NCBI C++ ToolKit
Classes | Macros | Enumerations | Enumerator | Functions | Variables | Friends
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  CBLAST_DB_Dialog::CExecuteAsync_CreateItems
 Private async class to off-load GUI. 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::SProgParams
 describes parameters for a BLAST program More...
 
struct  CBLASTParams::SProgInfo
 describes static attributes of 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  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  CClustalOmegaToolPanel
 
class  CClustalwToolPanel
 
class  CCreateNeedlemanWunschToolManager
 CCreateNeedlemanWunschToolManager. More...
 
class  CCreateNeedlemanWunschJob
 CCreateNeedlemanWunschJob. More...
 
class  CKalignToolPanel
 
class  CMafftToolPanel
 
class  CMuscleToolPanel
 
class  CNGAlignPanel
 
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"
 

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  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  {
  CClustalOmegaToolPanel::ID_CCLUSTALOMEGAPANEL = 10050, CClustalOmegaToolPanel::ID_PANEL = 10051, CClustalOmegaToolPanel::ID_CHECKBOX12 = 10053, CClustalOmegaToolPanel::ID_TEXTCTRL11 = 10052,
  CClustalOmegaToolPanel::ID_TEXTCTRL12 = 10055, CClustalOmegaToolPanel::ID_BITMAPBUTTON1 = 10056
}
 
enum  {
  CClustalwToolPanel::ID_CCLUSTALWPANEL = 10050, CClustalwToolPanel::ID_PANEL = 10051, CClustalwToolPanel::ID_CHECKBOX12 = 10053, CClustalwToolPanel::ID_TEXTCTRL11 = 10052,
  CClustalwToolPanel::ID_TEXTCTRL12 = 10055, CClustalwToolPanel::ID_BITMAPBUTTON1 = 10056
}
 
enum  {
  CKalignToolPanel::ID_CKALIGNPANEL = 10050, CKalignToolPanel::ID_PANEL = 10051, CKalignToolPanel::ID_CHECKBOX = 10000, CKalignToolPanel::ID_TEXTCTRL11 = 10052,
  CKalignToolPanel::ID_TEXTCTRL12 = 10055, CKalignToolPanel::ID_BITMAPBUTTON1 = 10056
}
 
enum  {
  CMafftToolPanel::ID_CMAFFTPANEL = 10050, CMafftToolPanel::ID_PANEL = 10051, CMafftToolPanel::ID_CHECKBOX1 = 10001, CMafftToolPanel::ID_CHECKBOX = 10000,
  CMafftToolPanel::ID_TEXTCTRL11 = 10052, CMafftToolPanel::ID_TEXTCTRL12 = 10055, CMafftToolPanel::ID_BITMAPBUTTON1 = 10056
}
 
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  { 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 ()
 
 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 TConstScopedObjectsCNeedlemanWunschToolParams::GetObjects () const
 
TConstScopedObjectsCNeedlemanWunschToolParams::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)
 
 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)
 
CMuscleToolParamsCMuscleToolPanel::GetData ()
 
const CMuscleToolParamsCMuscleToolPanel::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 SConstScopedObjectCNGAlignPanel::GetSubject () const
 
SConstScopedObjectCNGAlignPanel::SetSubject ()
 
const TConstScopedObjectsCNGAlignPanel::GetQueries () const
 
TConstScopedObjectsCNGAlignPanel::SetQueries ()
 
wxBitmap CNGAlignPanel::GetBitmapResource (const wxString &name)
 
wxIcon CNGAlignPanel::GetIconResource (const wxString &name)
 
void CNGAlignPanel::SetObjects (TConstScopedObjects *objects)
 
static bool CNGAlignPanel::ShowToolTips ()
 
 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 ()
 
CTaxTreeToolParamsCTaxTreeToolPanel::GetData ()
 
const CTaxTreeToolParamsCTaxTreeToolPanel::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 ()
 

Variables

CConstRef< CSeq_annotCAlignSpanView::m_OrigAnnot
 original data object passed to the view More...
 
