NCBI C++ ToolKit
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Search Toolkit Book for CQualityScoringMethod
CQualityScoringMethod - Like CSimpleScoringMethod, in that it calculate the quality of the alignment column and residue, based on how different each residue is from the columns consensus. More...
#include <gui/widgets/aln_score/quality_methods.hpp>
Public Types | |
enum | EOptions { fIgnoreEmptySpace = 0x01 , fIgnoreGaps = 0x02 , fScoreWholeColumn = 0x04 } |
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enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
Control filling of newly allocated memory. More... | |
typedef CObjectCounterLocker | TLockerType |
Default locker type for CRef. More... | |
typedef atomic< Uint8 > | TCounter |
Counter type is CAtomiCounter. More... | |
typedef Uint8 | TCount |
Alias for value type of counter. More... | |
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enum | EColorType { fBackground = 0x1 , fForeground = 0x2 } |
typedef float | TScore |
typedef vector< TScore > | TScoreVector |
typedef CAttrRangeCollection< TScore, TSeqPos > | TScoreColl |
Public Member Functions | |
CQualityScoringMethod () | |
CQualityScoringMethod. More... | |
CQualityScoringMethod (int colors) | |
CQualityScoringMethod (const CQualityScoringMethod &orig) | |
virtual | ~CQualityScoringMethod () |
void | CreateColorTable (int size) |
virtual TNCBIScore | GetSubstitutionScore (int aa1, int aa2) const =0 |
virtual string | GetAllowedSymbols () const =0 |
bool | IsScoreWholeColumn () const |
void | SetOptions (int options) |
int | GetOptions () const |
IScoringMethod implementation | |
virtual string | GetDescription () const |
returns a detailed description of the method that is used in UI More... | |
virtual bool | IsAverageable () const |
return "true" if scores could be averaged More... | |
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... | |
IColumnScoringMethod implementaion | |
virtual void | CalculateScores (char cons, const string &column, TScore &col_score, TScoreVector &scores) |
virtual bool | CanCalculateScores (const IScoringAlignment &aln) |
Do we have what it takes to calculate scores? e.g. a master row selected? More... | |
virtual const CRgbaColor & | GetColorForNoScore (EColorType type) const |
Call for display colors when CanCalculateScores returns false. More... | |
virtual void | SetColorForNoScore (EColorType type, const CRgbaColor &color) |
IUIToolWithGUI implementation | |
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... | |
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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... | |
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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 |
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virtual | ~IScoringMethod () |
virtual int | GetType () const =0 |
returns combination of EAlignType flags defining types of alignments that can be colored with this method More... | |
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virtual | ~IUITool () |
virtual IUITool * | Clone () const =0 |
virtual string | GetName () const =0 |
returns unique name of the method that is used in UI to identify it More... | |
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virtual | ~IColumnScoringMethod () |
virtual bool | NeedsTranslation () const |
virtual void | UpdateSettings (const IScoringAlignment &aln) |
Set alignment specifi settings. More... | |
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virtual | ~IUIToolWithGUI () |
virtual | ~IUIToolWithGUI () |
Protected Attributes | |
CRgbaColor | m_Worst |
CRgbaColor | m_Best |
CRgbaGradColorTable | m_ColorTable |
int | m_Options |
char | m_Space |
char | m_Gap |
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char | m_AmbiguousResidue = ' ' |
Ambiguous Residue, typically 'N' for nucleotides, 'X' for proteins. More... | |
std::function< bool(char c, char b)> | mf_CompareResidue |
Private Member Functions | |
void | x_Init (int colors) |
Friends | |
class | CQualityScoringPanel |
Additional Inherited Members | |
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static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
Define method to throw null pointer exception. More... | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
static EAllocFillMode | GetAllocFillMode (void) |
static void | SetAllocFillMode (EAllocFillMode mode) |
static void | SetAllocFillMode (const string &value) |
Set mode from configuration parameter value. More... | |
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static void | EnableDebugDump (bool on) |
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static const char * | GetAlignmentTagByType (IAlnExplorer::EAlignType type) |
returns symbolic label for the given alignment type, should be More... | |
static IAlnExplorer::EAlignType | GetAlignmentTypeByTag (const string &tag) |
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static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
Define possible object states. More... | |
static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
Heap signature was found. More... | |
static const TCount | eCounterBitsPlaceMask |
Mask for 'in heap' state flags. More... | |
static const int | eCounterStep = 1 << 2 |
Skip over the "in heap" bits. More... | |
static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
static const TCount | eCounterStateMask |
Valid object, and object in heap. More... | |
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static const int | sm_DefGradientSize = 32 |
default number of colors in gradient More... | |
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static const int | kAmbiguousResidueScore = 1000 |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
CQualityScoringMethod - Like CSimpleScoringMethod, in that it calculate the quality of the alignment column and residue, based on how different each residue is from the columns consensus.
Definition at line 50 of file quality_methods.hpp.
Definition at line 57 of file quality_methods.hpp.
CQualityScoringMethod::CQualityScoringMethod | ( | ) |
Definition at line 51 of file quality_methods.cpp.
References IScoringMethod::sm_DefGradientSize, and x_Init().
CQualityScoringMethod::CQualityScoringMethod | ( | int | colors | ) |
Definition at line 63 of file quality_methods.cpp.
CQualityScoringMethod::CQualityScoringMethod | ( | const CQualityScoringMethod & | orig | ) |
Definition at line 80 of file quality_methods.cpp.
