Inheritance diagram for SAccGuide:

Collaboration diagram for SAccGuide:

Classes
struct	SHints

struct	SSubMap

Public Types
typedef CSeq_id::EAccessionInfo	TAccInfo

typedef map< string, TAccInfo >	TPrefixes

typedef pair< string, TAccInfo >	TPair

typedef list< TPair >	TPairs

typedef map< string, TPair >	TBigSpecialMap

typedef pair< bm::bvector<>, TAccInfo >	TSmallSpecialOption

typedef multimap< string, TSmallSpecialOption >	TSmallSpecialMap

typedef unsigned int	TFormatCode

typedef pair< string, string >	TFallback

typedef map< const TAccInfo *, TFallback >	TFallbackMap

typedef map< TFormatCode, SSubMap >	TMainMap

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
	SAccGuide (void)

	SAccGuide (const string &filename)

	SAccGuide (ILineReader &lr)

void	AddRule (const CTempString &rule, SHints &hints)

const TAccInfo &	Find (TFormatCode fmt, const CTempString &acc_or_pfx, string *key_used=NULL) 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

Static Public Member Functions
static TFormatCode	s_Key (unsigned short letters, unsigned short digits)

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)

Public Attributes
unsigned int	count

TMainMap	rules

TPrefixes	general

TFallbackMap	fallbacks

Private Member Functions
void	x_Load (const string &filename)

void	x_Load (ILineReader &lr)

void	x_InitGeneral (void)

void	x_AddSpecial (SSubMap &submap, SHints &hints, TFormatCode fmt, CTempString from, CTempString to, TAccInfo value, const string *old_name, const CTempString &new_name)

Static Private Member Functions
static bm::bvector_size_type	x_SplitSpecial (CTempString &acc, TFormatCode fmt)

Additional Inherited Members
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 886 of file Seq_id.cpp.

Member Typedef Documentation

◆ TAccInfo

typedef CSeq_id::EAccessionInfo SAccGuide::TAccInfo

Definition at line 888 of file Seq_id.cpp.

◆ TBigSpecialMap

typedef map<string, TPair> SAccGuide::TBigSpecialMap

Definition at line 892 of file Seq_id.cpp.

◆ TFallback

typedef pair<string, string> SAccGuide::TFallback

Definition at line 896 of file Seq_id.cpp.

◆ TFallbackMap

typedef map<const TAccInfo*, TFallback> SAccGuide::TFallbackMap

Definition at line 897 of file Seq_id.cpp.

◆ TFormatCode

typedef unsigned int SAccGuide::TFormatCode

Definition at line 895 of file Seq_id.cpp.

◆ TMainMap

typedef map<TFormatCode, SSubMap> SAccGuide::TMainMap

Definition at line 905 of file Seq_id.cpp.

◆ TPair

typedef pair<string, TAccInfo> SAccGuide::TPair

Definition at line 890 of file Seq_id.cpp.

◆ TPairs

typedef list<TPair> SAccGuide::TPairs

Definition at line 891 of file Seq_id.cpp.

◆ TPrefixes

typedef map<string, TAccInfo> SAccGuide::TPrefixes

Definition at line 889 of file Seq_id.cpp.

◆ TSmallSpecialMap

typedef multimap<string, TSmallSpecialOption> SAccGuide::TSmallSpecialMap

Definition at line 894 of file Seq_id.cpp.

◆ TSmallSpecialOption

typedef pair<bm::bvector<>, TAccInfo> SAccGuide::TSmallSpecialOption

Definition at line 893 of file Seq_id.cpp.

Constructor & Destructor Documentation

◆ SAccGuide() [1/3]

SAccGuide::SAccGuide ( void )

Definition at line 1443 of file Seq_id.cpp.

References AddRule(), count, ERASE_ITERATE, ERR_POST_X, file, g_FindDataFile(), g_IsDataFileOld(), i, Info(), rules, STD_CATCH_ALL_X, x_InitGeneral(), and x_Load().

◆ SAccGuide() [2/3]

SAccGuide::SAccGuide ( const string & filename )

inline

Definition at line 942 of file Seq_id.cpp.

