CGuiObjectInfoSeq_align Class Reference

Search Toolkit Book for CGuiObjectInfoSeq_align

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

Inheritance diagram for CGuiObjectInfoSeq_align:

Collaboration diagram for CGuiObjectInfoSeq_align:

Public Types
using	TSignedSeqRanges = std::vector< TSignedSeqRange >
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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...
typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
virtual std::string	GetType () const
virtual std::string	GetSubtype () const
virtual std::string	GetLabel () const
virtual void	GetToolTip (ITooltipFormatter &tooltip, std::string &t_title, TSeqPos at_p=(TSeqPos) -1, bool *isGeneratedBySvc=NULL) const
virtual void	GetLinks (ITooltipFormatter &, bool) const
	Get a set of links. More...
virtual std::string	GetIcon () const
virtual std::string	GetViewCategory () const
	To share default view between different types. More...
void	SetAnchorRow (int anchor)
void	SetFlippedStrands (bool flipped=true)
void	SetReportInsertionSequences (bool report)
void	SetScale (double scale)
void	SetDataSource (const CConstRef< IAlnGraphicDataSource > &data_source)
virtual std::string	GetSRAReadStatus () const
virtual double	GetCoverage () const
Public Member Functions inherited from CObject
	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...
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 Member Functions inherited from IGuiObjectInfo
virtual	~IGuiObjectInfo ()
virtual void	GetToolTip (ITooltipFormatter &tooltip, string &t_title, TSeqPos at_p=(TSeqPos) -1, bool *isGeneratedBySvc=NULL) const =0
	Get tooltip. More...

Static Public Member Functions
static CGuiObjectInfoSeq_align *	CreateObject (SConstScopedObject &object, ICreateParams *params)
static bool	IsPolyA (const objects::CBioseq_Handle &bsh, TSeqPos start, TSeqPos stop)
static TSignedSeqRange	GetRangeAroundPosition (const TSeqPos at_p, double scale, const IAlnGraphicDataSource &data_source)
static size_t	GetInsertionRanges (const TSignedSeqRange &aln_range, const IAlnGraphicDataSource &data_source, TSignedSeqRanges *ranges=nullptr)
static std::string	GetSeqString (IAlnGraphicDataSource::TNumrow row, const IAlnGraphicDataSource &data_source, const TSignedSeqRange &seq_rng, bool flipped_strands)
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
static const size_t	kInsertionsPerTooltip = 3
static const float	kSequenceLevel = 0.25
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
void	x_AddUserObject (ITooltipFormatter &tooltip, const objects::CUser_field &user_object) const
void	x_GetAlignmentTooltip_Insert (const TSignedSeqRange &seq_r, ITooltipFormatter &tooltip) const
std::string	x_GetTooltipSequence (TSeqPos from, TSeqPos to, IAlnGraphicDataSource::TNumrow row) const
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Attributes
CConstRef< objects::CSeq_align >	m_Align
CRef< objects::CScope >	m_Scope
int	m_AnchorRow
	anchor sequence row number, default is -1 (unknown) More...
bool	m_FlippedStrands = false
bool	m_ReportInsertionSequences = true
double	m_Scale = 0.0
CConstRef< IAlnGraphicDataSource >	m_DataSource

Detailed Description

Definition at line 52 of file gui_object_info_seq_align.hpp.

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

• include/gui/widgets/seq_graphic/gui_object_info_seq_align.hpp
• src/gui/widgets/seq_graphic/gui_object_info_seq_align.cpp