CAlignmentSmear Class Reference

Search Toolkit Book for CAlignmentSmear

#include <gui/objutils/alignment_smear.hpp>

Inheritance diagram for CAlignmentSmear:

Collaboration diagram for CAlignmentSmear:

Public Types
enum	EAlignSmearStrand { eSmearStrand_Both , eSmearStrand_Pos , eSmearStrand_Neg }
typedef int	score_type
typedef CDenMapRunIterator< score_type >	runlen_iterator
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
	CAlignmentSmear (const objects::CBioseq_Handle &handle, TSeqPos start, TSeqPos stop, float window=1, EAlignSmearStrand strand_type=eSmearStrand_Both)
void	AddAnnot (const objects::CSeq_annot &seq_annot, ISeqTaskProgressCallback *p_cb=NULL)
	INPUT: More...
void	AddAlignments (const objects::SAnnotSelector &sel, ISeqTaskProgressCallback *p_cb=NULL)
	Smear all the alignments matched by this selector on my bioseq. More...
bool	AddAlignments (objects::CAlign_CI &align_iter, ISeqTaskProgressCallback *p_cb=NULL)
	Smear all the alignments in CAlign_CI. More...
void	AddAlignment (const CSparseAln &aln)
	Add this one alignment to my smear. More...
void	AddAlignment (const objects::CAlnMap &align)
	Add this one alignment to my smear. More...
void	MaskGaps ()
string	GetLabel () const
void	SetLabel (const string &label)
EAlignSmearStrand	GetStrandType () const
runlen_iterator	SmearSegBegin () const
	OUTPUT: More...
runlen_iterator	SmearGapBegin () const
score_type	GetMaxValue () 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

Static Public Member Functions
static bool	SeparateStrands (const objects::CSeq_annot &seq_annot)
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)

Private Types
typedef CDensityMap< score_type >	TSegMap
typedef CDensityMap< score_type >	TGapMap

Static Private Member Functions
static string	x_GetAnnotName (const objects::CSeq_annot &seq_annot)

Private Attributes
const objects::CBioseq_Handle &	m_BioseqHandle
TSegMap	m_AccumSeg
TGapMap	m_AccumGap
EAlignSmearStrand	m_StrandType
string	m_Label
unsigned long	m_CntAligns
unsigned long	m_CntMixes

Additional Inherited Members
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

Definition at line 58 of file alignment_smear.hpp.

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

• include/gui/objutils/alignment_smear.hpp
• src/gui/objutils/alignment_smear.cpp