Search Toolkit Book for CAutoDefSourceDescription

#include <objmgr/util/autodef_source_desc.hpp>

Inheritance diagram for CAutoDefSourceDescription:

Collaboration diagram for CAutoDefSourceDescription:

Public Types
typedef vector< string >	TStringVector

typedef vector< CAutoDefAvailableModifier >	TAvailableModifierVector

typedef vector< CAutoDefSourceModifierInfo >	TModifierVector

typedef list< string >	TDescString

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
	CAutoDefSourceDescription (const CBioSource &bs, string feature_clauses="")

	CAutoDefSourceDescription (CAutoDefSourceDescription *other)

	~CAutoDefSourceDescription ()

const CBioSource &	GetBioSource () const

void	GetAvailableModifiers (TAvailableModifierVector &modifier_list)

bool	IsTrickyHIV ()

string	GetComboDescription (IAutoDefCombo *mod_combo)

bool	AddQual (bool isOrgMod, int subtype, bool keepAfterSemicolon)

bool	RemoveQual (bool isOrgMod, int subtype)

int	Compare (const CAutoDefSourceDescription &s) const

bool	operator> (const CAutoDefSourceDescription &src) const

bool	operator< (const CAutoDefSourceDescription &src) const

const TModifierVector &	GetModifiers () const

const TDescString &	GetStrings () const

const string &	GetFeatureClauses () 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 Attributes
const CBioSource &	m_BS

TModifierVector	m_Modifiers

TDescString	m_DescStrings

string	m_FeatureClauses

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 CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 111 of file autodef_source_desc.hpp.

Member Typedef Documentation

◆ TAvailableModifierVector

typedef vector<CAutoDefAvailableModifier> CAutoDefSourceDescription::TAvailableModifierVector

Definition at line 119 of file autodef_source_desc.hpp.

◆ TDescString

typedef list<string> CAutoDefSourceDescription::TDescString

Definition at line 144 of file autodef_source_desc.hpp.

◆ TModifierVector

typedef vector<CAutoDefSourceModifierInfo> CAutoDefSourceDescription::TModifierVector

Definition at line 142 of file autodef_source_desc.hpp.

◆ TStringVector

typedef vector<string> CAutoDefSourceDescription::TStringVector

Definition at line 118 of file autodef_source_desc.hpp.

Constructor & Destructor Documentation

◆ CAutoDefSourceDescription() [1/2]

CAutoDefSourceDescription::CAutoDefSourceDescription	(	const CBioSource &	bs,
		string	feature_clauses = `""`
	)

Definition at line 50 of file autodef_source_desc.cpp.

References ITERATE, and ct::sort().

◆ CAutoDefSourceDescription() [2/2]

CAutoDefSourceDescription::CAutoDefSourceDescription ( CAutoDefSourceDescription * other )

Definition at line 70 of file autodef_source_desc.cpp.

References GetModifiers(), GetStrings(), ITERATE, m_DescStrings, m_FeatureClauses, and m_Modifiers.

◆ ~CAutoDefSourceDescription()

CAutoDefSourceDescription::~CAutoDefSourceDescription ( )

Definition at line 85 of file autodef_source_desc.cpp.

Member Function Documentation

◆ AddQual()

bool CAutoDefSourceDescription::AddQual	(	bool	isOrgMod,
		int	subtype,
		bool	keepAfterSemicolon
	)

Definition at line 95 of file autodef_source_desc.cpp.

References NStr::Find(), m_DescStrings, m_Modifiers, and val.

◆ Compare()

int CAutoDefSourceDescription::Compare ( const CAutoDefSourceDescription & s ) const

Definition at line 165 of file autodef_source_desc.cpp.

References NStr::Compare(), GetFeatureClauses(), GetStrings(), and m_DescStrings.

Referenced by operator<(), and operator>().

◆ GetAvailableModifiers()

void CAutoDefSourceDescription::GetAvailableModifiers ( TAvailableModifierVector & modifier_list )

Definition at line 206 of file autodef_source_desc.cpp.

References CBioSource_Base::CanGetOrg(), COrg_ref_Base::CanGetOrgname(), CBioSource_Base::CanGetSubtype(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), COrgName_Base::IsSetMod(), ITERATE, and m_BS.

◆ GetBioSource()

const CBioSource & CAutoDefSourceDescription::GetBioSource ( void ) const

Definition at line 89 of file autodef_source_desc.cpp.

