CGC_AssemblyDesc_Base Class Reference

Represents ASN.1 type GC-AssemblyDesc defined in file genome_collection.asn

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CGC_AssemblyDesc_Base –. More...

#include <objects/genomecoll/GC_AssemblyDesc_.hpp>

Inheritance diagram for CGC_AssemblyDesc_Base:

Collaboration diagram for CGC_AssemblyDesc_Base:

Public Types
enum	ERelease_type { eRelease_type_genbank = 1 , eRelease_type_refseq = 2 }
	release type: RefSeq / GenBank. More...
enum	ERelease_status {   eRelease_status_new = 0 , eRelease_status_gpipe = 5 , eRelease_status_public = 10 , eRelease_status_suppressed = 15 ,   eRelease_status_hup = 100 , eRelease_status_withdrawn = 105 }
	release status (numeric values have gaps for possible additional states More...
enum	ERelease_level { eRelease_level_major = 0 , eRelease_level_patch = 1 , eRelease_level_minor = 2 , eRelease_level_other = 255 }
	release level: Most of releases are major More...
enum class	E_memberIndex {   e__allMandatory = 0 , e_projects , e_name , e_submitter_name ,   e_display_name , e_long_name , e_filesafe_name , e_wgs_acc_prefix ,   e_wgs_acc_number , e_release_type , e_release_status , e_annot ,   e_synonyms , e_submitter_date , e_descr , e_partial ,   e_coverage , e_release_level , e_submitter_organization }
typedef list< CRef< CGC_Project > >	TProjects
typedef string	TName
typedef string	TSubmitter_name
typedef string	TDisplay_name
typedef CStringUTF8	TLong_name
typedef string	TFilesafe_name
typedef string	TWgs_acc_prefix
typedef int	TWgs_acc_number
typedef int	TRelease_type
typedef int	TRelease_status
typedef list< CRef< CSeq_annot > >	TAnnot
typedef list< CRef< CGC_DbTagAlias > >	TSynonyms
typedef CDate	TSubmitter_date
typedef CSeq_descr	TDescr
typedef bool	TPartial
typedef double	TCoverage
typedef int	TRelease_level
typedef CStringUTF8	TSubmitter_organization
typedef Tparent::CMemberIndex< E_memberIndex, 19 >	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
	CGC_AssemblyDesc_Base (void)
virtual	~CGC_AssemblyDesc_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetProjects (void) const
	project ID for this genome this is the ID for this asssembly and may reflect the submitter/source Check if a value has been assigned to Projects data member. More...
bool	CanGetProjects (void) const
	Check if it is safe to call GetProjects method. More...
void	ResetProjects (void)
	Reset Projects data member. More...
const TProjects &	GetProjects (void) const
	Get the Projects member data. More...
TProjects &	SetProjects (void)
	Assign a value to Projects data member. More...
bool	IsSetName (void) const
	Names of the assembly 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	IsSetSubmitter_name (void) const
	Check if a value has been assigned to Submitter_name data member. More...
bool	CanGetSubmitter_name (void) const
	Check if it is safe to call GetSubmitter_name method. More...
void	ResetSubmitter_name (void)
	Reset Submitter_name data member. More...
const TSubmitter_name &	GetSubmitter_name (void) const
	Get the Submitter_name member data. More...
void	SetSubmitter_name (const TSubmitter_name &value)
	Assign a value to Submitter_name data member. More...
void	SetSubmitter_name (TSubmitter_name &&value)
TSubmitter_name &	SetSubmitter_name (void)
	Assign a value to Submitter_name data member. More...
bool	IsSetDisplay_name (void) const
	Check if a value has been assigned to Display_name data member. More...
bool	CanGetDisplay_name (void) const
	Check if it is safe to call GetDisplay_name method. More...
void	ResetDisplay_name (void)
	Reset Display_name data member. More...
const TDisplay_name &	GetDisplay_name (void) const
	Get the Display_name member data. More...
void	SetDisplay_name (const TDisplay_name &value)
	Assign a value to Display_name data member. More...
void	SetDisplay_name (TDisplay_name &&value)
TDisplay_name &	SetDisplay_name (void)
	Assign a value to Display_name data member. More...
bool	IsSetLong_name (void) const
	Check if a value has been assigned to Long_name data member. More...
bool	CanGetLong_name (void) const
	Check if it is safe to call GetLong_name method. More...
void	ResetLong_name (void)
	Reset Long_name data member. More...
const TLong_name &	GetLong_name (void) const
	Get the Long_name member data. More...
void	SetLong_name (const TLong_name &value)
	Assign a value to Long_name data member. More...
void	SetLong_name (TLong_name &&value)
TLong_name &	SetLong_name (void)
	Assign a value to Long_name data member. More...
