#include <objects/genomecoll/GC_Sequence.hpp>

Inheritance diagram for CGC_Sequence:

Collaboration diagram for CGC_Sequence:

Public Types
enum	EChildrenSubset { eScaffold , eComponent , eAll }

typedef list< CConstRef< CGC_Sequence > >	TSequenceList

Public Types inherited from CGC_Sequence_Base
enum	EPatch_type { ePatch_type_novel = 0 , ePatch_type_fix = 1 , ePatch_type_other = 255 }

enum class	E_memberIndex { e__allMandatory = 0 , e_seq_id , e_seq_id_synonyms , e_descr , e_annot , e_sequences , e_structure , e_stats , e_patch_type , e_roles }

typedef CSeq_id	TSeq_id

typedef list< CRef< CGC_TypedSeqId > >	TSeq_id_synonyms

typedef CSeq_descr	TDescr

typedef list< CRef< CSeq_annot > >	TAnnot

typedef list< CRef< CGC_TaggedSequences > >	TSequences

typedef CDelta_ext	TStructure

typedef CGC_SequenceStats	TStats

typedef int	TPatch_type

typedef list< int >	TRoles

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
	CGC_Sequence (void)

	~CGC_Sequence (void)

CConstRef< CGC_AssemblyUnit >	GetAssemblyUnit () const
	Access the assembly unit the sequence belongs to. More...

CConstRef< CGC_Assembly >	GetFullAssembly () const
	Access the most specific full assembly the sequence belongs to This is needed because assemblies are packaged as sets of assemblies; knowing the unit is not always enough. More...

CConstRef< CGC_Replicon >	GetReplicon () const
	Access the replicon the sequence belongs to. More...

CConstRef< CGC_Sequence >	GetParent () const
	Access the parent sequence of this sequence. More...

CConstRef< CGC_Sequence >	GetTopLevelParent () const
	Access the top-most parent sequence of this sequence. More...

CGC_TaggedSequences::TState	GetParentRelation () const
	Access the relationship to the parent. More...

CConstRef< CSeq_id >	GetSynonymSeq_id (CGC_TypedSeqId::E_Choice type, CGC_SeqIdAlias::E_AliasTypes) const

CConstRef< CSeq_id >	GetSubmitterName () const

bool	HasRole (int Role) const

void	GetChildren (TSequenceList &children, EChildrenSubset subset=eAll, CGC_TaggedSequences::TState state=0, int level=0) const
	Get sub-sequences. More...

string	GetChrName () const
	Get name of chromosome that this sequence belongs to, if any. More...

string	GetUnitDisplayName () const
	Get full display name of assmebly unit. More...

bool	IsOrganelle () const
	Is this aN organelle sequence? More...

bool	CanGetLength () const
	Is the length statistic available? More...

TSeqPos	GetLength () const
	return the length of this sequence. More...

Public Member Functions inherited from CGC_Sequence_Base
	CGC_Sequence_Base (void)

virtual	~CGC_Sequence_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetSeq_id (void) const
	identifiers are: Local / gpipe-satellite / genbank / refseq local is merely local name (or maybe with WGS accession??) others are accession/ver/gi More...

bool	CanGetSeq_id (void) const
	Check if it is safe to call GetSeq_id method. More...

void	ResetSeq_id (void)
	Reset Seq_id data member. More...

const TSeq_id &	GetSeq_id (void) const
	Get the Seq_id member data. More...

void	SetSeq_id (TSeq_id &value)
	Assign a value to Seq_id data member. More...

TSeq_id &	SetSeq_id (void)
	Assign a value to Seq_id data member. More...

bool	IsSetSeq_id_synonyms (void) const
	Other known identifiers: Local / gpipe-satellite / genbank / refseq Check if a value has been assigned to Seq_id_synonyms data member. More...

bool	CanGetSeq_id_synonyms (void) const
	Check if it is safe to call GetSeq_id_synonyms method. More...

void	ResetSeq_id_synonyms (void)
	Reset Seq_id_synonyms data member. More...

const TSeq_id_synonyms &	GetSeq_id_synonyms (void) const
	Get the Seq_id_synonyms member data. More...

