GUI_PKG_ALIGNMENT

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