CConstRef< CSeq_alignCAlignSpanView::m_OrigAlign
 
CConstRef< CBioseqCAlignSpanView::m_OrigBioseq
 
vector< CConstRef< CSeq_align > > CAlignSpanView::m_InputAligns
 
CRef< IAlnMultiDataSourceCAlignSpanView::m_DataSource
 
CAnchoredAln CAlignSpanView::m_AnchoredAln
 
wxPanel * CAlignSpanView::m_Panel
 
wxStatusBar * CAlignSpanView::m_StatusBar
 
CAlnSpanWidgetCAlignSpanView::m_AlnWidget
 
auto_ptr< CAlnSpanVertModelCAlignSpanView::m_Model
 
CRef< CScopeCAlignSpanView::m_Scope
 
CRef< CSeq_idCAlignSpanView::m_Seq_id
 
string CAlignSpanView::m_RegPath
 
static CProjectViewTypeDescriptor CAlignSpanView::m_TypeDescr
 
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
 
CObjectListWidgetSelCMuscleToolPanel::m_LocationSel
 
CMuscleToolParams CMuscleToolPanel::m_data
 
TConstScopedObjectsCMuscleToolPanel::m_InputObjects
 
CObjectListWidgetCNGAlignPanel::m_QueryListCtrl
 
CObjectListWidgetCNGAlignPanel::m_SubjectListCtrl
 
SConstScopedObject CNGAlignPanel::m_Subject
 
TConstScopedObjects CNGAlignPanel::m_Queries
 
CObjectListWidgetSelCTaxTreeToolPanel::m_SeqIds
 
CTaxTreeToolParams CTaxTreeToolPanel::m_data
 
TConstScopedObjectsCTaxTreeToolPanel::m_InputObjects
 

Friends

class CAlignSpanView::CAlignSpanViewFactory
 
class CNeedlemanWunschToolParams::CAlignNeedlemanWunschPanel
 

IWMClient interface implementation

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

IView interface implementation

virtual const CViewTypeDescriptorCAlignSpanView::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
 

IVisibleRangeClient interface implementation

virtual void CAlignSpanView::OnVisibleRangeChanged (const CVisibleRange &vrange, IVisibleRangeClient *source)
 

CProjectViewBase internal overridables

virtual void CAlignSpanView::x_CreateMenuBarMenu ()
 initializes m_MenuBarMenu; override in derived classes More...
 
virtual const CObjectCAlignSpanView::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 IViewCAlignSpanViewFactory::CreateInstance () const
 creates a view instance More...
 
virtual IViewCAlignSpanViewFactory::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 CProjectViewTypeDescriptorCAlignSpanViewFactory::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...
 

CAlgoToolManagerParamsPanel implementation

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

IRegSettings interface implementation

virtual void CMuscleToolPanel::SetRegistryPath (const string &path)
 CAlgoToolManagerParamsPanel. More...
 
virtual void CMuscleToolPanel::LoadSettings ()
 
virtual void CMuscleToolPanel::SaveSettings () const
 override in derived classes More...
 

CAlgoToolManagerParamsPanel implementation

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

IRegSettings interface implementation

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

CAlgoToolManagerParamsPanel implementation

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

IRegSettings interface implementation

virtual void CTaxTreeToolPanel::SetRegistryPath (const string &path)
 CAlgoToolManagerParamsPanel. More...
 
virtual void CTaxTreeToolPanel::LoadSettings ()
 
virtual void CTaxTreeToolPanel::SaveSettings () const
 override in derived classes More...
 

Detailed Description

Macro Definition Documentation

#define NET_BLAST_DM_TOOL_NAME   "NCBI Net BLAST"
#define NET_BLAST_LOADER_LABEL   "RIDs from NCBI Net BLAST"

Definition at line 60 of file net_blast_ui_load_manager.hpp.

Referenced by CNetBLASTUIDataSource::OnLoadRIDs().

Enumeration Type Documentation

anonymous enum
Enumerator
ID_CBLAST_DB_DIALOG 
ID_SEARCH 
ID_RESET_BTN 
wxID_STATUS 
ID_TREECTRL 

Definition at line 173 of file blast_db_dialog.hpp.

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

Definition at line 165 of file blast_search_options_panel.hpp.

anonymous enum
Enumerator
ID_DBS_LOADING_TEXT 
ID_DBS_LOADING_PROGRESS 
ID_DBS_FAILED 
ID_DBS_TRY_AGAIN 

Definition at line 186 of file blast_search_options_panel.hpp.