TSeq_id_synonyms &	SetSeq_id_synonyms (void)
	Assign a value to Seq_id_synonyms 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	IsSetAnnot (void) const
	Feature annotation; Contains Pseudo Autosomal regions on chromosomes and scaffolds in the following format: Id = <ID of PAR (ex:"PAR#1")> Desc (set of Annot-descr) Name: "pseudo autosomal region" Region (seq-loc): int (seq-interval) Id: <GI of chromosome> From: <start-position of region> To : <end-position of region> Data: locs (set of seq-loc): List of int (seq-interval): Id: GI of scaffold From/to: position on scaffold that belongs to this PAR region. 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	IsSetSequences (void) const
	placed: populated both on chromosome and scaffold levels unlocalized: populated on chromosome level Check if a value has been assigned to Sequences data member. More...

bool	CanGetSequences (void) const
	Check if it is safe to call GetSequences method. More...

void	ResetSequences (void)
	Reset Sequences data member. More...

const TSequences &	GetSequences (void) const
	Get the Sequences member data. More...

TSequences &	SetSequences (void)
	Assign a value to Sequences data member. More...

bool	IsSetStructure (void) const
	locations of ordered scaffolds/components Check if a value has been assigned to Structure data member. More...

bool	CanGetStructure (void) const
	Check if it is safe to call GetStructure method. More...

void	ResetStructure (void)
	Reset Structure data member. More...

const TStructure &	GetStructure (void) const
	Get the Structure member data. More...

void	SetStructure (TStructure &value)
	Assign a value to Structure data member. More...

TStructure &	SetStructure (void)
	Assign a value to Structure data member. More...

bool	IsSetStats (void) const
	statistics 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	IsSetPatch_type (void) const
	Check if a value has been assigned to Patch_type data member. More...

bool	CanGetPatch_type (void) const
	Check if it is safe to call GetPatch_type method. More...

void	ResetPatch_type (void)
	Reset Patch_type data member. More...

TPatch_type	GetPatch_type (void) const
	Get the Patch_type member data. More...

void	SetPatch_type (TPatch_type value)
	Assign a value to Patch_type data member. More...

TPatch_type &	SetPatch_type (void)
	Assign a value to Patch_type data member. More...

bool	IsSetRoles (void) const
	sequence-role: what role(s) does this sequence have in the assembly Check if a value has been assigned to Roles data member. More...

bool	CanGetRoles (void) const
	Check if it is safe to call GetRoles method. More...

void	ResetRoles (void)
	Reset Roles data member. More...

const TRoles &	GetRoles (void) const
	Get the Roles member data. More...

TRoles &	SetRoles (void)
	Assign a value to Roles 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

Protected Member Functions
TSeqPos	x_GetLength () const

void	x_GetChildren (TSequenceList &children, EChildrenSubset subset, CGC_TaggedSequences::TState state, int level) const

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CGC_Assembly *	m_Assembly

CGC_AssemblyUnit *	m_AssemblyUnit

CGC_Replicon *	m_Replicon

CGC_Sequence *	m_ParentSequence

CGC_TaggedSequences::TState	m_ParentRel

TSeqPos	m_SeqLength

bool	m_SeqLengthRetrieved

Private Types
typedef CGC_Sequence_Base	Tparent

Private Member Functions
	CGC_Sequence (const CGC_Sequence &value)

CGC_Sequence &	operator= (const CGC_Sequence &value)

Friends
class	CGC_Assembly

class	CGC_Replicon

Additional Inherited Members
Static Public Member Functions inherited from CGC_Sequence_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EPatch_type (void)
	Access to EPatch_type'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)

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...

