Inheritance diagram for CPhrap_Read:

Collaboration diagram for CPhrap_Read:

Classes
struct	SReadDS

struct	SReadTag

Public Types
typedef map< string, CRef< CPhrap_Read > >	TReads

typedef vector< SReadTag >	TReadTags

typedef TSignedSeqPos	TStart

typedef CRange< TSignedSeqPos >	TRange

Public Types inherited from CPhrap_Seq
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_Read (const string &name, TPhrapReaderFlags flags)

virtual	~CPhrap_Read (void)

void	Read (CNcbiIstream &in)

void	AddReadLoc (TSignedSeqPos start, bool complemented)

TStart	GetStart (void) const

void	ReadQuality (CNcbiIstream &in)

void	ReadDS (CNcbiIstream &in)

virtual void	ReadTag (CNcbiIstream &in, char tag)

CRef< CSeq_entry >	CreateRead (void) const

bool	IsCircular (void) const

Public Member Functions inherited from CPhrap_Seq
	CPhrap_Seq (TPhrapReaderFlags flags)

	CPhrap_Seq (const string &name, TPhrapReaderFlags flags)

virtual	~CPhrap_Seq (void)

void	Read (CNcbiIstream &in)

void	ReadData (CNcbiIstream &in)

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

Private Member Functions
void	x_CreateFeat (CBioseq &bioseq) const

void	x_CreateDesc (CBioseq &bioseq) const

void	x_AddTagFeats (CRef< CSeq_annot > &annot) const

void	x_AddQualityFeat (CRef< CSeq_annot > &annot) const

Private Attributes
size_t	m_NumInfoItems

size_t	m_NumReadTags

TRange	m_HiQualRange

TStart	m_Start

SReadDS *	m_DS

TReadTags	m_Tags

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 CPhrap_Seq
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...

Detailed Description

Definition at line 402 of file phrap.cpp.

Member Typedef Documentation

◆ TRange

typedef CRange<TSignedSeqPos> CPhrap_Read::TRange

Definition at line 433 of file phrap.cpp.

◆ TReads

typedef map<string, CRef<CPhrap_Read> > CPhrap_Read::TReads

Definition at line 405 of file phrap.cpp.

◆ TReadTags

typedef vector<SReadTag> CPhrap_Read::TReadTags

Definition at line 431 of file phrap.cpp.

◆ TStart

typedef TSignedSeqPos CPhrap_Read::TStart

Definition at line 432 of file phrap.cpp.

Constructor & Destructor Documentation

◆ CPhrap_Read()

CPhrap_Read::CPhrap_Read	(	const string &	name,
		TPhrapReaderFlags	flags
	)

Definition at line 462 of file phrap.cpp.

◆ ~CPhrap_Read()

CPhrap_Read::~CPhrap_Read ( void )

virtual

Definition at line 473 of file phrap.cpp.

References m_DS.

Member Function Documentation

◆ AddReadLoc()

void CPhrap_Read::AddReadLoc	(	TSignedSeqPos	start,
		bool	complemented
	)

inline

Definition at line 589 of file phrap.cpp.

References _ASSERT, m_Start, and CPhrap_Seq::SetComplemented().

◆ CreateRead()

CRef< CSeq_entry > CPhrap_Read::CreateRead ( void ) const

Definition at line 784 of file phrap.cpp.

References _ASSERT, CPhrap_Seq::CreateBioseq(), CSeq_inst_Base::eRepr_raw, CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), x_CreateDesc(), and x_CreateFeat().

◆ GetStart()

TStart CPhrap_Read::GetStart ( void ) const

inline

Definition at line 437 of file phrap.cpp.

References m_Start.

Referenced by CPhrap_Contig::x_CreateAlignAll(), CPhrap_Contig::x_CreateAlignOptimized(), and CPhrap_Contig::x_CreateAlignPairs().

◆ IsCircular()

bool CPhrap_Read::IsCircular ( void ) const

Definition at line 489 of file phrap.cpp.

References CPhrap_Seq::GetAlignedFrom(), and m_Start.

◆ Read()

void CPhrap_Read::Read ( CNcbiIstream & in )

Definition at line 481 of file phrap.cpp.

References CheckStreamState(), in(), m_NumInfoItems, m_NumReadTags, and CPhrap_Seq::Read().