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

Definition at line 197 of file blast_search_params_panel.hpp.

anonymous enum
protected
Enumerator
ID_LOADING_TEXT 
ID_LOADING_PROGRESS 

Definition at line 218 of file blast_search_params_panel.hpp.

anonymous enum
Enumerator
ID_CCLEANUPALIGNMENTSPARAMSPANEL 
ID_LISTCTRL2 
ID_COMBOBOX 
ID_TEXTCTRL1 
ID_TEXTCTRL 
ID_CHECKBOX1 
ID_CHECKBOX2 
ID_CHECKBOX 
ID_CHECKBOX5 

Definition at line 181 of file cleanup_alignments_params_panel.hpp.

anonymous enum
Enumerator
ID_CFINDOVERLAPPANEL 
ID_LISTCTRL3 
ID_LISTCTRL4 
ID_TEXTCTRL2 
ID_TEXTCTRL4 
ID_TEXTCTRL5 

Definition at line 124 of file find_overlap_panel.hpp.

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

Definition at line 165 of file group_alignments_params_panel.hpp.

anonymous enum
Enumerator
ID_CBLASTSEARCHOPTIONSPANEL 
ID_LISTCTRL1 
ID_CHECKBOX6 
ID_CHECKBOX7 
ID_CHECKBOX8 
ID_CHECKBOX9 
ID_CHECKBOX10 

Definition at line 149 of file merge_alignments_params_panel.hpp.

anonymous enum
protected
Enumerator
ID_CNETBLASTDMSEARCHFORM 
ID_FILTER_INPUT 
ID_SUBMITTED_CHECK 
ID_COMPLETED_CHECK 
ID_FAILED_CHECK 
ID_RETRIEVED_CHECK 
ID_EXPIRED_CHECK 

Definition at line 139 of file net_blast_dm_search_form_panel.hpp.

anonymous enum
Enumerator
ID_NETBLASTLOADOPTIONPANEL 
ID_TEXTCTRL1 

Definition at line 94 of file net_blast_load_option_panel.hpp.

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

Definition at line 159 of file splign_panel.hpp.

anonymous enum
Enumerator
ID_CTreeBuilderPanel 
ID_LISTCTRL3 
ID_LISTCTRL4 
ID_TEXTCTRL2 
ID_TEXTCTRL3 
ID_TEXTCTRL4 
ID_TEXTCTRL5 

Definition at line 126 of file tree_builder_panel.hpp.

anonymous enum
Enumerator
ID_CCLUSTALOMEGAPANEL 
ID_PANEL 
ID_CHECKBOX12 
ID_TEXTCTRL11 
ID_TEXTCTRL12 
ID_BITMAPBUTTON1 

Definition at line 126 of file clustal_omega_tool_panel.hpp.

anonymous enum
Enumerator
ID_CCLUSTALWPANEL 
ID_PANEL 
ID_CHECKBOX12 
ID_TEXTCTRL11 
ID_TEXTCTRL12 
ID_BITMAPBUTTON1 

Definition at line 126 of file clustalw_tool_panel.hpp.

anonymous enum
Enumerator
ID_CKALIGNPANEL 
ID_PANEL 
ID_CHECKBOX 
ID_TEXTCTRL11 
ID_TEXTCTRL12 
ID_BITMAPBUTTON1 

Definition at line 130 of file kalign_tool_panel.hpp.

anonymous enum
Enumerator
ID_CMAFFTPANEL 
ID_PANEL 
ID_CHECKBOX1 
ID_CHECKBOX 
ID_TEXTCTRL11 
ID_TEXTCTRL12 
ID_BITMAPBUTTON1 

Definition at line 130 of file mafft_tool_panel.hpp.

anonymous enum
Enumerator
ID_CMUSCLEPANEL 
ID_PANEL 
ID_CHOICE2 
ID_CHECKBOX12 
ID_TEXTCTRL11 
ID_TEXTCTRL12 
ID_BITMAPBUTTON1 

Definition at line 130 of file muscle_tool_panel.hpp.

anonymous enum
Enumerator
ID_CNGALIGNPANEL 
ID_QUERY_LIST 
ID_SUBJ_LIST 

Definition at line 125 of file ngalign_panel.hpp.

anonymous enum
Enumerator
ID_CTAXTREETOOLPANEL 
ID_PANEL3 

Definition at line 128 of file taxtree_tool_panel.hpp.

which algorithm are we using?

Enumerator
eHitFilter 
eAlignmentManager 

Definition at line 106 of file cleanup_alignments_params_panel.hpp.

Enumerator
eInvalid 
eSubmit 
eMonitor 

submit request, monitor and retrieve results

eRetrieve 

monitor and retrieve resutlts

eFinished 

only retrieve resutlts

Definition at line 84 of file blast_search_task.hpp.

Enumerator
eJobDescrChanged 

Definition at line 86 of file net_blast_ui_data_source.hpp.