bool	IsSetFilesafe_name (void) const
	Check if a value has been assigned to Filesafe_name data member. More...
bool	CanGetFilesafe_name (void) const
	Check if it is safe to call GetFilesafe_name method. More...
void	ResetFilesafe_name (void)
	Reset Filesafe_name data member. More...
const TFilesafe_name &	GetFilesafe_name (void) const
	Get the Filesafe_name member data. More...
void	SetFilesafe_name (const TFilesafe_name &value)
	Assign a value to Filesafe_name data member. More...
void	SetFilesafe_name (TFilesafe_name &&value)
TFilesafe_name &	SetFilesafe_name (void)
	Assign a value to Filesafe_name data member. More...
bool	IsSetWgs_acc_prefix (void) const
	Check if a value has been assigned to Wgs_acc_prefix data member. More...
bool	CanGetWgs_acc_prefix (void) const
	Check if it is safe to call GetWgs_acc_prefix method. More...
void	ResetWgs_acc_prefix (void)
	Reset Wgs_acc_prefix data member. More...
const TWgs_acc_prefix &	GetWgs_acc_prefix (void) const
	Get the Wgs_acc_prefix member data. More...
void	SetWgs_acc_prefix (const TWgs_acc_prefix &value)
	Assign a value to Wgs_acc_prefix data member. More...
void	SetWgs_acc_prefix (TWgs_acc_prefix &&value)
TWgs_acc_prefix &	SetWgs_acc_prefix (void)
	Assign a value to Wgs_acc_prefix data member. More...
bool	IsSetWgs_acc_number (void) const
	Check if a value has been assigned to Wgs_acc_number data member. More...
bool	CanGetWgs_acc_number (void) const
	Check if it is safe to call GetWgs_acc_number method. More...
void	ResetWgs_acc_number (void)
	Reset Wgs_acc_number data member. More...
TWgs_acc_number	GetWgs_acc_number (void) const
	Get the Wgs_acc_number member data. More...
void	SetWgs_acc_number (TWgs_acc_number value)
	Assign a value to Wgs_acc_number data member. More...
TWgs_acc_number &	SetWgs_acc_number (void)
	Assign a value to Wgs_acc_number data member. More...
bool	IsSetRelease_type (void) const
	Check if a value has been assigned to Release_type data member. More...
bool	CanGetRelease_type (void) const
	Check if it is safe to call GetRelease_type method. More...
void	ResetRelease_type (void)
	Reset Release_type data member. More...
TRelease_type	GetRelease_type (void) const
	Get the Release_type member data. More...
void	SetRelease_type (TRelease_type value)
	Assign a value to Release_type data member. More...
TRelease_type &	SetRelease_type (void)
	Assign a value to Release_type data member. More...
bool	IsSetRelease_status (void) const
	Check if a value has been assigned to Release_status data member. More...
bool	CanGetRelease_status (void) const
	Check if it is safe to call GetRelease_status method. More...
void	ResetRelease_status (void)
	Reset Release_status data member. More...
TRelease_status	GetRelease_status (void) const
	Get the Release_status member data. More...
void	SetRelease_status (TRelease_status value)
	Assign a value to Release_status data member. More...
TRelease_status &	SetRelease_status (void)
	Assign a value to Release_status data member. More...
bool	IsSetAnnot (void) const
	in alt-loci units - contain alignment of this sequence to the primary unit Check if a value has been assigned to Annot data member. More...
bool	CanGetAnnot (void) const
	Check if it is safe to call GetAnnot method. More...
void	ResetAnnot (void)
	Reset Annot data member. More...
const TAnnot &	GetAnnot (void) const
	Get the Annot member data. More...
TAnnot &	SetAnnot (void)
	Assign a value to Annot data member. More...
bool	IsSetSynonyms (void) const
	Synonyms: Other releases of same assembly Check if a value has been assigned to Synonyms data member. More...
bool	CanGetSynonyms (void) const
	Check if it is safe to call GetSynonyms method. More...
void	ResetSynonyms (void)
	Reset Synonyms data member. More...
const TSynonyms &	GetSynonyms (void) const
	Get the Synonyms member data. More...
TSynonyms &	SetSynonyms (void)
	Assign a value to Synonyms data member. More...
bool	IsSetSubmitter_date (void) const
	Submitter release date Check if a value has been assigned to Submitter_date data member. More...
bool	CanGetSubmitter_date (void) const
	Check if it is safe to call GetSubmitter_date method. More...
void	ResetSubmitter_date (void)
	Reset Submitter_date data member. More...
const TSubmitter_date &	GetSubmitter_date (void) const
	Get the Submitter_date member data. More...
void	SetSubmitter_date (TSubmitter_date &value)
	Assign a value to Submitter_date data member. More...
TSubmitter_date &	SetSubmitter_date (void)
