CCreateGeneModelTask::s_GetGeneID(), and CCreateGeneModelTask::x_UpdateGeneOnSequence().

◆ sm_ProgramToAttr

CBLASTParams::TProgramAttrMap CBLASTParams::sm_ProgramToAttr

staticprotected

Macros

Typedefs

Enumerations

Functions

Variables

Friends

IWMClient interface implementation

IView interface implementation

IProjectView implementation

ISelectionClient Implementation

CProjectViewBase overridables

CProjectView callback overridables

IRegSettings interface implementation

CProjectViewBase internal overridables

CProjectView internal overridables

IExtension interface implementation

IProjectViewFactory interface implementation

IWMClient interface implementation

IView interface implementation

IProjectView implementation

ISelectionClient Implementation

CProjectViewBase overridables

CProjectView internal overridables

IExtension interface implementation

IProjectViewFactory interface implementation

IAppJob implementation

IAppJob implementation

IWaitPeriod implementation

CAlgoToolManagerParamsPanel implementation

CTaxIdHelper::ICallback interface implementation

CAlgoToolManagerParamsPanel implementation

CCompositeAppTask overridables

IUIToolManager interface implementation

IUIAlgoToolManager interface implementation

IExtension interface implementation

IRegSettings interface implementation

IRegSettings interface implementation

CAlgoToolManagerParamsPanel implementation

overriding IUIToolManager functions implemented in CAlgoToolManagerBase

IExtension interface implementation

overriding CAlgoToolManagerBase virtual functions

overriding IUIToolManager functions implemented in CAlgoToolManagerBase

IExtension interface implementation

overriding CAlgoToolManagerBase virtual functions

overriding IUIToolManager functions implemented in CAlgoToolManagerBase

IExtension interface implementation

overriding CAlgoToolManagerBase virtual functions

overriding IUIToolManager functions implemented in CAlgoToolManagerBase

IExtension interface implementation

overriding CAlgoToolManagerBase virtual functions

IWMClient interface implementation

IView interface implementation

IProjectView implementation

ISelectionClient Implementation

CProjectViewBase overridables

IVisibleRangeClient interface implementation

CProjectView internal overridables

IExtension interface implementation

IProjectViewFactory interface implementation

IWMClient interface implementation

IView interface implementation

IProjectView implementation

ISelectionClient Implementation

CProjectViewBase overridables

IVisibleRangeClient interface implementation

CProjectView internal overridables

IExtension interface implementation

IProjectViewFactory interface implementation

IRegSettings interface implementation

CAlgoToolManagerParamsPanel implementation

overriding IUIToolManager functions implemented in CAlgoToolManagerBase

IExtension interface implementation

overriding CAlgoToolManagerBase virtual functions

IRegSettings interface implementation

CAlgoToolManagerParamsPanel implementation

overriding IUIToolManager functions implemented in CAlgoToolManagerBase

IExtension interface implementation

overriding CAlgoToolManagerBase virtual functions

overriding IUIToolManager functions implemented in CAlgoToolManagerBase