Inheritance diagram for CPhrap_Seq:

Collaboration diagram for CPhrap_Seq:

Public Types
typedef map< TSeqPos, TSeqPos >	TPadMap

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
	CPhrap_Seq (TPhrapReaderFlags flags)

	CPhrap_Seq (const string &name, TPhrapReaderFlags flags)

virtual	~CPhrap_Seq (void)

void	Read (CNcbiIstream &in)

void	ReadData (CNcbiIstream &in)

virtual void	ReadTag (CNcbiIstream &in, char tag)=0

void	SetComplemented (bool value)

bool	IsComplemented (void) const

TPhrapReaderFlags	GetFlags (void) const

bool	FlagSet (EPhrapReaderFlags value) const

const string &	GetName (void) const

TSeqPos	GetPaddedLength (void) const

TSeqPos	GetUnpaddedLength (void) const

const string &	GetData (void) const

CRef< CSeq_id >	GetId (void) const

TSeqPos	GetPaddedPos (TSeqPos unpadded) const

TSeqPos	GetUnpaddedPos (TSeqPos padded, TSeqPos *link=0) const

CRef< CBioseq >	CreateBioseq (void) const

const TPadMap &	GetPadMap (void) const

TSeqPos	GetAlignedFrom (void) const

TSeqPos	GetAlignedTo (void) 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

Protected Member Functions
void	CreateComplementedDescr (CRef< CSeq_descr > &descr) const

void	CreatePadsFeat (CRef< CSeq_annot > &annot) const

void	SetAligned (TSeqPos from, TSeqPos to)

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

Private Member Functions
void	x_FillSeqData (CSeq_data &data) const

void	CopyFrom (CPhrap_Seq &seq)

Private Attributes
TPhrapReaderFlags	m_Flags

string	m_Name

TSeqPos	m_PaddedLength

TSeqPos	m_UnpaddedLength

string	m_Data

TPadMap	m_PadMap

bool	m_Complemented

TSeqPos	m_AlignedFrom

TSeqPos	m_AlignedTo

CRef< CSeq_id >	m_Id

Friends
class	CPhrap_Sequence

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...