Enumerator
eNone 
eLeft 
eRight 
eBoth 

Definition at line 55 of file needlemanwunsch_tool_params.hpp.

commands introduced by Net BLAST data source

Enumerator
eCmdRetriveBlastJobs 
eCmdMonitorBlastJobs 
eCmdDeleteBlastJobs 
eCmdExploreNetBLAST 
eCmdLoadRIDs 
eCmdBlastWinMask 

Definition at line 71 of file net_blast_ui_data_source.hpp.

Enumerator
eInvalidState 
eInitial 
eSubmitted 
eCompleted 
eFailed 
eRetrieved 
eExpired 

Definition at line 69 of file net_blast_job_descr.hpp.

Enumerator
eInvalid 
eSelectRID 
eSelectProject 
eCompleted 

Definition at line 95 of file net_blast_ui_load_manager.hpp.

enum CBLASTToolManager::EState
protected
Enumerator
eInvalid 
eOptions 
eParams 
eCompleted 

Definition at line 113 of file blast_tool_manager.hpp.

Enumerator
eInvalid 
eParams 
eCompleted 

Definition at line 126 of file text_align_load_manager.hpp.

Enumerator
eSequences 
eNCBIDB 
eLocalDB 

Definition at line 66 of file blast_search_params.hpp.

Enumerator
kGenomic 
kCDNA 
kProtein 
kNucleotide 

Definition at line 77 of file splign_panel.hpp.

Function Documentation

CAlignSpanView::CAlignSpanView ( )

Definition at line 91 of file align_span_view.cpp.

CMuscleToolPanel::CMuscleToolPanel ( )

Definition at line 69 of file muscle_tool_panel.cpp.

References Init().

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

Definition at line 74 of file muscle_tool_panel.cpp.

References CMuscleToolPanel::Create(), and CMuscleToolPanel::Init().

CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ( )
CNeedlemanWunschToolParams::CNeedlemanWunschToolParams ( const CNeedlemanWunschToolParams data)
CNGAlignPanel::CNGAlignPanel ( )

Definition at line 67 of file ngalign_panel.cpp.

References Init().

CNGAlignPanel::CNGAlignPanel ( wxWindow *  parent)

Definition at line 72 of file ngalign_panel.cpp.

References CNGAlignPanel::Create(), and CNGAlignPanel::Init().

void CNeedlemanWunschToolParams::Copy ( const CNeedlemanWunschToolParams data)
bool CNGAlignPanel::Create ( wxWindow *  parent,
wxWindowID  id = ID_CNGALIGNPANEL 
)
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 
)
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 
)
void CNGAlignPanel::CreateControls ( )
void CTaxTreeToolPanel::CreateControls ( )
void CMuscleToolPanel::CreateControls ( )
IView * CAlignSpanViewFactory::CreateInstance ( ) const
virtual

creates a view instance

Implements IViewFactory.

Definition at line 650 of file align_span_view.cpp.

IView * CAlignSpanViewFactory::CreateInstanceByFingerprint ( const TFingerprint fingerprint) const
virtual

if fingerprint is recognized - creates and returns a new instance

Implements IViewFactory.

Definition at line 656 of file align_span_view.cpp.

References NULL.

void CAlignSpanView::CreateViewWindow ( wxWindow *  parent)
virtual
CTaxTreeToolPanel::CTaxTreeToolPanel ( )

Definition at line 59 of file taxtree_tool_panel.cpp.

References Init().

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 
)
void CAlignSpanView::DestroyViewWindow ( )
virtual

destroy Window corresponding to the view

Implements CProjectViewBase.

Definition at line 171 of file align_span_view.cpp.

References CAlignSpanView::GetWindow(), CAlignSpanView::m_AlnWidget, CAlignSpanView::m_Panel, CAlignSpanView::m_StatusBar, and NULL.

int CNeedlemanWunschToolParams::GetBandSize ( ) const
inline
wxBitmap CNGAlignPanel::GetBitmapResource ( const wxString &  name)

Definition at line 138 of file ngalign_panel.cpp.

wxBitmap CTaxTreeToolPanel::GetBitmapResource ( const wxString &  name)

Definition at line 127 of file taxtree_tool_panel.cpp.

wxBitmap CMuscleToolPanel::GetBitmapResource ( const wxString &  name)

Definition at line 188 of file muscle_tool_panel.cpp.

Referenced by CMuscleToolPanel::CreateControls().

