#include <objects/genomecoll/GC_Assembly.hpp>

Inheritance diagram for CGC_Assembly:

Collaboration diagram for CGC_Assembly:

Public Types
enum	ESubset { eChromosome , eScaffold , eComponent , eTopLevel , eSubmitterPseudoScaffold , eAll }

enum	EFindSeqOption { eEnforceSingle , eChooseAny , eChooseBest }

typedef list< CConstRef< CGC_Sequence > >	TSequenceList

typedef list< CConstRef< CGC_AssemblyUnit > >	TAssemblyUnits

typedef list< CConstRef< CGC_Assembly > >	TFullAssemblies

Public Types inherited from CGC_Assembly_Base
enum	E_Choice { e_not_set = 0 , e_Unit , e_Assembly_set }
	Choice variants. More...

enum	E_ChoiceStopper { e_MaxChoice = 3 }
	Maximum+1 value of the choice variant enumerator. More...

typedef CGC_AssemblyUnit	TUnit

typedef CGC_AssemblySet	TAssembly_set

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_Assembly (void)

	~CGC_Assembly (void)

int	GetReleaseId () const
	Retrieve the release id for this assembly. More...

string	GetAccession () const
	Retrieve the accession for this assembly. More...

string	GetBestIdentifier () const
	Either accession or submitter-provided id. More...

const CGC_AssemblyDesc &	GetDesc () const
	Retrieve the full set of assembly descriptors. More...

TTaxId	GetTaxId () const
	Retrieve the tax-id for this assembly. More...

string	GetName () const
	Retrieve the name of this assembly. More...

string	GetDisplayName () const
	Get full label for assmebly; if this is a unit, full assembly name followed by unit name. More...

string	GetFileSafeName () const
	Retrieve the file-safe version of assembly name, if available; othwreise default to standard name. More...

string	GetFileSafeDisplayName () const
	Get file-safe version of full label for assmebly. More...

bool	IsRefSeq () const
	Is this assembly a RefSeq assembly? More...

bool	IsGenBank () const
	Is this assembly a GenBank assembly? More...

bool	IsOrganelle () const
	Is this a non-nuclear assembly unit? More...

CGC_AssemblyUnit::TClass	GetUnitClass () const
	If this is an assembly unit, get unit class. More...

void	CreateHierarchy (CGC_Assembly *target_set=NULL)
	Generate the internal up-pointers. More...

void	CreateIndex ()
	Generate the Seq-id index. More...

void	GetMolecules (TSequenceList &molecules, ESubset subset) const
	Retrieve a subset of molecules. More...

void	GetMoleculesByUnit (vector< TSequenceList > &molecules, ESubset subset) const
	Retrieve a subset of molecules separately for each unit, in the same order in which the units are returned by GetAssemblyUnits() More...

TAssemblyUnits	GetAssemblyUnits () const
	Retrieve a list of all assembly units contained in this assembly. More...

TFullAssemblies	GetFullAssemblies () const
	Retrieve a list of all full assemblies contained in this assembly Note that, if the assembly is a full assembly, then it will be the only assembly returned; also, if the assembly is not an assembly set, then the base assembly will be returned. More...

void	Find (const CSeq_id_Handle &id, TSequenceList &sequences) const
	Find all references to a given sequence within an assembly. More...

CConstRef< CGC_Sequence >	Find (const CSeq_id_Handle &id, EFindSeqOption find_option=eEnforceSingle) const
	Find a single sequence corresponding to the supplied id. More...

void	GetRepliconTypeLocRole (const CSeq_id_Handle &id, string &type, string &location, set< int > &role) const
	Returns replicon type, location and role. More...

void	PreWrite () const
	PreWrite() / PostRead() handle events for indexing of local structures. More...

void	PostRead ()

CConstRef< CGC_Assembly >	GetTargetSet () const
	Access the top-level target set that this assemhly belongs to. More...

bool	IsTargetSetReference () const
	Is this assembly the reference assembly of the target set, or part of it? More...

Public Member Functions inherited from CGC_Assembly_Base
	CGC_Assembly_Base (void)

virtual	~CGC_Assembly_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

virtual void	Reset (void)
	Reset the whole object. More...

virtual void	ResetSelection (void)
	Reset the selection (set it to e_not_set). More...

