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CGuiObjectInfoSeq_align Class Reference

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#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< Uint8TCounter
 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...
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 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_alignCreateObject (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< IAlnGraphicDataSourcem_DataSource

Detailed Description

Definition at line 52 of file gui_object_info_seq_align.hpp.

The documentation for this class was generated from the following files:
Modified on Sat Dec 02 09:21:26 2023 by rev. 669887