#include <objects/seqloc/Textseq_id.hpp>

Inheritance diagram for CTextseq_id:

Collaboration diagram for CTextseq_id:

Public Member Functions
	CTextseq_id (void)

virtual	~CTextseq_id (void)

CTextseq_id &	Set (const CTempString &acc_in, const CTempString &name_in=kEmptyStr, int version=0, const CTempString &release_in=kEmptyStr, bool allow_dot_version=true)
	Set all fields with a single call. More...

bool	Match (const CTextseq_id &tsip2) const
	Comparison functions. More...

int	Compare (const CTextseq_id &tsip2) const

bool	operator< (const CTextseq_id &tsip2) const

ostream &	AsFastaString (ostream &s, bool allow_version=true) const
	Format the contents FASTA string style. More...

Public Member Functions inherited from CTextseq_id_Base
	CTextseq_id_Base (void)

virtual	~CTextseq_id_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

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

bool	CanGetName (void) const
	Check if it is safe to call GetName method. More...

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

const TName &	GetName (void) const
	Get the Name member data. More...

void	SetName (const TName &value)
	Assign a value to Name data member. More...

void	SetName (TName &&value)

TName &	SetName (void)
	Assign a value to Name data member. More...

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

bool	CanGetAccession (void) const
	Check if it is safe to call GetAccession method. More...

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

const TAccession &	GetAccession (void) const
	Get the Accession member data. More...

void	SetAccession (const TAccession &value)
	Assign a value to Accession data member. More...

void	SetAccession (TAccession &&value)

TAccession &	SetAccession (void)
	Assign a value to Accession data member. More...

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

bool	CanGetRelease (void) const
	Check if it is safe to call GetRelease method. More...

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

const TRelease &	GetRelease (void) const
	Get the Release member data. More...

void	SetRelease (const TRelease &value)
	Assign a value to Release data member. More...

void	SetRelease (TRelease &&value)

TRelease &	SetRelease (void)
	Assign a value to Release data member. More...

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

bool	CanGetVersion (void) const
	Check if it is safe to call GetVersion method. More...

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

TVersion	GetVersion (void) const
	Get the Version member data. More...

void	SetVersion (TVersion value)
	Assign a value to Version data member. More...

TVersion &	SetVersion (void)
	Assign a value to Version 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 CTextseq_id_Base	Tparent

Private Member Functions
	CTextseq_id (const CTextseq_id &)

CTextseq_id &	operator= (const CTextseq_id &)

Additional Inherited Members
Public Types inherited from CTextseq_id_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_name , e_accession , e_release , e_version }

typedef string	TName

typedef string	TAccession

typedef string	TRelease

typedef int	TVersion

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...

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 50 of file Textseq_id.hpp.

Member Typedef Documentation

◆ Tparent

typedef CTextseq_id_Base CTextseq_id::Tparent

private

Definition at line 52 of file Textseq_id.hpp.

Constructor & Destructor Documentation

◆ CTextseq_id() [1/2]

CTextseq_id::CTextseq_id ( void )

inline

Definition at line 100 of file Textseq_id.hpp.

◆ ~CTextseq_id()

CTextseq_id::~CTextseq_id ( void )

virtual

Definition at line 52 of file Textseq_id.cpp.

◆ CTextseq_id() [2/2]

CTextseq_id::CTextseq_id ( const CTextseq_id & )

private

Member Function Documentation

◆ AsFastaString()

ostream & CTextseq_id::AsFastaString	(	ostream &	s,
		bool	allow_version = `true`
	)		const

Format the contents FASTA string style.

Definition at line 229 of file Textseq_id.cpp.

References CTextseq_id_Base::GetAccession(), CTextseq_id_Base::GetName(), CTextseq_id_Base::GetVersion(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetVersion(), and dtl::version.

Referenced by CSeq_id::x_WriteContentAsFasta().

◆ Compare()

int CTextseq_id::Compare ( const CTextseq_id & tsip2 ) const

Definition at line 178 of file Textseq_id.cpp.

References _ASSERT, CTextseq_id_Base::GetAccession(), CTextseq_id_Base::GetName(), CTextseq_id_Base::GetVersion(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), and CTextseq_id_Base::IsSetVersion().

Referenced by CSeq_id::CompareOrdered(), and operator<().

◆ Match()

bool CTextseq_id::Match ( const CTextseq_id & tsip2 ) const

Comparison functions.

Definition at line 143 of file Textseq_id.cpp.

References CSerialObject::Equals(), CTextseq_id_Base::GetAccession(), CTextseq_id_Base::GetName(), CTextseq_id_Base::GetVersion(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetName(), and CTextseq_id_Base::IsSetVersion().

Referenced by CSeq_id::Compare().

◆ operator<()

bool CTextseq_id::operator< ( const CTextseq_id & tsip2 ) const

inline

Definition at line 106 of file Textseq_id.hpp.

References Compare().

◆ operator=()

CTextseq_id& CTextseq_id::operator= ( const CTextseq_id & )

private

◆ Set()

CTextseq_id & CTextseq_id::Set	(	const CTempString &	acc_in,
		const CTempString &	name_in = `kEmptyStr`,
		int	version = `0`,
		const CTempString &	release_in = `kEmptyStr`,
		bool	allow_dot_version = `true`
	)

Set all fields with a single call.

Fields not specified will be reset.

Parameters

acc	New value of accession field (may end with a dot and a version unless allow_dot_version is false).
name	New value of name (locus) field.
version	New value of version field. If acc also specifies a non-zero version, the two values must agree.
release	New value of release field.
allow_dot_version	Whether to parse an optional dot-delimited version off the end of acc.

Definition at line 58 of file Textseq_id.cpp.

References CTempString::empty(), NStr::eTrunc_Both, NStr::IntToString(), NCBI_THROW, NPOS, CTextseq_id_Base::ResetAccession(), CTextseq_id_Base::ResetName(), CTextseq_id_Base::ResetRelease(), CTextseq_id_Base::ResetVersion(), CTempString::rfind(), CTextseq_id_Base::SetAccession(), CTextseq_id_Base::SetName(), CTextseq_id_Base::SetRelease(), CTextseq_id_Base::SetVersion(), NStr::StringToNonNegativeInt(), CTempString::substr(), NStr::TruncateSpaces_Unsafe(), and dtl::version.

Referenced by CSeq_id::Set().

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

include/objects/seqloc/Textseq_id.hpp
src/objects/seqloc/Textseq_id.cpp

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CTextseq_id() [1/2]

◆ ~CTextseq_id()

◆ CTextseq_id() [2/2]

Member Function Documentation

◆ AsFastaString()

◆ Compare()

◆ Match()

◆ operator<()

◆ operator=()

◆ Set()