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NCBI C++ ToolKit: CMatrixScoringMethod Class Reference

Search Toolkit Book for CMatrixScoringMethod

CMatrixScoringMethod. More...

#include <gui/widgets/aln_score/template_methods.hpp>

  CMatrixScoringMethod ()   virtual  ~CMatrixScoringMethod ()   virtual void  CreateColorTable (int size)   virtual IScoringMethod *  Clone () const   virtual bool  Load (CNcbiRegistry &reg)   virtual int  GetSupportedColorTypes () const   returns a combination of EColorType flags More...
  virtual const CRgbaColor &  GetColorForScore (TScore score, EColorType type) const   returns a color corresponding to a given score value. More...
  virtual void  CalculateScores (char cons, const string &column, TScore &col_score, TScoreVector &scores)   bool  CanCalculateScores (const IScoringAlignment &aln)   Do we have what it takes to calculate scores? e.g. a master row selected? More...
  const CRgbaColor &  GetColorForNoScore (EColorType type) const   Call for display colors when CanCalculateScores returns false. More...
  void  SetColorForNoScore (EColorType type, const CRgbaColor &color)   size_t  GetWindowSize () const   virtual const CMenuItem *  GetMenu ()   Returns a pointer to the submenu. More...
  virtual bool  HasPropertiesPanel () const   returns true if the method supports properties dialog More...
  virtual wxWindow *  CreatePropertiesPanel (wxWindow *parent)   This a factory method that shall produce a CPropertiesPanel representing properties of the method; the panel Apply() must take care of appying changes to the method. More...
    CTemplateScoringMethod ()   CTemplateScoringMethod. More...
  virtual  ~CTemplateScoringMethod ()   virtual bool  LoadInfo (CNcbiRegistry &reg)   loads only descriptive information More...
  virtual string  GetName () const   returns unique name of the method that is used in UI to identify it More...
  virtual string  GetDescription () const   returns a detailed description of the method that is used in UI More...
  virtual int  GetType () const   returns combination of EAlignType flags defining types of alignments that can be colored with this method More...
  virtual bool  IsAverageable () const   return "true" if scores could be averaged More...
  void  SetName (const string &s)   void  SetDescription (const string &s)   virtual bool  SaveInfo (CNcbiRegistry &reg)   saves only descriptive information More...
  virtual bool  Save (CNcbiRegistry &reg)     CObject (void)   Constructor. More...
    CObject (const CObject &src)   Copy constructor. More...
  virtual  ~CObject (void)   Destructor. More...
  CObject &  operator= (const CObject &src) THROWS_NONE   Assignment operator. More...
  bool  CanBeDeleted (void) const THROWS_NONE   Check if object can be deleted. More...
  bool  IsAllocatedInPool (void) const THROWS_NONE   Check if object is allocated in memory pool (not system heap) More...
  bool  Referenced (void) const THROWS_NONE   Check if object is referenced. More...
  bool  ReferencedOnlyOnce (void) const THROWS_NONE   Check if object is referenced only once. More...
  void  AddReference (void) const   Add reference to object. More...
  void  RemoveReference (void) const   Remove reference to object. More...
  void  ReleaseReference (void) const   Remove reference without deleting object. More...
  virtual void  DoNotDeleteThisObject (void)   Mark this object as not allocated in heap – do not delete this object. More...
  virtual void  DoDeleteThisObject (void)   Mark this object as allocated in heap – object can be deleted. More...
  void *  operator new (size_t size)   Define new operator for memory allocation. More...
  void *  operator new[] (size_t size)   Define new[] operator for 'array' memory allocation. More...
  void  operator delete (void *ptr)   Define delete operator for memory deallocation. More...
  void  operator delete[] (void *ptr)   Define delete[] operator for memory deallocation. More...
  void *  operator new (size_t size, void *place)   Define new operator. More...
  void  operator delete (void *ptr, void *place)   Define delete operator. More...
  void *  operator new (size_t size, CObjectMemoryPool *place)   Define new operator using memory pool. More...
  void  operator delete (void *ptr, CObjectMemoryPool *place)   Define delete operator. More...
  virtual void  DebugDump (CDebugDumpContext ddc, unsigned int depth) const   Define method for dumping debug information. More...
    CDebugDumpable (void)   virtual  ~CDebugDumpable (void)   void  DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const   void  DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const   void  DumpToConsole (void) const   virtual  ~IScoringMethod ()   virtual  ~IUITool ()   virtual  ~ITemplateUITool ()   ITemplateUITool. More...
   Public Member Functions inherited from IColumnScoringMethod virtual  ~IColumnScoringMethod ()   virtual bool  NeedsTranslation () const   virtual void  UpdateSettings (const IScoringAlignment &aln)   Set alignment specifi settings. More...
  virtual  ~IUIToolWithGUI ()   virtual  ~IUIToolWithGUI ()   virtual  ~IWindowScoringMethod ()   ◆ TRangeType ◆ CMatrixScoringMethod() CMatrixScoringMethod::CMatrixScoringMethod ( ) ◆ ~CMatrixScoringMethod() ◆ CalculateScores() ◆ CanCalculateScores() ◆ Clone() ◆ CreateColorTable() void CMatrixScoringMethod::CreateColorTable ( int  size ) virtual

Definition at line 1015 of file template_methods.cpp.

