#include <objects/seqset/Bioseq_set.hpp>

Inheritance diagram for CBioseq_set:

Collaboration diagram for CBioseq_set:

Public Types
enum	ELabelType { eType , eContent , eBoth }

Public Types inherited from CBioseq_set_Base
enum	EClass { eClass_not_set = 0 , eClass_nuc_prot = 1 , eClass_segset = 2 , eClass_conset = 3 , eClass_parts = 4 , eClass_gibb = 5 , eClass_gi = 6 , eClass_genbank = 7 , eClass_pir = 8 , eClass_pub_set = 9 , eClass_equiv = 10 , eClass_swissprot = 11 , eClass_pdb_entry = 12 , eClass_mut_set = 13 , eClass_pop_set = 14 , eClass_phy_set = 15 , eClass_eco_set = 16 , eClass_gen_prod_set = 17 , eClass_wgs_set = 18 , eClass_named_annot = 19 , eClass_named_annot_prod = 20 , eClass_read_set = 21 , eClass_paired_end_reads = 22 , eClass_small_genome_set = 23 , eClass_other = 255 }

enum class	E_memberIndex { e__allMandatory = 0 , e_id , e_coll , e_level , e_class , e_release , e_date , e_descr , e_seq_set , e_annot }

typedef CObject_id	TId

typedef CDbtag	TColl

typedef int	TLevel

typedef EClass	TClass

typedef string	TRelease

typedef CDate	TDate

typedef CSeq_descr	TDescr

typedef list< CRef< CSeq_entry > >	TSeq_set

typedef list< CRef< CSeq_annot > >	TAnnot

typedef Tparent::CMemberIndex< E_memberIndex, 10 >	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
	CBioseq_set (void)

	~CBioseq_set (void)

CSeq_entry *	GetParentEntry (void) const

CConstRef< CBioseq_set >	GetParentSet (void) const

void	GetLabel (string *label, ELabelType type) const

const CBioseq &	GetNucFromNucProtSet (void) const

const CBioseq &	GetGenomicFromGenProdSet (void) const

const CBioseq &	GetMasterFromSegSet (void) const

bool	NeedsDocsumTitle () const

Public Member Functions inherited from CBioseq_set_Base
	CBioseq_set_Base (void)

virtual	~CBioseq_set_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetId (void) const
	Check if a value has been assigned to Id data member. 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...

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

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

bool	IsSetColl (void) const
	to identify a collection Check if a value has been assigned to Coll data member. More...

bool	CanGetColl (void) const
	Check if it is safe to call GetColl method. More...

void	ResetColl (void)
	Reset Coll data member. More...

const TColl &	GetColl (void) const
	Get the Coll member data. More...

void	SetColl (TColl &value)
	Assign a value to Coll data member. More...

TColl &	SetColl (void)
	Assign a value to Coll data member. More...

bool	IsSetLevel (void) const
	nesting level Check if a value has been assigned to Level data member. More...

bool	CanGetLevel (void) const
	Check if it is safe to call GetLevel method. More...

void	ResetLevel (void)
	Reset Level data member. More...

TLevel	GetLevel (void) const
	Get the Level member data. More...

void	SetLevel (TLevel value)
	Assign a value to Level data member. More...

TLevel &	SetLevel (void)
	Assign a value to Level 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...

void	SetDefaultClass (void)
	Assign default value to 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	IsSetRelease (void) const
	Check if a value has been assigned to Release data member. More...

bool	CanGetRelease (void) const
	Check if it is safe to call GetRelease method. More...

void	ResetRelease (void)
	Reset Release data member. More...

const TRelease &	GetRelease (void) const
	Get the Release member data. More...

void	SetRelease (const TRelease &value)
	Assign a value to Release data member. More...

void	SetRelease (TRelease &&value)

TRelease &	SetRelease (void)
	Assign a value to Release data member. More...

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

bool	CanGetDate (void) const
	Check if it is safe to call GetDate method. More...

void	ResetDate (void)
	Reset Date data member. More...

const TDate &	GetDate (void) const
	Get the Date member data. More...

void	SetDate (TDate &value)
	Assign a value to Date data member. More...

TDate &	SetDate (void)
	Assign a value to Date data member. More...

bool	IsSetDescr (void) const
	Check if a value has been assigned to Descr data member. 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	IsSetSeq_set (void) const
	Check if a value has been assigned to Seq_set data member. More...

bool	CanGetSeq_set (void) const
	Check if it is safe to call GetSeq_set method. More...

void	ResetSeq_set (void)
	Reset Seq_set data member. More...

const TSeq_set &	GetSeq_set (void) const
	Get the Seq_set member data. More...

TSeq_set &	SetSeq_set (void)
	Assign a value to Seq_set data member. More...

bool	IsSetAnnot (void) const
	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...

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 bool	NeedsDocsumTitle (EClass set_class)

Static Public Member Functions inherited from CBioseq_set_Base
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 CBioseq_set_Base	Tparent

Private Member Functions
	CBioseq_set (const CBioseq_set &)

CBioseq_set &	operator= (const CBioseq_set &)

void	SetParentEntry (CSeq_entry *entry)

Private Attributes
CSeq_entry *	m_ParentEntry

Friends
class	CSeq_entry

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...