NCBI C++ ToolKit
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CAlignmentConfig Class Reference

Search Toolkit Book for CAlignmentConfig

File Description: More...

#include <gui/widgets/seq_graphic/alignment_conf.hpp>

+ Inheritance diagram for CAlignmentConfig:
+ Collaboration diagram for CAlignmentConfig:

Public Types

enum  ELabelPosition { ePos_Above , ePos_Side , ePos_NoLabel }
 
enum  ECompactMode { eNormal , eCompact , eExtremeCompact }
 
enum  EHideSraAlignments { eHide_None = 0x0 , eHide_Duplicates = 0x1 , eHide_BadReads = 0x2 , eHide_Both = 0x3 }
 
enum  EUnalignedTailsMode { eTails_Hide , eTails_ShowGlyph , eTails_ShowSequence }
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CAlignmentConfig ()
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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...
 
- Public Member Functions inherited from CDebugDumpable
 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
 

Public Attributes

CGlTextureFont m_LabelFont
 
CGlTextureFont m_SeqFont
 
ELabelPosition m_LabelPos
 
EUnalignedTailsMode m_UnalignedTailsMode
 
int m_BarHeight
 
bool m_ShowLabel
 
bool m_ShowIdenticalBases
 
bool m_ShowUnalignedTailsForTrans2GenomicAln
 
ECompactMode m_CompactMode
 Alignment layout compact mode. More...
 
bool m_Dirty
 Dirty flag indicates any unsaved changes. More...
 
Colors.
CRgbaColor m_BG
 
CRgbaColor m_FG
 
CRgbaColor m_Label
 
CRgbaColor m_Sequence
 
CRgbaColor m_SeqMismatch
 
CRgbaColor m_TailColor
 
CRgbaColor m_Insertion
 
CRgbaColor m_Gap
 
CRgbaColor m_Intron
 
CRgbaColor m_NonConsensus
 
CRgbaColor m_SmearColorMin
 
CRgbaColor m_SmearColorMax
 
CRgbaColor m_UnalignedFG
 
CRgbaColor m_UnalignedSequence
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
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...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
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...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

File Description:

CAlignmentConfig: the data structure holding alignment rendering parameters

Definition at line 48 of file alignment_conf.hpp.

Member Enumeration Documentation

◆ ECompactMode

Enumerator
eNormal 

no compact mode

eCompact 

compact mode

eExtremeCompact 

extreme compact mode

Definition at line 57 of file alignment_conf.hpp.

◆ EHideSraAlignments

Enumerator
eHide_None 
eHide_Duplicates 
eHide_BadReads 
eHide_Both 

Definition at line 63 of file alignment_conf.hpp.

◆ ELabelPosition

Enumerator
ePos_Above 

above the rendered bar

ePos_Side 

always on 5' side

ePos_NoLabel 

no label

Definition at line 51 of file alignment_conf.hpp.

◆ EUnalignedTailsMode

Enumerator
eTails_Hide 
eTails_ShowGlyph 
eTails_ShowSequence 

Definition at line 70 of file alignment_conf.hpp.

Constructor & Destructor Documentation

◆ CAlignmentConfig()

CAlignmentConfig::CAlignmentConfig ( )
inline

Definition at line 76 of file alignment_conf.hpp.

Member Data Documentation

◆ m_BarHeight

int CAlignmentConfig::m_BarHeight

◆ m_BG

CRgbaColor CAlignmentConfig::m_BG

◆ m_CompactMode

ECompactMode CAlignmentConfig::m_CompactMode

Alignment layout compact mode.

It is a run-time setting depending on the number of total alignments shown on screen.

Definition at line 121 of file alignment_conf.hpp.

Referenced by CAlignGlyph::GetBarHeight(), CAlignmentTrack::x_AddAlignmentLayout(), CAlignGlyph::x_DrawInserts(), CAlignGlyph::x_DrawStrandIndicators(), and CAlignGlyph::x_UpdateBoundingBox().

◆ m_Dirty

bool CAlignmentConfig::m_Dirty
mutable

Dirty flag indicates any unsaved changes.

Definition at line 124 of file alignment_conf.hpp.

Referenced by CAlignmentTrack::x_SaveAlignmentSettings().

◆ m_FG

CRgbaColor CAlignmentConfig::m_FG

◆ m_Gap

CRgbaColor CAlignmentConfig::m_Gap

◆ m_Insertion

CRgbaColor CAlignmentConfig::m_Insertion

◆ m_Intron

CRgbaColor CAlignmentConfig::m_Intron

◆ m_Label

CRgbaColor CAlignmentConfig::m_Label

◆ m_LabelFont

CGlTextureFont CAlignmentConfig::m_LabelFont

◆ m_LabelPos

ELabelPosition CAlignmentConfig::m_LabelPos

◆ m_NonConsensus

CRgbaColor CAlignmentConfig::m_NonConsensus

◆ m_SeqFont

CGlTextureFont CAlignmentConfig::m_SeqFont

◆ m_SeqMismatch

CRgbaColor CAlignmentConfig::m_SeqMismatch

◆ m_Sequence

CRgbaColor CAlignmentConfig::m_Sequence

◆ m_ShowIdenticalBases

bool CAlignmentConfig::m_ShowIdenticalBases

◆ m_ShowLabel

bool CAlignmentConfig::m_ShowLabel

◆ m_ShowUnalignedTailsForTrans2GenomicAln

bool CAlignmentConfig::m_ShowUnalignedTailsForTrans2GenomicAln

◆ m_SmearColorMax

CRgbaColor CAlignmentConfig::m_SmearColorMax

◆ m_SmearColorMin

CRgbaColor CAlignmentConfig::m_SmearColorMin

◆ m_TailColor

CRgbaColor CAlignmentConfig::m_TailColor

◆ m_UnalignedFG

CRgbaColor CAlignmentConfig::m_UnalignedFG

◆ m_UnalignedSequence

CRgbaColor CAlignmentConfig::m_UnalignedSequence

◆ m_UnalignedTailsMode

EUnalignedTailsMode CAlignmentConfig::m_UnalignedTailsMode

The documentation for this class was generated from the following file:
Modified on Sat Jun 15 11:50:47 2024 by modify_doxy.py rev. 669887