Detailed Description

Definition at line 62 of file GC_Sequence.hpp.

Member Typedef Documentation

◆ Tparent

typedef CGC_Sequence_Base CGC_Sequence::Tparent

private

Definition at line 64 of file GC_Sequence.hpp.

◆ TSequenceList

typedef list< CConstRef<CGC_Sequence> > CGC_Sequence::TSequenceList

Definition at line 98 of file GC_Sequence.hpp.

Member Enumeration Documentation

◆ EChildrenSubset

enum CGC_Sequence::EChildrenSubset

Enumerator
eScaffold
eComponent
eAll

Definition at line 99 of file GC_Sequence.hpp.

Constructor & Destructor Documentation

◆ CGC_Sequence() [1/2]

CGC_Sequence::CGC_Sequence ( void )

Definition at line 56 of file GC_Sequence.cpp.

◆ ~CGC_Sequence()

CGC_Sequence::~CGC_Sequence ( void )

Definition at line 69 of file GC_Sequence.cpp.

◆ CGC_Sequence() [2/2]

CGC_Sequence::CGC_Sequence ( const CGC_Sequence & value )

private

Member Function Documentation

◆ CanGetLength()

bool CGC_Sequence::CanGetLength ( void ) const

Is the length statistic available?

Definition at line 283 of file GC_Sequence.cpp.

References x_GetLength().

Referenced by CGC_Assembly_Parser::x_AddBioseq(), and CSeq_loc_Mapper::x_AddVirtualBioseq().

◆ GetAssemblyUnit()

CConstRef< CGC_AssemblyUnit > CGC_Sequence::GetAssemblyUnit ( ) const

Access the assembly unit the sequence belongs to.

Definition at line 74 of file GC_Sequence.cpp.

References m_AssemblyUnit.

Referenced by CTableDataGCAssembly::GetStringValue(), and GetUnitDisplayName().

◆ GetChildren()

void CGC_Sequence::GetChildren	(	TSequenceList &	children,
		EChildrenSubset	subset = `eAll`,
		CGC_TaggedSequences::TState	state = `0`,
		int	level = `0`
	)		const

Get sub-sequences.

Parameters

subset	subset of children to get; default is all children
stats	get only children with this state; default is all children
lebel	get children up to this level; default is all levels

Definition at line 204 of file GC_Sequence.cpp.

References x_GetChildren().

◆ GetChrName()

string CGC_Sequence::GetChrName ( ) const

Get name of chromosome that this sequence belongs to, if any.

Definition at line 261 of file GC_Sequence.cpp.

References GetReplicon(), and GetTopLevelParent().

Referenced by IsOrganelle().

◆ GetFullAssembly()

CConstRef< CGC_Assembly > CGC_Sequence::GetFullAssembly ( ) const

Access the most specific full assembly the sequence belongs to This is needed because assemblies are packaged as sets of assemblies; knowing the unit is not always enough.

Definition at line 79 of file GC_Sequence.cpp.

References m_Assembly.

◆ GetLength()

TSeqPos CGC_Sequence::GetLength ( void ) const

return the length of this sequence.

if not available throws CUnassignedMember exception.

Definition at line 288 of file GC_Sequence.cpp.

References eGet, NCBI_THROW, result, and x_GetLength().

Referenced by CGC_Assembly_Parser::x_AddBioseq(), and CSeq_loc_Mapper::x_AddVirtualBioseq().

◆ GetParent()

CConstRef< CGC_Sequence > CGC_Sequence::GetParent ( void ) const

Access the parent sequence of this sequence.

Definition at line 89 of file GC_Sequence.cpp.

References m_ParentSequence.

Referenced by CTableDataGCAssembly::GetObjectValue(), CTableDataGCAssembly::GetStringValue(), CGencollIdMapper::x_CanSeqMeetSpec(), and CGencollIdMapper::x_FillGpipeTopRole().