References m_BS.

◆ GetComboDescription()

string CAutoDefSourceDescription::GetComboDescription ( IAutoDefCombo * mod_combo )

Definition at line 195 of file autodef_source_desc.cpp.

References CBioSource_Base::GetOrg(), IAutoDefCombo::GetSourceDescriptionString(), COrg_ref_Base::GetTaxname(), and m_BS.

◆ GetFeatureClauses()

const string& CAutoDefSourceDescription::GetFeatureClauses ( ) const

inline

Definition at line 146 of file autodef_source_desc.hpp.

References m_FeatureClauses.

Referenced by Compare().

◆ GetModifiers()

const TModifierVector& CAutoDefSourceDescription::GetModifiers ( void ) const

inline

Definition at line 143 of file autodef_source_desc.hpp.

References m_Modifiers.

Referenced by CAutoDefSourceDescription().

◆ GetStrings()

const TDescString& CAutoDefSourceDescription::GetStrings ( void ) const

inline

Definition at line 145 of file autodef_source_desc.hpp.

References m_DescStrings.

Referenced by CAutoDefSourceDescription(), and Compare().

◆ IsTrickyHIV()

bool CAutoDefSourceDescription::IsTrickyHIV ( )

Definition at line 239 of file autodef_source_desc.cpp.

References CBioSource_Base::CanGetOrg(), COrg_ref_Base::CanGetOrgname(), CBioSource_Base::CanGetSubtype(), NStr::Equal(), CSubSource_Base::eSubtype_clone, COrgMod_Base::eSubtype_isolate, COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetSubtype(), COrg_ref_Base::GetTaxname(), COrgName_Base::IsSetMod(), ITERATE, and m_BS.

◆ operator<()

bool CAutoDefSourceDescription::operator< ( const CAutoDefSourceDescription & src ) const

inline

Definition at line 137 of file autodef_source_desc.hpp.

References Compare().

◆ operator>()

bool CAutoDefSourceDescription::operator> ( const CAutoDefSourceDescription & src ) const

inline

Definition at line 132 of file autodef_source_desc.hpp.

References Compare().

◆ RemoveQual()

bool CAutoDefSourceDescription::RemoveQual	(	bool	isOrgMod,
		int	subtype
	)

Definition at line 138 of file autodef_source_desc.cpp.

References m_Modifiers.

Member Data Documentation

◆ m_BS

const CBioSource& CAutoDefSourceDescription::m_BS

private

Definition at line 149 of file autodef_source_desc.hpp.

Referenced by GetAvailableModifiers(), GetBioSource(), GetComboDescription(), and IsTrickyHIV().

◆ m_DescStrings

TDescString CAutoDefSourceDescription::m_DescStrings

private

Definition at line 151 of file autodef_source_desc.hpp.

Referenced by AddQual(), CAutoDefSourceDescription(), Compare(), and GetStrings().

◆ m_FeatureClauses

string CAutoDefSourceDescription::m_FeatureClauses

private

Definition at line 152 of file autodef_source_desc.hpp.

Referenced by CAutoDefSourceDescription(), and GetFeatureClauses().

◆ m_Modifiers

TModifierVector CAutoDefSourceDescription::m_Modifiers

private

Definition at line 150 of file autodef_source_desc.hpp.

Referenced by AddQual(), CAutoDefSourceDescription(), GetModifiers(), and RemoveQual().

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

include/objmgr/util/autodef_source_desc.hpp
src/objmgr/util/autodef_source_desc.cpp

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAvailableModifierVector

◆ TDescString

◆ TModifierVector

◆ TStringVector

Constructor & Destructor Documentation

◆ CAutoDefSourceDescription() [1/2]

◆ CAutoDefSourceDescription() [2/2]

◆ ~CAutoDefSourceDescription()

Member Function Documentation

◆ AddQual()

◆ Compare()

◆ GetAvailableModifiers()

◆ GetBioSource()

◆ GetComboDescription()

◆ GetFeatureClauses()

◆ GetModifiers()

◆ GetStrings()

◆ IsTrickyHIV()

◆ operator<()

◆ operator>()

◆ RemoveQual()

Member Data Documentation

◆ m_BS

◆ m_DescStrings

◆ m_FeatureClauses

◆ m_Modifiers