E_Choice	Which (void) const
	Which variant is currently selected. More...

void	CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...

void	ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...

void	Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...

void	Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...

bool	IsUnit (void) const
	Check if variant Unit is selected. More...

const TUnit &	GetUnit (void) const
	Get the variant data. More...

TUnit &	SetUnit (void)
	Select the variant. More...

void	SetUnit (TUnit &value)
	Select the variant and set its data. More...

bool	IsAssembly_set (void) const
	Check if variant Assembly_set is selected. More...

const TAssembly_set &	GetAssembly_set (void) const
	Get the variant data. More...

TAssembly_set &	SetAssembly_set (void)
	Select the variant. More...

void	SetAssembly_set (TAssembly_set &value)
	Select the variant and set its data. 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

Private Types
typedef CGC_Assembly_Base	Tparent

typedef map< CSeq_id_Handle, TSequenceList >	TSequenceIndex

Private Member Functions
	CGC_Assembly (const CGC_Assembly &value)

CGC_Assembly &	operator= (const CGC_Assembly &value)

void	x_Index (CGC_Assembly &assm, CGC_Replicon &replicon)
	indexing infrastructure More...

void	x_Index (CGC_Assembly &assm, CGC_Sequence &seq)

void	x_Index (CGC_AssemblyUnit &unit, CGC_Replicon &replicon)

void	x_Index (CGC_AssemblyUnit &unit, CGC_Sequence &seq)

void	x_Index (CGC_Replicon &replicon, CGC_Sequence &seq)

void	x_Index (CGC_Sequence &parent, CGC_Sequence &seq, CGC_TaggedSequences::TState relation)

void	x_Index (CGC_Sequence &seq, CGC_TaggedSequences::TState relation)

void	x_Index (CGC_Assembly &root)

const list< CRef< CDbtag > > &	x_GetId () const

string	x_GetSubmitterId () const

Private Attributes
CMutex	m_Mutex

TSequenceIndex	m_SequenceMap

CGC_Assembly *	m_TargetSet

Additional Inherited Members
Static Public Member Functions inherited from CGC_Assembly_Base
static string	SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). 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...

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

Detailed Description

Definition at line 62 of file GC_Assembly.hpp.

Member Typedef Documentation

◆ TAssemblyUnits

typedef list< CConstRef<CGC_AssemblyUnit> > CGC_Assembly::TAssemblyUnits

Definition at line 68 of file GC_Assembly.hpp.

◆ TFullAssemblies

typedef list< CConstRef<CGC_Assembly> > CGC_Assembly::TFullAssemblies

Definition at line 69 of file GC_Assembly.hpp.

◆ Tparent

typedef CGC_Assembly_Base CGC_Assembly::Tparent

private

Definition at line 64 of file GC_Assembly.hpp.

◆ TSequenceIndex

typedef map<CSeq_id_Handle, TSequenceList> CGC_Assembly::TSequenceIndex

private

Definition at line 194 of file GC_Assembly.hpp.

◆ TSequenceList

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

Definition at line 67 of file GC_Assembly.hpp.

Member Enumeration Documentation

◆ EFindSeqOption

enum CGC_Assembly::EFindSeqOption

Enumerator
eEnforceSingle
eChooseAny
eChooseBest

Definition at line 156 of file GC_Assembly.hpp.

◆ ESubset

enum CGC_Assembly::ESubset

Enumerator
eChromosome
eScaffold
eComponent
eTopLevel
eSubmitterPseudoScaffold
eAll

Definition at line 124 of file GC_Assembly.hpp.

Constructor & Destructor Documentation

◆ CGC_Assembly() [1/2]

CGC_Assembly::CGC_Assembly ( void )

Definition at line 66 of file GC_Assembly.cpp.

◆ ~CGC_Assembly()

CGC_Assembly::~CGC_Assembly ( void )

Definition at line 73 of file GC_Assembly.cpp.

◆ CGC_Assembly() [2/2]

CGC_Assembly::CGC_Assembly ( const CGC_Assembly & value )

private

Member Function Documentation

◆ CreateHierarchy()

void CGC_Assembly::CreateHierarchy ( CGC_Assembly * target_set = NULL )

Generate the internal up-pointers.

Definition at line 460 of file GC_Assembly.cpp.

References CGC_AssemblySet_Base::eSet_type_assembly_set, CGC_AssemblySet_Base::eSet_type_full_assembly, eUnknown, CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), m_TargetSet, NCBI_THROW, NON_CONST_ITERATE, NULL, CGC_Assembly_Base::SetAssembly_set(), and x_Index().

