Search Toolkit Book for CSeq_align_Mapper

#include <objmgr/impl/seq_align_mapper.hpp>

Inheritance diagram for CSeq_align_Mapper:

Collaboration diagram for CSeq_align_Mapper:

Public Member Functions
	CSeq_align_Mapper (const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper)

	~CSeq_align_Mapper (void)

Public Member Functions inherited from CSeq_align_Mapper_Base
	CSeq_align_Mapper_Base (const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper)

	~CSeq_align_Mapper_Base (void)

void	Convert (void)
	Map the whole alignment through the linked seq-loc mapper. More...

void	Convert (size_t row)
	Map a single row of the alignment through the linked seq-loc mapper. More...

CRef< CSeq_align >	GetDstAlign (void) const
	Create mapped alignment. More...

size_t	GetDim (void) const
	Some of the following methods use only the first segment to get information about rows. More...

const CSeq_id_Handle &	GetRowId (size_t idx) const
	Get seq-id for the given row. More...

const TSegments &	GetSegments () const
	Get parsed segments. More...

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

Protected Member Functions
virtual CSeq_align_Mapper_Base *	CreateSubAlign (const CSeq_align &align)

virtual CSeq_align_Mapper_Base *	CreateSubAlign (const CSpliced_seg &spliced, const CSpliced_exon &exon)

Protected Member Functions inherited from CSeq_align_Mapper_Base
	CSeq_align_Mapper_Base (CSeq_loc_Mapper_Base &loc_mapper)

CSeq_loc_Mapper_Base &	GetLocMapper (void) const

size_t	GetMaxDim (void) const
	Get max number of rows of all segments. More...

void	InitExon (const CSpliced_seg &spliced, const CSpliced_exon &exon)

void	x_Init (const CSeq_align &align)

SAlignment_Segment &	x_InsertSeg (TSegments::iterator &where, int len, size_t dim, bool reverse)

void	x_InvalidateScores (SAlignment_Segment *seg=NULL)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
typedef CSeq_loc_Conversion_Set::TRange	TRange

typedef CSeq_loc_Conversion_Set::TRangeMap	TRangeMap

typedef CSeq_loc_Conversion_Set::TIdMap	TIdMap

typedef CSeq_loc_Conversion_Set::TConvByIndex	TConvByIndex

Private Member Functions
	CSeq_align_Mapper (CSeq_loc_Mapper_Base &loc_mapper)

void	Convert (CSeq_loc_Conversion_Set &cvts)

void	x_ConvertAlignCvt (CSeq_loc_Conversion_Set &cvts)

void	x_ConvertRowCvt (CSeq_loc_Conversion &cvt, size_t row)

void	x_ConvertRowCvt (TIdMap &cvts, size_t row)

CSeq_id_Handle	x_ConvertSegmentCvt (TSegments::iterator &seg_it, CSeq_loc_Conversion &cvt, size_t row)

CSeq_id_Handle	x_ConvertSegmentCvt (TSegments::iterator &seg_it, TIdMap &id_map, size_t row)

Friends
class	CSeq_loc_Conversion_Set

Additional Inherited Members
Public Types inherited from CSeq_align_Mapper_Base
typedef CSeq_align::C_Segs::TDendiag	TDendiag

typedef CSeq_align::C_Segs::TStd	TStd

typedef list< SAlignment_Segment >	TSegments

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...

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 Types inherited from CSeq_align_Mapper_Base
enum	EAlignFlags { eAlign_Normal , eAlign_Empty , eAlign_MultiId , eAlign_MultiDim }

typedef vector< CRef< CSeq_align_Mapper_Base > >	TSubAligns

Protected Attributes inherited from CSeq_align_Mapper_Base
CRef< CSeq_align >	m_DstAlign

TSubAligns	m_SubAligns

TSegments	m_Segs

EAlignFlags	m_AlignFlags