#include <objects/seqalign/Sparse_seg.hpp>

Inheritance diagram for CSparse_seg:

Collaboration diagram for CSparse_seg:

Public Types
typedef int	TDim
	types More...

Public Types inherited from CSparse_seg_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_master_id , e_rows , e_row_scores , e_ext }

typedef CSeq_id	TMaster_id

typedef vector< CRef< CSparse_align > >	TRows

typedef vector< CRef< CScore > >	TRow_scores

typedef vector< CRef< CSparse_seg_ext > >	TExt

typedef Tparent::CMemberIndex< E_memberIndex, 5 >	TmemberIndex

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
	CSparse_seg (void)

	~CSparse_seg (void)

void	Validate (bool full_test=false) const
	Validators. More...

TDim	CheckNumRows (void) const

CRange< TSeqPos >	GetSeqRange (TDim row) const

TSeqPos	GetSeqStart (TDim row) const

TSeqPos	GetSeqStop (TDim row) const

const CSeq_id &	GetSeq_id (TDim row) const

ENa_strand	GetSeqStrand (TDim row) const

Public Member Functions inherited from CSparse_seg_Base
	CSparse_seg_Base (void)

virtual	~CSparse_seg_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetMaster_id (void) const
	Check if a value has been assigned to Master_id data member. More...

bool	CanGetMaster_id (void) const
	Check if it is safe to call GetMaster_id method. More...

void	ResetMaster_id (void)
	Reset Master_id data member. More...

const TMaster_id &	GetMaster_id (void) const
	Get the Master_id member data. More...

void	SetMaster_id (TMaster_id &value)
	Assign a value to Master_id data member. More...

TMaster_id &	SetMaster_id (void)
	Assign a value to Master_id data member. More...

bool	IsSetRows (void) const
	pairwise alignments constituting this multiple alignment Check if a value has been assigned to Rows data member. More...

bool	CanGetRows (void) const
	Check if it is safe to call GetRows method. More...

void	ResetRows (void)
	Reset Rows data member. More...

const TRows &	GetRows (void) const
	Get the Rows member data. More...

TRows &	SetRows (void)
	Assign a value to Rows data member. More...

bool	IsSetRow_scores (void) const
	per-row scores Check if a value has been assigned to Row_scores data member. More...

bool	CanGetRow_scores (void) const
	Check if it is safe to call GetRow_scores method. More...

void	ResetRow_scores (void)
	Reset Row_scores data member. More...

const TRow_scores &	GetRow_scores (void) const
	Get the Row_scores member data. More...

TRow_scores &	SetRow_scores (void)
	Assign a value to Row_scores data member. More...

bool	IsSetExt (void) const
	index of extra items Check if a value has been assigned to Ext data member. More...

bool	CanGetExt (void) const
	Check if it is safe to call GetExt method. More...

void	ResetExt (void)
	Reset Ext data member. More...

const TExt &	GetExt (void) const
	Get the Ext member data. More...

TExt &	SetExt (void)
	Assign a value to Ext data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. 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...

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 Types
typedef CSparse_seg_Base	Tparent

Private Member Functions
	CSparse_seg (const CSparse_seg &value)

CSparse_seg &	operator= (const CSparse_seg &value)

Additional Inherited Members
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

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 CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

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...