Referenced by CTableDataGCAssembly::Init(), PostRead(), and CAdvancedAlignCleanup::SetParams().

◆ CreateIndex()

void CGC_Assembly::CreateIndex ( )

Generate the Seq-id index.

Definition at line 511 of file GC_Assembly.cpp.

References map_checker< Container >::empty(), CGC_TaggedSequences_Base::eState_placed, CSeq_id_Handle::GetHandle(), CGC_Sequence::GetReplicon(), CGC_Sequence_Base::GetSeq_id(), CGC_Sequence_Base::GetSeq_id_synonyms(), CGC_Sequence_Base::GetSequences(), set< Key, Compare >::insert(), CGC_Sequence_Base::IsSetSeq_id_synonyms(), CGC_Sequence_Base::IsSetSequences(), ITERATE, m_Mutex, and m_SequenceMap.

Referenced by Find().

◆ Find() [1/2]

CConstRef< CGC_Sequence > CGC_Assembly::Find	(	const CSeq_id_Handle &	id,
		EFindSeqOption	find_option = `eEnforceSingle`
	)		const

Find a single sequence corresponding to the supplied id.

Flag find_option specifies what to do if more than one sequence is found with this id.

eEnforceSingle: throw an exception. This is the default
eChooseAny: arbitrarily choose one of the sequences
eChooseBest: choose the best sequneces available with this id. Criteria are: – Choose a sequence from the reference full assembly in preference to a sequence from another full assembly – Choose a sequence from the primary unit in preference to a sequence from another unit – Choose a top-level sequence in preference to a non-top-level sequence – Choose a scaffold in preference to a component – If there's more than one sequence that's "best" by the above criteria, choose one arbitrarily

Definition at line 384 of file GC_Assembly.cpp.

References CreateIndex(), eChooseBest, eEnforceSingle, map_checker< Container >::empty(), map_checker< Container >::end(), eUnknown, map_checker< Container >::find(), GetSeqId(), m_SequenceMap, and NCBI_THROW.

◆ Find() [2/2]

void CGC_Assembly::Find	(	const CSeq_id_Handle &	id,
		TSequenceList &	sequences
	)		const

Find all references to a given sequence within an assembly.

Definition at line 412 of file GC_Assembly.cpp.

References CreateIndex(), map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::find(), and m_SequenceMap.

Referenced by CAttachedHandles::Attach(), CSeqUtils::GetChrGI(), GetRepliconTypeLocRole(), and s_FindGaps().

◆ GetAccession()

string CGC_Assembly::GetAccession ( void ) const

Retrieve the accession for this assembly.

Definition at line 99 of file GC_Assembly.cpp.

References ITERATE, and x_GetId().

Referenced by CAssemblyObjectLoader::Execute(), GetBestIdentifier(), CGencollSvc::GetGCAssembly(), CAssemblyInfo::IsSameAssembly(), CTabularFormatter_AssemblyInfo::Print(), s_GetAssemblySeqIds(), and CGBDocument::x_InitializeAssembly().

◆ GetAssemblyUnits()

CGC_Assembly::TAssemblyUnits CGC_Assembly::GetAssemblyUnits ( ) const

Retrieve a list of all assembly units contained in this assembly.

Definition at line 266 of file GC_Assembly.cpp.

References CGC_Assembly_Base::GetAssembly_set(), GetAssemblyUnits(), CGC_AssemblySet_Base::GetPrimary_assembly(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsUnit(), ITERATE, and tmp.

Referenced by GetAssemblyUnits(), and GetFullAssemblies().

◆ GetBestIdentifier()

string CGC_Assembly::GetBestIdentifier ( ) const

Either accession or submitter-provided id.

Definition at line 113 of file GC_Assembly.cpp.

References GetAccession(), and x_GetSubmitterId().

◆ GetDesc()

const CGC_AssemblyDesc & CGC_Assembly::GetDesc ( void ) const

Retrieve the full set of assembly descriptors.

Definition at line 133 of file GC_Assembly.cpp.

References eUnknown, CGC_Assembly_Base::GetAssembly_set(), CGC_AssemblySet_Base::GetDesc(), CGC_AssemblyUnit_Base::GetDesc(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), and NCBI_THROW.

