@Gb_qual.hpp User-defined methods of the data storage class. More...

#include <objects/seqfeat/Gb_qual.hpp>

Inheritance diagram for CGb_qual:

Collaboration diagram for CGb_qual:

Public Types
typedef CStaticArraySet< const char *, PNocase_CStr >	TLegalRepeatTypeSet

typedef CStaticArraySet< const char *, PNocase_CStr >	TLegalPseudogeneSet

typedef CStaticArraySet< const char *, PNocase_CStr >	TLegalRecombinationClassSet

Public Types inherited from CGb_qual_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_qual , e_val }

typedef string	TQual

typedef string	TVal

typedef Tparent::CMemberIndex< E_memberIndex, 3 >	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...

Public Member Functions
	CGb_qual (void)

	CGb_qual (const TQual &qual, const TVal &val)

	~CGb_qual (void)

int	Compare (const CGb_qual &gbqual) const

Public Member Functions inherited from CGb_qual_Base
	CGb_qual_Base (void)

virtual	~CGb_qual_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

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

bool	CanGetQual (void) const
	Check if it is safe to call GetQual method. More...

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

const TQual &	GetQual (void) const
	Get the Qual member data. More...

void	SetQual (const TQual &value)
	Assign a value to Qual data member. More...

void	SetQual (TQual &&value)

TQual &	SetQual (void)
	Assign a value to Qual data member. More...

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

bool	CanGetVal (void) const
	Check if it is safe to call GetVal method. More...

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

const TVal &	GetVal (void) const
	Get the Val member data. More...

void	SetVal (const TVal &value)
	Assign a value to Val data member. More...

void	SetVal (TVal &&value)

TVal &	SetVal (void)
	Assign a value to Val 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

Static Public Member Functions
static void	ParseExperiment (const string &orig, string &category, string &experiment, string &doi)

static string	BuildExperiment (const string &category, const string &experiment, const string &doi)

static bool	CleanupRptUnitSeq (string &val)

static bool	CleanupReplace (string &val)

static bool	CleanupRptUnitRange (string &val)

static const TLegalRepeatTypeSet &	GetSetOfLegalRepeatTypes (void)

static bool	IsValidRptTypeValue (const string &val)

static bool	FixRptTypeValue (string &val)

static const TLegalPseudogeneSet &	GetSetOfLegalPseudogenes (void)

static bool	IsValidPseudogeneValue (const string &val)

static bool	FixPseudogeneValue (string &val)

static const TLegalRecombinationClassSet &	GetSetOfLegalRecombinationClassValues (void)

static bool	FixRecombinationClassValue (string &val)

static bool	IsLegalMobileElementValue (const string &val)

static void	GetMobileElementValueElements (const string &val, string &element_type, string &element_name)

static bool	FixMobileElementValue (string &val)

static bool	IsIllegalQualName (const string &val)

static void	ParseInferenceString (string val, string &category, string &type_str, bool &is_same_species, string &database, string &accession, string &program, string &version, string &acc_list)

static string	CleanupAndRepairInference (const string &orig_inference)

static bool	IsLegalInferenceDatabase (const string &db)

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)

Private Types
typedef CGb_qual_Base	Tparent

Private Member Functions
	CGb_qual (const CGb_qual &value)

CGb_qual &	operator= (const CGb_qual &value)

Static Private Member Functions
static bool	x_CleanupRptAndReplaceSeq (string &val)

Additional Inherited Members
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

@Gb_qual.hpp User-defined methods of the data storage class.

This file was originally generated by application DATATOOL using the following specifications: 'seqfeat.asn'.

New methods or data members can be added to it if needed. See also: Gb_qual_.hpp

Definition at line 60 of file Gb_qual.hpp.

Member Typedef Documentation

◆ TLegalPseudogeneSet

typedef CStaticArraySet<const char *, PNocase_CStr> CGb_qual::TLegalPseudogeneSet

Definition at line 87 of file Gb_qual.hpp.

◆ TLegalRecombinationClassSet

typedef CStaticArraySet<const char *, PNocase_CStr> CGb_qual::TLegalRecombinationClassSet

Definition at line 93 of file Gb_qual.hpp.

◆ TLegalRepeatTypeSet

typedef CStaticArraySet<const char *, PNocase_CStr> CGb_qual::TLegalRepeatTypeSet

Definition at line 81 of file Gb_qual.hpp.

◆ Tparent

typedef CGb_qual_Base CGb_qual::Tparent

private

Definition at line 62 of file Gb_qual.hpp.

Constructor & Destructor Documentation

◆ CGb_qual() [1/3]

CGb_qual::CGb_qual ( void )

inline

Definition at line 125 of file Gb_qual.hpp.

◆ CGb_qual() [2/3]

CGb_qual::CGb_qual	(	const TQual &	qual,
		const TVal &	val
	)

inline

Definition at line 130 of file Gb_qual.hpp.

References CGb_qual_Base::SetQual(), CGb_qual_Base::SetVal(), and val.

◆ ~CGb_qual()

CGb_qual::~CGb_qual ( void )

Definition at line 56 of file Gb_qual.cpp.