◆ GetParentRelation()

CGC_TaggedSequences::TState CGC_Sequence::GetParentRelation ( ) const

Access the relationship to the parent.

Definition at line 95 of file GC_Sequence.cpp.

References m_ParentRel.

Referenced by CTableDataGCAssembly::GetStringValue(), and CGencollIdMapper::x_FillGpipeTopRole().

◆ GetReplicon()

CConstRef< CGC_Replicon > CGC_Sequence::GetReplicon ( ) const

Access the replicon the sequence belongs to.

Definition at line 84 of file GC_Sequence.cpp.

References m_Replicon.

Referenced by CGC_Assembly::CreateIndex(), GetChrName(), and CTableDataGCAssembly::GetStringValue().

◆ GetSubmitterName()

CConstRef< CSeq_id > CGC_Sequence::GetSubmitterName ( ) const

Definition at line 169 of file GC_Sequence.cpp.

References NStr::EqualNocase(), CGC_Sequence_Base::GetSeq_id_synonyms(), CGC_Sequence_Base::IsSetSeq_id_synonyms(), and ITERATE.

Referenced by CGencollIdMapper::x_Init().

◆ GetSynonymSeq_id()

CConstRef< CSeq_id > CGC_Sequence::GetSynonymSeq_id	(	CGC_TypedSeqId::E_Choice	type,
		CGC_SeqIdAlias::E_AliasTypes	alias_type
	)		const

Definition at line 109 of file GC_Sequence.cpp.

References CGC_TypedSeqId_Base::e_External, CGC_TypedSeqId_Base::e_Genbank, CGC_SeqIdAlias::e_Gi, CGC_SeqIdAlias::e_Gpipe, CGC_SeqIdAlias::e_None, CGC_TypedSeqId_Base::e_Private, CGC_SeqIdAlias::e_Public, CGC_TypedSeqId_Base::e_Refseq, eUnknown, CGC_Sequence_Base::GetSeq_id_synonyms(), CConstRef< C, Locker >::IsNull(), CGC_Sequence_Base::IsSetSeq_id_synonyms(), ITERATE, and NCBI_THROW.

Referenced by CTableDataGCAssembly::GetObjectValue(), CTableDataGCAssembly::GetStringValue(), and CGencollIdMapper::x_FillGpipeTopRole().

◆ GetTopLevelParent()

CConstRef< CGC_Sequence > CGC_Sequence::GetTopLevelParent ( ) const

Access the top-most parent sequence of this sequence.

Definition at line 101 of file GC_Sequence.cpp.

Referenced by GetChrName().

◆ GetUnitDisplayName()

string CGC_Sequence::GetUnitDisplayName ( ) const

Get full display name of assmebly unit.

Definition at line 272 of file GC_Sequence.cpp.

References GetAssemblyUnit().

◆ HasRole()

bool CGC_Sequence::HasRole ( int Role ) const

Definition at line 191 of file GC_Sequence.cpp.

References CGC_Sequence_Base::CanGetRoles(), CGC_Sequence_Base::GetRoles(), and ITERATE.

Referenced by CGencollIdMapper::x_CanSeqMeetSpec(), CGencollIdMapper::x_FillGpipeTopRole(), x_GetLength(), CGencollIdMapper::x_MakeSpecForSeq(), CGencollIdMapper::x_RecursiveSeqFix(), and CGencollIdMapper::x_StripPseudoSeq().

◆ IsOrganelle()

bool CGC_Sequence::IsOrganelle ( ) const

Is this aN organelle sequence?

Definition at line 278 of file GC_Sequence.cpp.

References GetChrName().

◆ operator=()

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

private

◆ x_GetChildren()

void CGC_Sequence::x_GetChildren	(	TSequenceList &	children,
		EChildrenSubset	subset,
		CGC_TaggedSequences::TState	state,
		int	level
	)		const

protected

Definition at line 212 of file GC_Sequence.cpp.