References _ASSERT, eConsensus, eNonConsesus, CTemplateScoringMethod::eThreeColorGradient, CRgbaGradColorTable::FillGradient(), m_CalculateRange, CTemplateScoringMethod::m_ColorGradType, m_ColorTable, m_ConsensusMaxScore, m_ConsensusMinScore, m_MaxColor, m_MaxScore, m_MidColor, m_MinColor, m_MinScore, m_NonConsensusMaxScore, m_NonConsensusMinScore, m_UseConsensus, CRgbaGradColorTable::SetSize(), ncbi::grid::netcache::search::fields::size, x_CalculateConsensusRange(), and x_CalculateNonConsensusRange().

Referenced by CMatrixScoringMethod(), Load(), and CMatrixScoringPanel::OnApply().

◆ CreatePropertiesPanel() wxWindow * CMatrixScoringMethod::CreatePropertiesPanel ( wxWindow *  parent ) virtual ◆ GetColorForNoScore() ◆ GetColorForScore()

returns a color corresponding to a given score value.

It is recommended that this method be implemented using color table, on-the-fly creation of colors is expensive.

Implements IScoringMethod.

Definition at line 1253 of file template_methods.cpp.

References _ASSERT, IScoringMethod::fBackground, CRgbaGradColorTable::GetSize(), int, m_ColorTable, m_MaxScore, m_MinScore, max(), min(), and ncbi::grid::netcache::search::fields::size.

◆ GetMenu()

Returns a pointer to the submenu.

If the pointer is not NULL, then this submenu is integrated into the application's menu. If method is derived from CCommandTarget it will recieve command events.

Implements IUIToolWithGUI.

Definition at line 1278 of file template_methods.cpp.

References NULL.

◆ GetSupportedColorTypes() int CMatrixScoringMethod::GetSupportedColorTypes ( ) const virtual ◆ GetWindowSize() size_t CMatrixScoringMethod::GetWindowSize ( ) const virtual ◆ HasPropertiesPanel() bool CMatrixScoringMethod::HasPropertiesPanel ( ) const virtual ◆ Load()

Reimplemented from CTemplateScoringMethod.

Definition at line 1048 of file template_methods.cpp.

References columns, NStr::CompareNocase(), CreateColorTable(), eConsensus, eNonConsesus, IRegistry::EnumerateEntries(), NStr::fSplit_Tokenize, IRegistry::Get(), IRegistry::GetBool(), IRegistry::GetDouble(), CRgbaGradColorTable::GetSize(), IRegistry::GetString(), IRegistry::HasEntry(), i, int, ITERATE, kMatrixSize, CTemplateScoringMethod::LoadInfo(), m_CalculateRange, m_ColorTable, m_ConsensusMaxScore, m_ConsensusMinScore, m_MaxColor, m_MaxScore, m_MinColor, m_NonConsensusMaxScore, m_NonConsensusMinScore, m_UndefColor, m_UseConsensus, m_vScore, max(), min(), NCBISM_Blosum45, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, CNcbiMatrix< T >::Resize(), SNCBIPackedScoreMatrix::scores, NStr::Split(), NStr::StringToDouble(), SNCBIPackedScoreMatrix::symbols, NStr::TruncateSpaces(), x_BaseToIndex(), and CTemplateScoringMethod::x_GetColor().

◆ SetColorForNoScore() ◆ x_BaseToIndex() int CMatrixScoringMethod::x_BaseToIndex ( char  c ) staticprotected ◆ x_CalculateConsensusRange() void CMatrixScoringMethod::x_CalculateConsensusRange ( ) protected ◆ x_CalculateNonConsensusRange() void CMatrixScoringMethod::x_CalculateNonConsensusRange ( ) protected ◆ x_CreateScoreTable() void CMatrixScoringMethod::x_CreateScoreTable ( CNcbiRegistry &  reg ) protected ◆ CMatrixScoringPanel ◆ m_CalculateRange unsigned char CMatrixScoringMethod::m_CalculateRange protected ◆ m_ColorTable ◆ m_ConsensusMaxScore TScore CMatrixScoringMethod::m_ConsensusMaxScore protected ◆ m_ConsensusMinScore TScore CMatrixScoringMethod::m_ConsensusMinScore protected ◆ m_MaxColor ◆ m_MaxScore TScore CMatrixScoringMethod::m_MaxScore protected ◆ m_MidColor ◆ m_MinColor ◆ m_MinScore TScore CMatrixScoringMethod::m_MinScore protected ◆ m_NonConsensusMaxScore TScore CMatrixScoringMethod::m_NonConsensusMaxScore protected ◆ m_NonConsensusMinScore TScore CMatrixScoringMethod::m_NonConsensusMinScore protected ◆ m_UndefColor ◆ m_UseConsensus bool CMatrixScoringMethod::m_UseConsensus protected ◆ m_vScore ◆ m_WindowSize size_t CMatrixScoringMethod::m_WindowSize protected

The documentation for this class was generated from the following files:

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