CTaxTreeToolParams& CTaxTreeToolPanel::GetData ( void  )
inline
const CTaxTreeToolParams& CTaxTreeToolPanel::GetData ( void  ) const
inline

Definition at line 113 of file taxtree_tool_panel.hpp.

References CTaxTreeToolPanel::m_data.

CMuscleToolParams& CMuscleToolPanel::GetData ( void  )
inline
const CMuscleToolParams& CMuscleToolPanel::GetData ( void  ) const
inline

Definition at line 115 of file muscle_tool_panel.hpp.

References CMuscleToolPanel::m_data.

string CAlignSpanViewFactory::GetExtensionIdentifier ( ) const
virtual

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

Implements IExtension.

Definition at line 624 of file align_span_view.cpp.

string CAlignSpanViewFactory::GetExtensionLabel ( ) const
virtual

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

Implements IExtension.

Definition at line 631 of file align_span_view.cpp.

int CNeedlemanWunschToolParams::GetFirstSeqFreeEnds ( ) const
inline
int CNeedlemanWunschToolParams::GetGapExtendCost ( ) const
inline
int CNeedlemanWunschToolParams::GetGapOpenCost ( ) const
inline
wxIcon CNGAlignPanel::GetIconResource ( const wxString &  name)

Definition at line 146 of file ngalign_panel.cpp.

wxIcon CTaxTreeToolPanel::GetIconResource ( const wxString &  name)

Definition at line 135 of file taxtree_tool_panel.cpp.

wxIcon CMuscleToolPanel::GetIconResource ( const wxString &  name)

Definition at line 193 of file muscle_tool_panel.cpp.

int CNeedlemanWunschToolParams::GetMatchCost ( ) const
inline
int CNeedlemanWunschToolParams::GetMismatchCost ( ) const
inline
const TConstScopedObjects& CNeedlemanWunschToolParams::GetObjects ( ) const
inline
const CProjectViewTypeDescriptor & CAlignSpanViewFactory::GetProjectViewTypeDescriptor ( ) const
virtual

returns a Descriptor for the View Type supported by the Factory

Implements IProjectViewFactory.

Definition at line 645 of file align_span_view.cpp.

References CAlignSpanView::m_TypeDescr.

const TConstScopedObjects& CNGAlignPanel::GetQueries ( void  ) const
inline

Definition at line 104 of file ngalign_panel.hpp.

References CNGAlignPanel::m_Queries.

Referenced by CNGAlignTool::x_CreateLoadingJob().

int CNeedlemanWunschToolParams::GetSecondSeqFreeEnds ( ) const
inline
void CAlignSpanView::GetSelection ( CSelectionEvent evt) const
virtual
void CAlignSpanView::GetSelection ( TConstScopedObjects objects) const
virtual

shall return data objects representing selected things, return one data object for every selected thing.

Implementation shall not clear the container as it can be used for accumulating objects.

Reimplemented from CProjectView.

Definition at line 479 of file align_span_view.cpp.

References _ASSERT, GetIdHandle(), CProjectViewBase::GetScope(), CAlnSpanWidget::GetSelection(), CRef< C, Locker >::IsNull(), ITERATE, CAlignSpanView::m_AlnWidget, NULL, CSeq_loc::SetId(), CSeq_loc::SetInt(), and CProjectViewBase::x_HasProject().

const SConstScopedObject& CNGAlignPanel::GetSubject ( void  ) const
inline

Definition at line 101 of file ngalign_panel.hpp.

References CNGAlignPanel::m_Subject.

Referenced by CNGAlignTool::x_CreateLoadingJob().

const CViewTypeDescriptor & CAlignSpanView::GetTypeDescriptor ( ) const
virtual

return an object providing meta information about thei view type

Implements CProjectViewBase.

Definition at line 217 of file align_span_view.cpp.

References CAlignSpanView::m_TypeDescr.

void CAlignSpanView::GetVisibleRanges ( CVisibleRange vrange) const
virtual

populate a visible range event for broadcasting

Populate a visible range event prior to broadcasting.

Reimplemented from CProjectView.

Definition at line 549 of file align_span_view.cpp.

References CVisibleRange::AddLocation(), CAlnSpanWidget::GetSelection(), ITERATE, CAlignSpanView::m_AlnWidget, and CProjectViewBase::x_HasProject().

wxWindow * CAlignSpanView::GetWindow ( )
virtual

returns a pointer to the wxWindow representing the client

Implements CProjectViewBase.

Definition at line 98 of file align_span_view.cpp.

References _ASSERT, and CAlignSpanView::m_Panel.

