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

Search Toolkit Book for CGC_AssemblyUnit_Base

#include <objects/genomecoll/GC_AssemblyUnit_.hpp>

Inheritance diagram for CGC_AssemblyUnit_Base:

Collaboration diagram for CGC_AssemblyUnit_Base:

Public Types
enum	EClass { eClass_haploid_unit = 1 , eClass_alt_loci = 2 , eClass_assembly_patch = 3 , eClass_other = 255 }
	'class' defines the semantics of how to interpret this item More...

enum class	E_memberIndex { e__allMandatory = 0 , e_id , e_class , e_desc , e_mols , e_other_sequences , e_stats , e_unplaced_stats , e_unplaced_unlocalized_stats }

typedef list< CRef< CDbtag > >	TId

typedef int	TClass

typedef CGC_AssemblyDesc	TDesc

typedef list< CRef< CGC_Replicon > >	TMols

typedef list< CRef< CGC_TaggedSequences > >	TOther_sequences

typedef CGC_SequenceStats	TStats

typedef list< CRef< CGC_Scaf_stats > >	TUnplaced_stats

typedef list< CRef< CGC_Scaf_stats > >	TUnplaced_unlocalized_stats

typedef Tparent::CMemberIndex< E_memberIndex, 9 >	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_AssemblyUnit_Base (void)

virtual	~CGC_AssemblyUnit_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetId (void) const
	The identifier of this assembly Contains: GenColl internal id, GenColl accession.version, AGP id, UCSC name, Ensembl name Types of DbTags used: db "GenColl", tag id <assembly-release-id> db "GenColl", tag str <assembly-accession.version> db "AGP", tag id <agp-sumbission-id> db "GenColl_Chain", tag id <assembly-chain-id> "Ensembl_name" and "UCSC_name" will not appear in the Unit level since these organizations do not define assembly-units. More...

bool	CanGetId (void) const
	Check if it is safe to call GetId method. More...

void	ResetId (void)
	Reset Id data member. More...

const TId &	GetId (void) const
	Get the Id member data. More...

TId &	SetId (void)
	Assign a value to Id data member. More...

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

bool	CanGetClass (void) const
	Check if it is safe to call GetClass method. More...

void	ResetClass (void)
	Reset Class data member. More...

TClass	GetClass (void) const
	Get the Class member data. More...

void	SetClass (TClass value)
	Assign a value to Class data member. More...

TClass &	SetClass (void)
	Assign a value to Class data member. More...

bool	IsSetDesc (void) const
	descriptors live in a shared data block Check if a value has been assigned to Desc data member. More...

bool	CanGetDesc (void) const
	Check if it is safe to call GetDesc method. More...

void	ResetDesc (void)
	Reset Desc data member. More...

const TDesc &	GetDesc (void) const
	Get the Desc member data. More...

void	SetDesc (TDesc &value)
	Assign a value to Desc data member. More...

TDesc &	SetDesc (void)
	Assign a value to Desc data member. More...

bool	IsSetMols (void) const
	collections of molecules for this assembly Check if a value has been assigned to Mols data member. More...

bool	CanGetMols (void) const
	Check if it is safe to call GetMols method. More...

void	ResetMols (void)
	Reset Mols data member. More...

const TMols &	GetMols (void) const
	Get the Mols member data. More...

TMols &	SetMols (void)
	Assign a value to Mols data member. More...

bool	IsSetOther_sequences (void) const
	On primary assembly-unit: here will be the unplaced sequences On alt-loci: list of sequences aligned/unaligned to primary unit Check if a value has been assigned to Other_sequences data member. More...

bool	CanGetOther_sequences (void) const
	Check if it is safe to call GetOther_sequences method. More...

void	ResetOther_sequences (void)
	Reset Other_sequences data member. More...

const TOther_sequences &	GetOther_sequences (void) const
	Get the Other_sequences member data. More...

TOther_sequences &	SetOther_sequences (void)
	Assign a value to Other_sequences data member. More...

bool	IsSetStats (void) const
	statistics "stats" field holds stats for all chromosomes combined: ordered/unordered scaffolds "unplaced-stats" holds stats for ChrUn which is omitted from "stats" Check if a value has been assigned to Stats data member. More...

bool	CanGetStats (void) const
	Check if it is safe to call GetStats method. More...

void	ResetStats (void)
	Reset Stats data member. More...

const TStats &	GetStats (void) const
	Get the Stats member data. More...

void	SetStats (TStats &value)
	Assign a value to Stats data member. More...

TStats &	SetStats (void)
	Assign a value to Stats data member. More...

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

bool	CanGetUnplaced_stats (void) const
	Check if it is safe to call GetUnplaced_stats method. More...

void	ResetUnplaced_stats (void)
	Reset Unplaced_stats data member. More...

const TUnplaced_stats &	GetUnplaced_stats (void) const
	Get the Unplaced_stats member data. More...

TUnplaced_stats &	SetUnplaced_stats (void)
	Assign a value to Unplaced_stats data member. More...

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

bool	CanGetUnplaced_unlocalized_stats (void) const
	Check if it is safe to call GetUnplaced_unlocalized_stats method. More...

void	ResetUnplaced_unlocalized_stats (void)
	Reset Unplaced_unlocalized_stats data member. More...

const TUnplaced_unlocalized_stats &	GetUnplaced_unlocalized_stats (void) const
	Get the Unplaced_unlocalized_stats member data. More...

TUnplaced_unlocalized_stats &	SetUnplaced_unlocalized_stats (void)
	Assign a value to Unplaced_unlocalized_stats 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()	EClass (void)
	Access to EClass'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_AssemblyUnit_Base (const CGC_AssemblyUnit_Base &)

CGC_AssemblyUnit_Base &	operator= (const CGC_AssemblyUnit_Base &)

Private Attributes
Uint4	m_set_State [1]

list< CRef< CDbtag > >	m_Id

int	m_Class

CRef< TDesc >	m_Desc

list< CRef< CGC_Replicon > >	m_Mols

list< CRef< CGC_TaggedSequences > >	m_Other_sequences

CRef< TStats >	m_Stats

list< CRef< CGC_Scaf_stats > >	m_Unplaced_stats

list< CRef< CGC_Scaf_stats > >	m_Unplaced_unlocalized_stats

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_AssemblyUnit_Base –.

Definition at line 81 of file GC_AssemblyUnit_.hpp.

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

include/objects/genomecoll/GC_AssemblyUnit_.hpp
src/objects/genomecoll/GC_AssemblyUnit_.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description