◆ CGb_qual() [3/3]

CGb_qual::CGb_qual ( const CGb_qual & value )

private

Member Function Documentation

◆ BuildExperiment()

string CGb_qual::BuildExperiment	(	const string &	category,
		const string &	experiment,
		const string &	doi
	)

static

Definition at line 114 of file Gb_qual.cpp.

References NStr::IsBlank().

Referenced by BOOST_AUTO_TEST_CASE().

◆ CleanupAndRepairInference()

string CGb_qual::CleanupAndRepairInference ( const string & orig_inference )

static

Definition at line 735 of file Gb_qual.cpp.

References ArraySize(), i, ITERATE, kInferenceDBChoices, kNumInferenceDBChoices, ReplaceIfNotFound(), NStr::ReplaceInPlace(), and valid_inf_prefixes.

Referenced by BOOST_AUTO_TEST_CASE(), and CNewCleanup_imp::x_CleanupAndRepairInference().

◆ CleanupReplace()

bool CGb_qual::CleanupReplace ( string & val )

static

Definition at line 150 of file Gb_qual.cpp.

References val, and x_CleanupRptAndReplaceSeq().

Referenced by CNewCleanup_imp::GBQualBC().

◆ CleanupRptUnitRange()

bool CGb_qual::CleanupRptUnitRange ( string & val )

static

Definition at line 158 of file Gb_qual.cpp.

References NStr::Find(), NStr::IsBlank(), NPOS, NStr::ReplaceInPlace(), and val.

Referenced by CNewCleanup_imp::GBQualBC(), and CNewCleanup_imp::x_CleanupRptUnit().

◆ CleanupRptUnitSeq()

bool CGb_qual::CleanupRptUnitSeq ( string & val )

static

Definition at line 144 of file Gb_qual.cpp.

References val, and x_CleanupRptAndReplaceSeq().

Referenced by CNewCleanup_imp::GBQualBC(), and CNewCleanup_imp::x_CleanupRptUnit().

◆ Compare()

int CGb_qual::Compare ( const CGb_qual & gbqual ) const

inline

Definition at line 138 of file Gb_qual.hpp.

References CGb_qual_Base::GetQual(), and CGb_qual_Base::GetVal().

◆ FixMobileElementValue()

bool CGb_qual::FixMobileElementValue ( string & val )

static

Definition at line 469 of file Gb_qual.cpp.

References NStr::Equal(), GetMobileElementValueElements(), NStr::IsBlank(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and CNewCleanup_imp::GBQualBC().

◆ FixPseudogeneValue()

bool CGb_qual::FixPseudogeneValue ( string & val )

static

Definition at line 314 of file Gb_qual.cpp.

References CStaticArraySearchBase< KeyValueGetter, KeyCompare >::end(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::find(), GetSetOfLegalPseudogenes(), and val.

Referenced by CNewCleanup_imp::GBQualBC().

◆ FixRecombinationClassValue()

bool CGb_qual::FixRecombinationClassValue ( string & val )

static

Definition at line 345 of file Gb_qual.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CTempString::size(), NStr::StartsWith(), NStr::ToLower(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and CNewCleanup_imp::GBQualSeqFeatBC().

◆ FixRptTypeValue()

bool CGb_qual::FixRptTypeValue ( string & val )

static

Definition at line 224 of file Gb_qual.cpp.

References CStaticArraySearchBase< KeyValueGetter, KeyCompare >::end(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::find(), GetRptTypeValue(), GetSetOfLegalRepeatTypes(), NStr::Join(), NON_CONST_ITERATE, origin, NStr::Split(), and val.

Referenced by CNewCleanup_imp::GBQualBC().

◆ GetMobileElementValueElements()

void CGb_qual::GetMobileElementValueElements	(	const string &	val,
		string &	element_type,
		string &	element_name
	)

static

Definition at line 433 of file Gb_qual.cpp.

References NStr::Find(), and val.

Referenced by FixMobileElementValue(), and IsLegalMobileElementValue().

◆ GetSetOfLegalPseudogenes()

const CGb_qual::TLegalPseudogeneSet & CGb_qual::GetSetOfLegalPseudogenes ( void )

static

Definition at line 285 of file Gb_qual.cpp.

References DEFINE_STATIC_ARRAY_MAP_WITH_COPY.

Referenced by CGenericPropsPanel::CreateControls(), FixPseudogeneValue(), and IsValidPseudogeneValue().

◆ GetSetOfLegalRecombinationClassValues()

const CGb_qual::TLegalRecombinationClassSet & CGb_qual::GetSetOfLegalRecombinationClassValues ( void )

static

Definition at line 329 of file Gb_qual.cpp.

References DEFINE_STATIC_ARRAY_MAP_WITH_COPY.

Referenced by BOOST_AUTO_TEST_CASE(), CSingleGbQualSubPanel::CreateControls(), and CImpFeatValidator::Validate().

◆ GetSetOfLegalRepeatTypes()

const CGb_qual::TLegalRepeatTypeSet & CGb_qual::GetSetOfLegalRepeatTypes ( void )

static

Definition at line 178 of file Gb_qual.cpp.