References eAll, eComponent, eGC_SequenceRole_component, eGC_SequenceRole_scaffold, eScaffold, eUnknown, CGC_Sequence_Base::GetSequences(), max(), NCBI_THROW, and tag.

Referenced by GetChildren().

◆ x_GetLength()

TSeqPos CGC_Sequence::x_GetLength ( ) const

protected

Definition at line 297 of file GC_Sequence.cpp.

References CGC_SequenceStats_Base::CanGetAll_scaf(), CGC_Sequence_Base::CanGetStats(), eGC_SequenceRole_chromosome, CGC_Scaf_stats_Base::eStats_category_total_length, CGC_Sequence_Base::GetStats(), HasRole(), ITERATE, m_SeqLength, and m_SeqLengthRetrieved.

Referenced by CanGetLength(), and GetLength().

Friends And Related Function Documentation

◆ CGC_Assembly

friend class CGC_Assembly

friend

Definition at line 65 of file GC_Sequence.hpp.

◆ CGC_Replicon

friend class CGC_Replicon

friend

Definition at line 66 of file GC_Sequence.hpp.

Member Data Documentation

◆ m_Assembly

CGC_Assembly* CGC_Sequence::m_Assembly

protected

Definition at line 130 of file GC_Sequence.hpp.

Referenced by GetFullAssembly(), and CGC_Assembly::x_Index().

◆ m_AssemblyUnit

CGC_AssemblyUnit* CGC_Sequence::m_AssemblyUnit

protected

Definition at line 131 of file GC_Sequence.hpp.

Referenced by GetAssemblyUnit(), and CGC_Assembly::x_Index().

◆ m_ParentRel

CGC_TaggedSequences::TState CGC_Sequence::m_ParentRel

protected

Definition at line 134 of file GC_Sequence.hpp.

Referenced by GetParentRelation(), and CGC_Assembly::x_Index().

◆ m_ParentSequence

CGC_Sequence* CGC_Sequence::m_ParentSequence

protected

Definition at line 133 of file GC_Sequence.hpp.

Referenced by GetParent(), and CGC_Assembly::x_Index().

◆ m_Replicon

CGC_Replicon* CGC_Sequence::m_Replicon

protected

Definition at line 132 of file GC_Sequence.hpp.

Referenced by GetReplicon(), and CGC_Assembly::x_Index().

◆ m_SeqLength

TSeqPos CGC_Sequence::m_SeqLength

mutableprotected

Definition at line 137 of file GC_Sequence.hpp.

Referenced by x_GetLength().

◆ m_SeqLengthRetrieved

bool CGC_Sequence::m_SeqLengthRetrieved

mutableprotected

Definition at line 138 of file GC_Sequence.hpp.

Referenced by x_GetLength().

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

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

◆ TSequenceList

Member Enumeration Documentation

◆ EChildrenSubset

Constructor & Destructor Documentation

◆ CGC_Sequence() [1/2]

◆ ~CGC_Sequence()

◆ CGC_Sequence() [2/2]

Member Function Documentation

◆ CanGetLength()

◆ GetAssemblyUnit()

◆ GetChildren()

◆ GetChrName()

◆ GetFullAssembly()

◆ GetLength()

◆ GetParent()

◆ GetParentRelation()

◆ GetReplicon()

◆ GetSubmitterName()

◆ GetSynonymSeq_id()

◆ GetTopLevelParent()

◆ GetUnitDisplayName()

◆ HasRole()

◆ IsOrganelle()

◆ operator=()

◆ x_GetChildren()

◆ x_GetLength()

Friends And Related Function Documentation

◆ CGC_Assembly

◆ CGC_Replicon

Member Data Documentation

◆ m_Assembly

◆ m_AssemblyUnit

◆ m_ParentRel

◆ m_ParentSequence

◆ m_Replicon

◆ m_SeqLength

◆ m_SeqLengthRetrieved