#include <objects/seq/Delta_ext.hpp>

Inheritance diagram for CDelta_ext:

Collaboration diagram for CDelta_ext:

Public Member Functions
	CDelta_ext (void)

	~CDelta_ext (void)

CDelta_seq &	AddLiteral (TSeqPos len)
	add a literal segment at the end this variant adds a gap literal More...

CDelta_seq &	AddLiteral (const CTempString &iupac_seq, CSeq_inst::EMol mol, bool do_pack=true)
	add a literal segment at the end this variant adds a non-gap literal More...

void	AddAndSplit (const CTempString &src, CSeq_data::E_Choice format, TSeqPos length, bool gaps_ok=false, bool allow_packing=true)
	add a chunk of sequence, splitting it as necessary for the sake of compactness (isolating ambiguous portions and optionally gaps) More...

CDelta_seq &	AddSeqRange (const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_plus)
	add a segment that refers to another segment More...

Public Member Functions inherited from CDelta_ext_Base
	CDelta_ext_Base (void)

virtual	~CDelta_ext_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

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

bool	CanGet (void) const
	Check if it is safe to call Get method. More...

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

const Tdata &	Get (void) const
	Get the member data. More...

Tdata &	Set (void)
	Assign a value to data member. More...

	operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...

	operator Tdata & (void)
	Conversion operator to 'Tdata' type. 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 CDelta_ext_Base	Tparent

Private Member Functions
	CDelta_ext (const CDelta_ext &value)

CDelta_ext &	operator= (const CDelta_ext &value)

Additional Inherited Members
Public Types inherited from CDelta_ext_Base
typedef list< CRef< CDelta_seq > >	Tdata

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 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...

Detailed Description

Definition at line 59 of file Delta_ext.hpp.

Member Typedef Documentation

◆ Tparent

typedef CDelta_ext_Base CDelta_ext::Tparent

private

Definition at line 61 of file Delta_ext.hpp.

Constructor & Destructor Documentation

◆ CDelta_ext() [1/2]

CDelta_ext::CDelta_ext ( void )

inline

Definition at line 98 of file Delta_ext.hpp.

◆ ~CDelta_ext()

CDelta_ext::~CDelta_ext ( void )

Definition at line 62 of file Delta_ext.cpp.

◆ CDelta_ext() [2/2]

CDelta_ext::CDelta_ext ( const CDelta_ext & value )

private

Member Function Documentation

◆ AddAndSplit()

void CDelta_ext::AddAndSplit	(	const CTempString &	src,
		CSeq_data::E_Choice	format,
		TSeqPos	length,
		bool	gaps_ok = `false`,
		bool	allow_packing = `true`
	)

add a chunk of sequence, splitting it as necessary for the sake of compactness (isolating ambiguous portions and optionally gaps)

Definition at line 183 of file Delta_ext.cpp.

References CTempString::data(), data, CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeqUtil::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeqUtil::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeqUtil::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqUtil::e_Ncbistdaa, CSeqUtil::e_not_set, CSeqConvert::Pack(), CDelta_ext_Base::Set(), CSeq_literal_Base::SetLength(), and CSeq_literal_Base::SetSeq_data().

Referenced by CFastaReader::AssembleSeq(), CGapsEditor::ConvertNs2Gaps(), and CBioseq::PackAsDeltaSeq().

◆ AddLiteral() [1/2]

CDelta_seq & CDelta_ext::AddLiteral	(	const CTempString &	iupac_seq,
		CSeq_inst::EMol	mol,
		bool	do_pack = `true`
	)

add a literal segment at the end this variant adds a non-gap literal

Definition at line 89 of file Delta_ext.cpp.

References CTempString::data(), CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eUnknown, CTempString::length(), NCBI_THROW, CSeqportUtil::Pack(), CDelta_ext_Base::Set(), and CTempString::size().

◆ AddLiteral() [2/2]

CDelta_seq & CDelta_ext::AddLiteral ( TSeqPos len )

add a literal segment at the end this variant adds a gap literal

Definition at line 69 of file Delta_ext.cpp.

References ctll::empty(), CDelta_ext_Base::Get(), len, and CDelta_ext_Base::Set().

Referenced by CGapsEditor::ConvertNs2Gaps(), and SeqLocToBioseq().

◆ AddSeqRange()

CDelta_seq & CDelta_ext::AddSeqRange	(	const CSeq_id &	id,
		TSeqPos	from,
		TSeqPos	to,
		ENa_strand	strand = `eNa_strand_plus`
	)

add a segment that refers to another segment

Definition at line 219 of file Delta_ext.cpp.

References CDelta_ext_Base::Set().

◆ operator=()

CDelta_ext& CDelta_ext::operator= ( const CDelta_ext & value )

private

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

include/objects/seq/Delta_ext.hpp
src/objects/seq/Delta_ext.cpp

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CDelta_ext() [1/2]

◆ ~CDelta_ext()

◆ CDelta_ext() [2/2]

Member Function Documentation

◆ AddAndSplit()

◆ AddLiteral() [1/2]

◆ AddLiteral() [2/2]

◆ AddSeqRange()

◆ operator=()