Referenced by CAlignSpanView::DestroyViewWindow().

void CNeedlemanWunschToolParams::Init ( void  )
void CNGAlignPanel::Init ( void  )
void CTaxTreeToolPanel::Init ( void  )

Definition at line 94 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::m_SeqIds, and NULL.

Referenced by CTaxTreeToolPanel::CTaxTreeToolPanel().

void CMuscleToolPanel::Init ( void  )

Definition at line 105 of file muscle_tool_panel.cpp.

References CMuscleToolPanel::m_LocationSel, and NULL.

Referenced by CMuscleToolPanel::CMuscleToolPanel().

void CNeedlemanWunschToolParams::LoadSettings ( )
virtual
void CNGAlignPanel::LoadSettings ( )
virtual
void CMuscleToolPanel::LoadSettings ( )
virtual
void CTaxTreeToolPanel::LoadSettings ( )
virtual
void CAlignSpanView::LoadSettings ( )
virtual
void CMuscleToolPanel::OnMusclePathClick ( wxCommandEvent &  event)

Definition at line 242 of file muscle_tool_panel.cpp.

References _ASSERT, CMuscleToolPanel::ID_TEXTCTRL12, and wxT.

void CAlignSpanView::OnProjectChanged ( CProjectViewEvent evt)
virtual
void CAlignSpanView::OnVisibleRangeChanged ( const CVisibleRange vrange,
IVisibleRangeClient source 
)
virtual

Reimplemented from CProjectView.

Definition at line 561 of file align_span_view.cpp.

void CAlignSpanView::OnWidgetRangeChanged ( )
virtual

Reimplemented from CProjectView.

Definition at line 566 of file align_span_view.cpp.

References CAlignSpanView::x_UpdateStatusMessage().

void CAlignSpanView::OnWidgetSelChanged ( )
virtual
void CNeedlemanWunschToolParams::operator= ( const CNeedlemanWunschToolParams data)
bool CNeedlemanWunschToolParams::operator== ( const CNeedlemanWunschToolParams data) const
void CAlignSpanViewFactory::RegisterIconAliases ( wxFileArtProvider provider)
virtual

called by the framework to give Factory a chance to register images used by view

Implements IViewFactory.

Definition at line 638 of file align_span_view.cpp.

References CUIObject::GetIconAlias(), IProjectViewFactory::GetViewTypeDescriptor(), wxFileArtProvider::RegisterFileAlias(), ToWxString(), and wxT.

void CNGAlignPanel::RestoreDefaults ( )
virtual

override in derived classes

Restores the default options for the panel

Implements CAlgoToolManagerParamsPanel.

Definition at line 282 of file ngalign_panel.cpp.

void CMuscleToolPanel::RestoreDefaults ( )
virtual

override in derived classes

Restores the default options for the panel

Implements CAlgoToolManagerParamsPanel.

Definition at line 261 of file muscle_tool_panel.cpp.

References CMuscleToolPanel::GetData(), and CMuscleToolParams::Init().

void CTaxTreeToolPanel::RestoreDefaults ( )
virtual

override in derived classes

Restores the default options for the panel

Implements CAlgoToolManagerParamsPanel.

Definition at line 173 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::GetData(), and CTaxTreeToolParams::Init().

void CNeedlemanWunschToolParams::SaveSettings ( ) const
virtual
void CNGAlignPanel::SaveSettings ( ) const
virtual
void CMuscleToolPanel::SaveSettings ( ) const
virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 232 of file muscle_tool_panel.cpp.

References CMuscleToolPanel::m_LocationSel, and CObjectListWidgetSel::SaveSettings().

void CTaxTreeToolPanel::SaveSettings ( ) const
virtual

override in derived classes

Implements CAlgoToolManagerParamsPanel.

Definition at line 163 of file taxtree_tool_panel.cpp.

References CTaxTreeToolPanel::m_SeqIds, and CObjectListWidgetSel::SaveSettings().

void CAlignSpanView::SaveSettings ( ) const
virtual
void CNeedlemanWunschToolParams::SetBandSize ( int  value)
inline
void CTaxTreeToolPanel::SetData ( const CTaxTreeToolParams data)
inline
void CMuscleToolPanel::SetData ( const CMuscleToolParams data)
inline

Definition at line 116 of file muscle_tool_panel.hpp.

References CMuscleToolPanel::m_data.