◆ ReadDS()

void CPhrap_Read::ReadDS ( CNcbiIstream & in )

Definition at line 514 of file phrap.cpp.

References CT_POS_TYPE, CPhrap_Seq::GetName(), in(), ITERATE, CPhrap_Read::SReadDS::m_Chem, CPhrap_Read::SReadDS::m_ChromatFile, CPhrap_Read::SReadDS::m_Direction, m_DS, CPhrap_Read::SReadDS::m_Dye, CPhrap_Read::SReadDS::m_PhdFile, CPhrap_Read::SReadDS::m_Template, CPhrap_Read::SReadDS::m_Time, NCBI_THROW2, ReadLine(), NStr::Split(), and tag.

◆ ReadQuality()

void CPhrap_Read::ReadQuality ( CNcbiIstream & in )

Definition at line 495 of file phrap.cpp.

References CheckStreamState(), fPhrap_OldVersion, CPhrap_Seq::GetFlags(), in(), m_HiQualRange, COpenRange< Position >::Set(), and CPhrap_Seq::SetAligned().

◆ ReadTag()

void CPhrap_Read::ReadTag	(	CNcbiIstream &	in,
		char	tag
	)

virtual

Implements CPhrap_Seq.

Definition at line 562 of file phrap.cpp.

References _ASSERT, CheckStreamState(), CT_POS_TYPE, in(), CPhrap_Read::SReadTag::m_Date, CPhrap_Read::SReadTag::m_End, CPhrap_Read::SReadTag::m_Program, CPhrap_Read::SReadTag::m_Start, m_Tags, CPhrap_Read::SReadTag::m_Type, NCBI_THROW2, and tag.

◆ x_AddQualityFeat()

void CPhrap_Read::x_AddQualityFeat ( CRef< CSeq_annot > & annot ) const

private

◆ x_AddTagFeats()

void CPhrap_Read::x_AddTagFeats ( CRef< CSeq_annot > & annot ) const

private

◆ x_CreateDesc()

void CPhrap_Read::x_CreateDesc ( CBioseq & bioseq ) const

private

◆ x_CreateFeat()

void CPhrap_Read::x_CreateFeat ( CBioseq & bioseq ) const

private

Definition at line 717 of file phrap.cpp.

References CPhrap_Seq::CreatePadsFeat(), CBioseq_Base::SetAnnot(), x_AddQualityFeat(), and x_AddTagFeats().

Referenced by CreateRead().

Member Data Documentation

◆ m_DS

SReadDS* CPhrap_Read::m_DS

private

Definition at line 457 of file phrap.cpp.

Referenced by ReadDS(), x_CreateDesc(), and ~CPhrap_Read().

◆ m_HiQualRange

TRange CPhrap_Read::m_HiQualRange

private

Definition at line 455 of file phrap.cpp.

Referenced by ReadQuality(), and x_AddQualityFeat().

◆ m_NumInfoItems

size_t CPhrap_Read::m_NumInfoItems

private

Definition at line 453 of file phrap.cpp.

Referenced by Read().

◆ m_NumReadTags

size_t CPhrap_Read::m_NumReadTags

private

Definition at line 454 of file phrap.cpp.

Referenced by Read(), and x_AddTagFeats().

◆ m_Start

TStart CPhrap_Read::m_Start

private

Definition at line 456 of file phrap.cpp.

Referenced by AddReadLoc(), GetStart(), and IsCircular().

◆ m_Tags

TReadTags CPhrap_Read::m_Tags

private

Definition at line 458 of file phrap.cpp.

Referenced by ReadTag(), and x_AddTagFeats().

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

src/objtools/readers/phrap.cpp

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TRange

◆ TReads

◆ TReadTags

◆ TStart

Constructor & Destructor Documentation

◆ CPhrap_Read()

◆ ~CPhrap_Read()

Member Function Documentation

◆ AddReadLoc()

◆ CreateRead()

◆ GetStart()

◆ IsCircular()

◆ Read()

◆ ReadDS()

◆ ReadQuality()

◆ ReadTag()

◆ x_AddQualityFeat()

◆ x_AddTagFeats()

◆ x_CreateDesc()

◆ x_CreateFeat()

Member Data Documentation

◆ m_DS

◆ m_HiQualRange

◆ m_NumInfoItems

◆ m_NumReadTags

◆ m_Start

◆ m_Tags