References x_Load().

◆ SAccGuide() [3/3]

SAccGuide::SAccGuide ( ILineReader & lr )

inline

Definition at line 945 of file Seq_id.cpp.

References x_Load().

Member Function Documentation

◆ AddRule()

void SAccGuide::AddRule	(	const CTempString &	rule,
		SHints &	hints
	)

Definition at line 1030 of file Seq_id.cpp.

Referenced by SAccGuide(), and x_Load().

◆ Find()

const SAccGuide::TAccInfo & SAccGuide::Find	(	TFormatCode	fmt,
		const CTempString &	acc_or_pfx,
		string *	key_used = `NULL`
	)		const

◆ s_Key()

static TFormatCode SAccGuide::s_Key	(	unsigned short	letters,
		unsigned short	digits
	)

inlinestatic

Definition at line 952 of file Seq_id.cpp.

Referenced by AddRule(), and CSeq_id::x_IdentifyAccession().

◆ x_AddSpecial()

void SAccGuide::x_AddSpecial	(	SSubMap &	submap,
		SHints &	hints,
		TFormatCode	fmt,
		CTempString	from,
		CTempString	to,
		TAccInfo	value,
		const string *	old_name,
		const CTempString &	new_name
	)

private

◆ x_InitGeneral()

void SAccGuide::x_InitGeneral ( void )

private

Definition at line 1484 of file Seq_id.cpp.

References CSeq_id::eAcc_general_nuc, map_checker< Container >::empty(), general, and NULL.

Referenced by SAccGuide().

◆ x_Load() [1/2]

void SAccGuide::x_Load ( const string & filename )

private

Definition at line 1499 of file Seq_id.cpp.

References in(), and ILineReader::New().

Referenced by SAccGuide().

◆ x_Load() [2/2]

void SAccGuide::x_Load ( ILineReader & lr )

private

Definition at line 1505 of file Seq_id.cpp.

References AddRule(), and in().

◆ x_SplitSpecial()

bm::bvector_size_type SAccGuide::x_SplitSpecial	(	CTempString &	acc,
		TFormatCode	fmt
	)

staticprivate

Definition at line 1596 of file Seq_id.cpp.

References _ASSERT, CTempString::erase(), isalpha(), kBVSizes, kMaxSmallSpecialDigits, result, CTempString::size(), NStr::StringToNumeric(), and CTempString::substr().

Referenced by Find(), and x_AddSpecial().

Member Data Documentation

◆ count

unsigned int SAccGuide::count

Definition at line 955 of file Seq_id.cpp.

Referenced by AddRule(), and SAccGuide().

◆ fallbacks

TFallbackMap SAccGuide::fallbacks

Definition at line 958 of file Seq_id.cpp.

Referenced by AddRule(), and x_AddSpecial().

◆ general

TPrefixes SAccGuide::general

Definition at line 957 of file Seq_id.cpp.

Referenced by AddRule(), and x_InitGeneral().

◆ rules

TMainMap SAccGuide::rules

Definition at line 956 of file Seq_id.cpp.

Referenced by AddRule(), Find(), SAccGuide::SHints::FindSubMap(), and SAccGuide().

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

src/objects/seqloc/Seq_id.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Static Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAccInfo

◆ TBigSpecialMap

◆ TFallback

◆ TFallbackMap

◆ TFormatCode

◆ TMainMap

◆ TPair

◆ TPairs

◆ TPrefixes

◆ TSmallSpecialMap

◆ TSmallSpecialOption

Constructor & Destructor Documentation

◆ SAccGuide() [1/3]

◆ SAccGuide() [2/3]

◆ SAccGuide() [3/3]

Member Function Documentation

◆ AddRule()

◆ Find()

◆ s_Key()

◆ x_AddSpecial()

◆ x_InitGeneral()

◆ x_Load() [1/2]

◆ x_Load() [2/2]

◆ x_SplitSpecial()

Member Data Documentation

◆ count

◆ fallbacks

◆ general

◆ rules