Referenced by CMuscleTool::x_CreateParamsPanelIfNeeded().

void CNeedlemanWunschToolParams::SetFirstSeqFreeEnds ( int  value)
inline
void CNeedlemanWunschToolParams::SetGapExtendCost ( int  value)
inline
void CNeedlemanWunschToolParams::SetGapOpenCost ( int  value)
inline
void CNeedlemanWunschToolParams::SetMatchCost ( int  value)
inline
void CNeedlemanWunschToolParams::SetMismatchCost ( int  value)
inline
TConstScopedObjects& CNeedlemanWunschToolParams::SetObjects ( void  )
inline
void CNGAlignPanel::SetObjects ( TConstScopedObjects objects)
void CTaxTreeToolPanel::SetObjects ( map< string, TConstScopedObjects > *  objects)
void CMuscleToolPanel::SetObjects ( map< string, TConstScopedObjects > *  objects)
TConstScopedObjects& CNGAlignPanel::SetQueries ( void  )
inline

Definition at line 105 of file ngalign_panel.hpp.

References CNGAlignPanel::m_Queries.

Referenced by CNGAlignPanel::TransferDataFromWindow().

virtual void CNeedlemanWunschToolParams::SetRegistryPath ( const string path)
inlinevirtual
void CMuscleToolPanel::SetRegistryPath ( const string reg_path)
virtual
void CTaxTreeToolPanel::SetRegistryPath ( const string reg_path)
virtual
void CAlignSpanView::SetRegistryPath ( const string reg_path)
virtual

Implements IRegSettings.

Definition at line 184 of file align_span_view.cpp.

References CAlignSpanView::m_RegPath.

void CNeedlemanWunschToolParams::SetSecondSeqFreeEnds ( int  value)
inline
SConstScopedObject& CNGAlignPanel::SetSubject ( void  )
inline

Definition at line 102 of file ngalign_panel.hpp.

References CNGAlignPanel::m_Subject.

Referenced by CNGAlignPanel::TransferDataFromWindow().

bool CNGAlignPanel::ShowToolTips ( )
static

Definition at line 134 of file ngalign_panel.cpp.

bool CTaxTreeToolPanel::ShowToolTips ( )
static

Definition at line 123 of file taxtree_tool_panel.cpp.

bool CMuscleToolPanel::ShowToolTips ( )
static

Definition at line 182 of file muscle_tool_panel.cpp.

Referenced by CMuscleToolPanel::CreateControls().

int CAlignSpanViewFactory::TestInputObjects ( TConstScopedObjects objects)
virtual

tests input objects (probably using object conversion, or not) and returns a combination of ETestResult flags better name is IsCompatibleWith()

Implements IProjectViewFactory.

Definition at line 668 of file align_span_view.cpp.

References IProjectViewFactory::fCanShowAll, IProjectViewFactory::fCanShowSeparated, IProjectViewFactory::fCanShowSome, i, and type.

bool CNGAlignPanel::TransferDataFromWindow ( )
virtual
bool CTaxTreeToolPanel::TransferDataFromWindow ( )
virtual
bool CMuscleToolPanel::TransferDataFromWindow ( )
virtual
void CAlignSpanView::x_CreateMenuBarMenu ( )
protectedvirtual

initializes m_MenuBarMenu; override in derived classes

Reimplemented from CProjectViewBase.

Definition at line 127 of file align_span_view.cpp.

References CwxTableListCtrl::eCmdExportToCSV, CProjectViewBase::m_MenuBarMenu, wxID_ANY, wxT, and CAlignSpanView::x_InitMenuResources().

const CObject * CAlignSpanView::x_GetOrigObject ( ) const
protectedvirtual
void CAlignSpanView::x_InitMenuResources ( )
protected

Definition at line 104 of file align_span_view.cpp.

Referenced by CAlignSpanView::x_CreateMenuBarMenu().

void CAlignSpanView::x_InitWidget ( )
protected
void CAlignSpanView::x_OnSetSelection ( CSelectionEvent evt)
protectedvirtual

override in derived classes in order to handle selection broadcast

override this function in derived classes

Reimplemented from CProjectView.

Definition at line 533 of file align_span_view.cpp.

References CSelectionEvent::HasObjectSelection(), and CAlignSpanView::x_UpdateStatusMessage().

void CAlignSpanView::x_PostAttachToProject ( )
protectedvirtual
objects::CScope * CAlignSpanView::x_PreAttachToProject ( TConstScopedObjects objects)
protectedvirtual
void CAlignSpanView::x_Update ( )
protectedvirtual
void CAlignSpanView::x_UpdateStatusMessage ( )
protectedvirtual
CMuscleToolPanel::~CMuscleToolPanel ( )

Definition at line 99 of file muscle_tool_panel.cpp.