	Assign a value to Submitter_date data member. More...
bool	IsSetDescr (void) const
	Various attributes assigned at this level: biosrc, comments, publications... More...
bool	CanGetDescr (void) const
	Check if it is safe to call GetDescr method. More...
void	ResetDescr (void)
	Reset Descr data member. More...
const TDescr &	GetDescr (void) const
	Get the Descr member data. More...
void	SetDescr (TDescr &value)
	Assign a value to Descr data member. More...
TDescr &	SetDescr (void)
	Assign a value to Descr data member. More...
bool	IsSetPartial (void) const
	flag: is this assembly partial? **NOTE: not set = not known!! Check if a value has been assigned to Partial data member. More...
bool	CanGetPartial (void) const
	Check if it is safe to call GetPartial method. More...
void	ResetPartial (void)
	Reset Partial data member. More...
TPartial	GetPartial (void) const
	Get the Partial member data. More...
void	SetPartial (TPartial value)
	Assign a value to Partial data member. More...
TPartial &	SetPartial (void)
	Assign a value to Partial data member. More...
bool	IsSetCoverage (void) const
	level of coverage for this assembly **NOTE: not set = not known!! Check if a value has been assigned to Coverage data member. More...
bool	CanGetCoverage (void) const
	Check if it is safe to call GetCoverage method. More...
void	ResetCoverage (void)
	Reset Coverage data member. More...
TCoverage	GetCoverage (void) const
	Get the Coverage member data. More...
void	SetCoverage (TCoverage value)
	Assign a value to Coverage data member. More...
TCoverage &	SetCoverage (void)
	Assign a value to Coverage data member. More...
bool	IsSetRelease_level (void) const
	Check if a value has been assigned to Release_level data member. More...
bool	CanGetRelease_level (void) const
	Check if it is safe to call GetRelease_level method. More...
void	ResetRelease_level (void)
	Reset Release_level data member. More...
void	SetDefaultRelease_level (void)
	Assign default value to Release_level data member. More...
TRelease_level	GetRelease_level (void) const
	Get the Release_level member data. More...
void	SetRelease_level (TRelease_level value)
	Assign a value to Release_level data member. More...
TRelease_level &	SetRelease_level (void)
	Assign a value to Release_level data member. More...
bool	IsSetSubmitter_organization (void) const
	organization which submitted this assembly. More...
bool	CanGetSubmitter_organization (void) const
	Check if it is safe to call GetSubmitter_organization method. More...
void	ResetSubmitter_organization (void)
	Reset Submitter_organization data member. More...
const TSubmitter_organization &	GetSubmitter_organization (void) const
	Get the Submitter_organization member data. More...
void	SetSubmitter_organization (const TSubmitter_organization &value)
	Assign a value to Submitter_organization data member. More...
void	SetSubmitter_organization (TSubmitter_organization &&value)
TSubmitter_organization &	SetSubmitter_organization (void)
	Assign a value to Submitter_organization 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 const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ERelease_type (void)
	Access to ERelease_type's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ERelease_status (void)
	Access to ERelease_status's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ERelease_level (void)
	Access to ERelease_level's attributes (values, names) as defined in spec. 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)

Private Types
typedef CSerialObject	Tparent

Private Member Functions
	CGC_AssemblyDesc_Base (const CGC_AssemblyDesc_Base &)
CGC_AssemblyDesc_Base &	operator= (const CGC_AssemblyDesc_Base &)

Private Attributes
Uint4	m_set_State [2]
list< CRef< CGC_Project > >	m_Projects
string	m_Name
string	m_Submitter_name
string	m_Display_name
CStringUTF8	m_Long_name
string	m_Filesafe_name
string	m_Wgs_acc_prefix
int	m_Wgs_acc_number
int	m_Release_type
int	m_Release_status
list< CRef< CSeq_annot > >	m_Annot
list< CRef< CGC_DbTagAlias > >	m_Synonyms
CRef< TSubmitter_date >	m_Submitter_date
CRef< TDescr >	m_Descr
bool	m_Partial
double	m_Coverage
int	m_Release_level
CStringUTF8	m_Submitter_organization

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

CGC_AssemblyDesc_Base –.

Definition at line 81 of file GC_AssemblyDesc_.hpp.

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

• include/objects/genomecoll/GC_AssemblyDesc_.hpp
• src/objects/genomecoll/GC_AssemblyDesc_.cpp