CBioseq_set Class Reference

Search Toolkit Book for CBioseq_set

#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...

Detailed Description

Definition at line 54 of file Bioseq_set.hpp.

Member Typedef Documentation

Tparent

typedef CBioseq_set_Base CBioseq_set::Tparent

private

Definition at line 56 of file Bioseq_set.hpp.

Member Enumeration Documentation

ELabelType

enum CBioseq_set::ELabelType

Enumerator
eType
eContent
eBoth

Definition at line 74 of file Bioseq_set.hpp.

Constructor & Destructor Documentation

CBioseq_set() [1/2]

CBioseq_set::CBioseq_set ( void  )

inline

Definition at line 110 of file Bioseq_set.hpp.

~CBioseq_set()

CBioseq_set::~CBioseq_set

(

void

)

Definition at line 61 of file Bioseq_set.cpp.

CBioseq_set() [2/2]

CBioseq_set::CBioseq_set ( const CBioseq_set &  )

private

Member Function Documentation

GetGenomicFromGenProdSet()

const CBioseq & CBioseq_set::GetGenomicFromGenProdSet

(

void

)

const

Definition at line 251 of file Bioseq_set.cpp.

References CBioseq_set_Base::eClass_gen_prod_set, CSeq_inst_Base::eMol_dna, ENUM_METHOD_NAME, eUnknown, CBioseq_set_Base::GetClass(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetMol(), CBioseq_set_Base::GetSeq_set(), CSeq_inst_Base::IsSetMol(), ITERATE, and NCBI_THROW.

Referenced by s_GetGenProdContent().

GetLabel()

void CBioseq_set::GetLabel	(	string *	label,
		ELabelType	type
	)		const

Definition at line 107 of file Bioseq_set.cpp.

References ConstBegin(), eContent, eType, CEnumeratedTypeValues::FindName(), CBioseq_set_Base::GetClass(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CBioseq_set_Base::GetSeq_set(), CSeq_id::GetSeqIdString(), CBioseq_set_Base::IsSetClass(), CBioseq_set_Base::IsSetSeq_set(), label, len, max(), s_has_accession(), s_has_gb(), s_is_na(), si, and NStr::SizetToString().

Referenced by CSeq_entry::GetLabel(), s_GetBioseq_setContent(), and CDescPlacementPanel::x_AddToStrings().

GetMasterFromSegSet()

const CBioseq & CBioseq_set::GetMasterFromSegSet

(

void

)

const

Definition at line 275 of file Bioseq_set.cpp.

References CBioseq_set_Base::eClass_segset, ENUM_METHOD_NAME, eUnknown, CBioseq_set_Base::GetClass(), CBioseq_set_Base::GetSeq_set(), ITERATE, and NCBI_THROW.

Referenced by GetNucFromNucProtSet(), s_GetIdLabel(), and s_GetSegsetContent().

GetNucFromNucProtSet()

const CBioseq & CBioseq_set::GetNucFromNucProtSet

(

void

)

const

Definition at line 227 of file Bioseq_set.cpp.

References CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_segset, ENUM_METHOD_NAME, eUnknown, CBioseq_set_Base::GetClass(), GetMasterFromSegSet(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CBioseq::IsNa(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), ITERATE, and NCBI_THROW.

Referenced by CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CRemoveSequencesDlg::CollectLabelsAll(), CRBSubpanel::CollectLabelsAll(), CWithdrawSequences::GetNames(), CSequesterSets::OnAccept(), CRemoveSequencesDlg::OnSelect(), CLengthSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), seqsubmit_split::SCompare< SLongestFirstCompare >::operator()(), s_GetIdLabel(), s_GetNucProtContent(), CLengthSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CRBSubpanel::SetSubsets(), CSegregateSetsBase::TakeFromSet(), and CSequenceEditingEventHandler::x_CacheSelectedLocations().

GetParentEntry()

CSeq_entry * CBioseq_set::GetParentEntry ( void  ) const

inline

Definition at line 122 of file Bioseq_set.hpp.

References m_ParentEntry.

Referenced by CAutogeneratedExtendedCleanup::ExtendedCleanupSeqEntry(), GetParentSet(), CValidError_bioseqset::ValidateSetTitle(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), and CSeqMasterIndex::x_Initialize().

GetParentSet()

CConstRef< CBioseq_set > CBioseq_set::GetParentSet

(

void

)

const

Definition at line 294 of file Bioseq_set.cpp.

References GetParentEntry(), CSeq_entry::GetParentEntry(), CSeq_entry_Base::GetSet(), and CSeq_entry_Base::IsSet().

Referenced by CCleanup::AddPartialToProteinTitle(), and CNewCleanup_imp::x_RemoveNestedGenBankSet().

NeedsDocsumTitle() [1/2]

bool CBioseq_set::NeedsDocsumTitle

(

)

const

Definition at line 343 of file Bioseq_set.cpp.

References CBioseq_set_Base::GetClass(), and CBioseq_set_Base::IsSetClass().

Referenced by AddOrgToDefline(), CheckDeflineMatches(), CountDefLineConflicts(), CEditObjectSet::GetEditCommand(), CMacroFunction_RefreshDefline::s_RefreshDeflineCommand(), UpdateAllDefinitionLine(), and CValidError_bioseqset::ValidateSetTitle().

NeedsDocsumTitle() [2/2]

bool CBioseq_set::NeedsDocsumTitle ( EClass  set_class )

static

Definition at line 330 of file Bioseq_set.cpp.

References CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_phy_set, and CBioseq_set_Base::eClass_pop_set.

operator=()

CBioseq_set& CBioseq_set::operator= ( const CBioseq_set &  )

private

SetParentEntry()

void CBioseq_set::SetParentEntry ( CSeq_entry *  entry )

inlineprivate

Definition at line 116 of file Bioseq_set.hpp.

References m_ParentEntry.

Referenced by CSeq_entry::Parentize(), and CSeq_entry::ParentizeOneLevel().

Friends And Related Function Documentation

CSeq_entry

friend class CSeq_entry

friend

Definition at line 101 of file Bioseq_set.hpp.

Member Data Documentation

m_ParentEntry

CSeq_entry* CBioseq_set::m_ParentEntry

private

Definition at line 99 of file Bioseq_set.hpp.

Referenced by GetParentEntry(), and SetParentEntry().

---

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

• include/objects/seqset/Bioseq_set.hpp
• src/objects/seqset/Bioseq_set.cpp