CNeedlemanWunschToolParams::~CNeedlemanWunschToolParams ( )

Definition at line 49 of file needlemanwunsch_tool_params.cpp.

CNGAlignPanel::~CNGAlignPanel ( )

Definition at line 95 of file ngalign_panel.cpp.

CTaxTreeToolPanel::~CTaxTreeToolPanel ( )

Definition at line 88 of file taxtree_tool_panel.cpp.

Variable Documentation

CAlnSpanWidget* CAlignSpanView::m_AlnWidget
private
CAnchoredAln CAlignSpanView::m_AnchoredAln
private

Definition at line 150 of file align_span_view.hpp.

int CNeedlemanWunschToolParams::m_BandSize
private
CTaxTreeToolParams CTaxTreeToolPanel::m_data
CMuscleToolParams CMuscleToolPanel::m_data

Definition at line 129 of file muscle_tool_panel.hpp.

Referenced by CMuscleToolPanel::GetData(), and CMuscleToolPanel::SetData().

CRef<IAlnMultiDataSource> CAlignSpanView::m_DataSource
private

Definition at line 149 of file align_span_view.hpp.

Referenced by CAlignSpanView::x_InitWidget().

int CNeedlemanWunschToolParams::m_FirstSeqFreeEnds
private
int CNeedlemanWunschToolParams::m_GapExtendCost
private
int CNeedlemanWunschToolParams::m_GapOpenCost
private
vector< CConstRef<CSeq_align> > CAlignSpanView::m_InputAligns
private
TConstScopedObjects* CTaxTreeToolPanel::m_InputObjects

Definition at line 134 of file taxtree_tool_panel.hpp.

TConstScopedObjects* CMuscleToolPanel::m_InputObjects

Definition at line 141 of file muscle_tool_panel.hpp.

CObjectListWidgetSel* CMuscleToolPanel::m_LocationSel
int CNeedlemanWunschToolParams::m_MatchCost
private
int CNeedlemanWunschToolParams::m_MismatchCost
private
auto_ptr<CAlnSpanVertModel> CAlignSpanView::m_Model
private
TConstScopedObjects CNeedlemanWunschToolParams::m_Objects
private
CConstRef<CSeq_align> CAlignSpanView::m_OrigAlign
private
CConstRef<CSeq_annot> CAlignSpanView::m_OrigAnnot
private

original data object passed to the view

Definition at line 142 of file align_span_view.hpp.

Referenced by CAlignSpanView::x_GetOrigObject(), CAlignSpanView::x_InitWidget(), and CAlignSpanView::x_PreAttachToProject().

CConstRef<CBioseq> CAlignSpanView::m_OrigBioseq
private
wxPanel* CAlignSpanView::m_Panel
private
TConstScopedObjects CNGAlignPanel::m_Queries

Definition at line 133 of file ngalign_panel.hpp.

Referenced by CNGAlignPanel::GetQueries(), and CNGAlignPanel::SetQueries().

CObjectListWidget* CNGAlignPanel::m_QueryListCtrl
string CNeedlemanWunschToolParams::m_RegPath
private
string CAlignSpanView::m_RegPath
private
CRef<CScope> CAlignSpanView::m_Scope
private

Definition at line 157 of file align_span_view.hpp.

int CNeedlemanWunschToolParams::m_SecondSeqFreeEnds
private
CRef<CSeq_id> CAlignSpanView::m_Seq_id
private

Definition at line 158 of file align_span_view.hpp.

CObjectListWidgetSel* CTaxTreeToolPanel::m_SeqIds
wxStatusBar* CAlignSpanView::m_StatusBar
private
SConstScopedObject CNGAlignPanel::m_Subject

Definition at line 132 of file ngalign_panel.hpp.

Referenced by CNGAlignPanel::GetSubject(), and CNGAlignPanel::SetSubject().

CObjectListWidget* CNGAlignPanel::m_SubjectListCtrl
CProjectViewTypeDescriptor CAlignSpanView::m_TypeDescr
staticprivate

Friends

friend class CAlignNeedlemanWunschPanel
friend

Definition at line 53 of file needlemanwunsch_tool_params.hpp.

friend class CAlignSpanViewFactory
friend

Definition at line 65 of file align_span_view.hpp.

Modified on Thu Feb 22 13:23:43 2018 by modify_doxy.py rev. 546573