References m_ColorTable, and orig.
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Definition at line 58 of file quality_methods.cpp.
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Implements IColumnScoringMethod.
Reimplemented in CConservationScoringMethod.
Definition at line 137 of file quality_methods.cpp.
References _ASSERT, column, GetAllowedSymbols(), GetSubstitutionScore(), i, IsScoreWholeColumn(), ITERATE, IColumnScoringMethod::kAmbiguousResidueScore, IColumnScoringMethod::m_AmbiguousResidue, m_Gap, m_Space, NCBI_FSM_DIM, and r().
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Do we have what it takes to calculate scores? e.g. a master row selected?
Implements IColumnScoringMethod.
Definition at line 203 of file quality_methods.cpp.
void CQualityScoringMethod::CreateColorTable | ( | int | size | ) |
Definition at line 112 of file quality_methods.cpp.
References _ASSERT, CRgbaGradColorTable::FillGradient(), m_Best, m_ColorTable, m_Worst, CRgbaGradColorTable::SetSize(), and ncbi::grid::netcache::search::fields::size.
Referenced by CQualityScoringPanel::OnApply(), CConservationScoringPanel::OnApply(), x_Init(), and CConservationScoringMethod::x_Init().
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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.
Implements IUIToolWithGUI.
Reimplemented in CConservationScoringMethod.
Definition at line 377 of file quality_methods.cpp.
References CQualityScoringPanel.
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pure virtual |
Implemented in CConservationScoringMethod, CQualityScoringMethodAA, and CQualityScoringMethodNA.
Referenced by CalculateScores().
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Call for display colors when CanCalculateScores returns false.
Implements IScoringMethod.
Definition at line 209 of file quality_methods.cpp.
References _ASSERT.
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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.
Reimplemented in CConservationScoringMethod.
Definition at line 229 of file quality_methods.cpp.
References _ASSERT, IScoringMethod::fBackground, CRgbaGradColorTable::GetSize(), int, kMaxScore, m_ColorTable, min(), and ncbi::grid::netcache::search::fields::size.
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returns a detailed description of the method that is used in UI
Implements IUITool.
Reimplemented in CConservationScoringMethod.
Definition at line 125 of file quality_methods.cpp.
References QUALITY_DESCR.
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 249 of file quality_methods.cpp.
int CQualityScoringMethod::GetOptions | ( | void | ) | const |
Definition at line 100 of file quality_methods.cpp.
References m_Options.
Referenced by CQualityScoringPanel::Init().
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pure virtual |
Implemented in CConservationScoringMethod, CQualityScoringMethodAA, and CQualityScoringMethodNA.
Referenced by CalculateScores().
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returns a combination of EColorType flags
Implements IScoringMethod.
Reimplemented in CConservationScoringMethod.
Definition at line 223 of file quality_methods.cpp.
References IScoringMethod::fBackground.
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returns true if the method supports properties dialog
Implements IUIToolWithGUI.
Definition at line 255 of file quality_methods.cpp.
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return "true" if scores could be averaged
Implements IScoringMethod.
Definition at line 131 of file quality_methods.cpp.
bool CQualityScoringMethod::IsScoreWholeColumn | ( | ) | const |
Definition at line 106 of file quality_methods.cpp.
References fScoreWholeColumn, m_Options, and true.
Referenced by CalculateScores().
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Implements IScoringMethod.
Definition at line 217 of file quality_methods.cpp.
void CQualityScoringMethod::SetOptions | ( | int | options | ) |
Definition at line 91 of file quality_methods.cpp.
References fIgnoreGaps, m_Gap, m_Options, and m_Space.
Referenced by CQualityScoringPanel::OnApply(), and x_Init().
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Definition at line 70 of file quality_methods.cpp.
References colors, CreateColorTable(), fIgnoreEmptySpace, m_Best, m_Worst, CRgbaColor::Set(), and SetOptions().
Referenced by CQualityScoringMethod().
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Definition at line 63 of file quality_methods.hpp.
Referenced by CreatePropertiesPanel().
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Definition at line 114 of file quality_methods.hpp.
Referenced by CreateColorTable(), CQualityScoringPanel::CreateControls(), CConservationScoringPanel::CreateControls(), CQualityScoringPanel::OnApply(), CConservationScoringPanel::OnApply(), x_Init(), and CConservationScoringMethod::x_Init().
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Definition at line 115 of file quality_methods.hpp.
Referenced by CConservationScoringMethod::CConservationScoringMethod(), CQualityScoringMethod(), CreateColorTable(), CQualityScoringPanel::CreateControls(), CConservationScoringPanel::CreateControls(), GetColorForScore(), and CConservationScoringMethod::GetColorForScore().
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Definition at line 119 of file quality_methods.hpp.
Referenced by CalculateScores(), and SetOptions().
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Definition at line 117 of file quality_methods.hpp.
Referenced by GetOptions(), IsScoreWholeColumn(), and SetOptions().
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Definition at line 118 of file quality_methods.hpp.
Referenced by CalculateScores(), and SetOptions().
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Definition at line 113 of file quality_methods.hpp.
Referenced by CreateColorTable(), CQualityScoringPanel::CreateControls(), CConservationScoringPanel::CreateControls(), CQualityScoringPanel::OnApply(), CConservationScoringPanel::OnApply(), x_Init(), and CConservationScoringMethod::x_Init().