References DEFINE_STATIC_ARRAY_MAP_WITH_COPY.

Referenced by FixRptTypeValue(), and IsValidRptTypeValue().

◆ IsIllegalQualName()

bool CGb_qual::IsIllegalQualName ( const string & val )

static

Definition at line 508 of file Gb_qual.cpp.

References ArraySize(), NStr::EqualNocase(), i, s_IllegalQualNameStrings, and val.

Referenced by BOOST_AUTO_TEST_CASE().

◆ IsLegalInferenceDatabase()

bool CGb_qual::IsLegalInferenceDatabase ( const string & db )

static

Definition at line 784 of file Gb_qual.cpp.

References NStr::Equal(), i, kInferenceDBChoices, and kNumInferenceDBChoices.

Referenced by CValidError_feat::ValidateInferenceAccession().

◆ IsLegalMobileElementValue()

bool CGb_qual::IsLegalMobileElementValue ( const string & val )

static

Definition at line 454 of file Gb_qual.cpp.

References NStr::Equal(), GetMobileElementValueElements(), NStr::IsBlank(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and CSingleFeatValidator::x_ValidateGbquals().

◆ IsValidPseudogeneValue()

bool CGb_qual::IsValidPseudogeneValue ( const string & val )

static

Definition at line 303 of file Gb_qual.cpp.

References CStaticArraySearchBase< KeyValueGetter, KeyCompare >::end(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::find(), GetSetOfLegalPseudogenes(), and val.

Referenced by CSingleFeatValidator::x_ValidateGbQual().

◆ IsValidRptTypeValue()

bool CGb_qual::IsValidRptTypeValue ( const string & val )

static

Definition at line 258 of file Gb_qual.cpp.

References CStaticArraySearchBase< KeyValueGetter, KeyCompare >::end(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::find(), GetRptTypeValue(), GetSetOfLegalRepeatTypes(), ITERATE, NStr::Split(), and val.

Referenced by CFeatureItem::x_AddRptTypeQual(), and CSingleFeatValidator::x_ValidateGbquals().

◆ operator=()

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

private

◆ ParseExperiment()

void CGb_qual::ParseExperiment	(	const string &	orig,
		string &	category,
		string &	experiment,
		string &	doi
	)

static

Definition at line 83 of file Gb_qual.cpp.

References ArraySize(), NStr::EndsWith(), NStr::Find(), i, NPOS, orig, NStr::StartsWith(), NStr::TruncateSpacesInPlace(), and valid_inf_categories.

Referenced by BOOST_AUTO_TEST_CASE().

◆ ParseInferenceString()

void CGb_qual::ParseInferenceString	(	string	val,
		string &	category,
		string &	type_str,
		bool &	is_same_species,
		string &	database,
		string &	accession,
		string &	program,
		string &	version,
		string &	acc_list
	)

static

Definition at line 573 of file Gb_qual.cpp.

References database, NStr::eNocase, NStr::EqualNocase(), NStr::Find(), i, NStr::IsBlank(), ITERATE, kInferenceDBChoices, match(), NPOS, NStr::ReplaceInPlace(), s_FindInArray(), NStr::StartsWith(), NStr::TruncateSpacesInPlace(), val, and dtl::version.

◆ x_CleanupRptAndReplaceSeq()

bool CGb_qual::x_CleanupRptAndReplaceSeq ( string & val )

staticprivate

Definition at line 128 of file Gb_qual.cpp.

References NStr::Equal(), NStr::IsBlank(), orig, NStr::ReplaceInPlace(), NStr::ToLower(), and val.

Referenced by CleanupReplace(), and CleanupRptUnitSeq().

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

include/objects/seqfeat/Gb_qual.hpp
src/objects/seqfeat/Gb_qual.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TLegalPseudogeneSet

◆ TLegalRecombinationClassSet

◆ TLegalRepeatTypeSet

◆ Tparent

Constructor & Destructor Documentation

◆ CGb_qual() [1/3]

◆ CGb_qual() [2/3]

◆ ~CGb_qual()

◆ CGb_qual() [3/3]

Member Function Documentation

◆ BuildExperiment()

◆ CleanupAndRepairInference()

◆ CleanupReplace()

◆ CleanupRptUnitRange()

◆ CleanupRptUnitSeq()

◆ Compare()

◆ FixMobileElementValue()

◆ FixPseudogeneValue()

◆ FixRecombinationClassValue()

◆ FixRptTypeValue()

◆ GetMobileElementValueElements()

◆ GetSetOfLegalPseudogenes()

◆ GetSetOfLegalRecombinationClassValues()

◆ GetSetOfLegalRepeatTypes()

◆ IsIllegalQualName()

◆ IsLegalInferenceDatabase()

◆ IsLegalMobileElementValue()

◆ IsValidPseudogeneValue()

◆ IsValidRptTypeValue()

◆ operator=()

◆ ParseExperiment()

◆ ParseInferenceString()

◆ x_CleanupRptAndReplaceSeq()