Query-anchored alignment can be 2 or multi-dimentional. More...

#include <objtools/alnmgr/pairwise_aln.hpp>

Inheritance diagram for CAnchoredAln:

Collaboration diagram for CAnchoredAln:

Public Types
typedef int	TDim

typedef vector< CRef< CPairwiseAln > >	TPairwiseAlnVector

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
	CAnchoredAln (void)
	Default constructor. More...

	CAnchoredAln (const CAnchoredAln &c)
	NB: Copy constructor is deep on pairwise_alns so that pairwise_alns can be modified. More...

CAnchoredAln &	operator= (const CAnchoredAln &c)
	NB: Assignment operator is deep on pairwise_alns so that pairwise_alns can be modified. More...

TDim	GetDim (void) const
	How many rows. More...

const TAlnSeqIdIRef &	GetId (TDim row) const
	Seq ids of the rows. More...

const TPairwiseAlnVector &	GetPairwiseAlns (void) const
	The vector of pairwise alns. More...

TDim	GetAnchorRow (void) const
	Which is the anchor row? More...

const TAlnSeqIdIRef &	GetAnchorId (void) const
	What is the seq id of the anchor? More...

int	GetScore (void) const
	What is the total score? More...

void	SetDim (TDim dim)
	Modify the number of rows. More...

TPairwiseAlnVector &	SetPairwiseAlns (void)
	Modify pairwise alns. More...

void	SetAnchorRow (TDim anchor_row)
	Modify anchor row (never do this unless you are creating a new alignment and know what you're doing). More...

void	SetScore (int score)
	Set the total score. More...

int &	SetScore (void)
	Non-const access to the total score. More...

bool	SplitStrands (void)
	Split rows with mixed dir into separate rows returns true if the operation was performed. 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

Private Attributes
TDim	m_AnchorRow

TPairwiseAlnVector	m_PairwiseAlns

int	m_Score

Static Private Attributes
static const TDim	kInvalidAnchorRow = -1

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...