Referenced by Convert_GC_Assembly_Seq_id(), GetFileSafeName(), CGCAsssemblyHandler::GetLabel(), GetName(), GetTaxId(), IsGenBank(), and IsRefSeq().

◆ GetDisplayName()

string CGC_Assembly::GetDisplayName ( ) const

Get full label for assmebly; if this is a unit, full assembly name followed by unit name.

Definition at line 164 of file GC_Assembly.cpp.

References CGC_AssemblyUnit::GetDisplayName(), GetName(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), and kEmptyStr.

◆ GetFileSafeDisplayName()

string CGC_Assembly::GetFileSafeDisplayName ( ) const

Get file-safe version of full label for assmebly.

Definition at line 184 of file GC_Assembly.cpp.

References CGC_AssemblyUnit::GetFileSafeDisplayName(), GetFileSafeName(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), and kEmptyStr.

◆ GetFileSafeName()

string CGC_Assembly::GetFileSafeName ( ) const

Retrieve the file-safe version of assembly name, if available; othwreise default to standard name.

Definition at line 176 of file GC_Assembly.cpp.

References GetDesc(), CGC_AssemblyDesc_Base::GetFilesafe_name(), GetName(), CGC_AssemblyDesc_Base::IsSetFilesafe_name(), and NStr::Replace().

Referenced by GetFileSafeDisplayName(), and CGC_AssemblyUnit::GetFileSafeDisplayName().

◆ GetFullAssemblies()

CGC_Assembly::TFullAssemblies CGC_Assembly::GetFullAssemblies ( ) const

Retrieve a list of all full assemblies contained in this assembly Note that, if the assembly is a full assembly, then it will be the only assembly returned; also, if the assembly is not an assembly set, then the base assembly will be returned.

Definition at line 290 of file GC_Assembly.cpp.

References CGC_AssemblySet_Base::eSet_type_assembly_set, CGC_AssemblySet_Base::eSet_type_full_assembly, CGC_Assembly_Base::GetAssembly_set(), GetAssemblyUnits(), CGC_Assembly_Base::IsAssembly_set(), ITERATE, and tmp.

◆ GetMolecules()

void CGC_Assembly::GetMolecules	(	TSequenceList &	molecules,
		ESubset	subset
	)		const

Retrieve a subset of molecules.

Definition at line 865 of file GC_Assembly.cpp.

References s_Extract().

Referenced by Convert_GC_Assembly_Seq_id(), Convert_GC_Assembly_Seq_loc_Chromosomes(), Convert_GC_Assembly_Seq_loc_TopLevel(), CTableDataGCAssembly::Init(), s_GetAssemblySeqIds(), and CVcfLoadingJob::x_CreateProjectItems().

◆ GetMoleculesByUnit()

void CGC_Assembly::GetMoleculesByUnit	(	vector< TSequenceList > &	molecules,
		ESubset	subset
	)		const

Retrieve a subset of molecules separately for each unit, in the same order in which the units are returned by GetAssemblyUnits()

Definition at line 871 of file GC_Assembly.cpp.

References s_Extract().

◆ GetName()

string CGC_Assembly::GetName ( void ) const

Retrieve the name of this assembly.

Definition at line 147 of file GC_Assembly.cpp.

References CGC_Assembly_Base::GetAssembly_set(), GetDesc(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), kEmptyStr, and CConstRef< C, Locker >::Reset().

Referenced by Convert_GC_Assembly_Seq_id(), GetDisplayName(), CGC_AssemblyUnit::GetDisplayName(), GetFileSafeName(), CGCAsssemblyHandler::GetLabel(), IsOrganelle(), CAssemblyInfo::IsSameAssembly(), and CTabularFormatter_AssemblyInfo::Print().

◆ GetReleaseId()

int CGC_Assembly::GetReleaseId ( ) const

Retrieve the release id for this assembly.

Definition at line 84 of file GC_Assembly.cpp.

References ITERATE, and x_GetId().

◆ GetRepliconTypeLocRole()

void CGC_Assembly::GetRepliconTypeLocRole	(	const CSeq_id_Handle &	id,
		string &	type,
		string &	location,
		set< int > &	role
	)		const

Returns replicon type, location and role.

Definition at line 425 of file GC_Assembly.cpp.

References eGC_SequenceRole_chromosome, eGC_SequenceRole_pseudo_scaffold, eGC_SequenceRole_scaffold, Find(), set< Key, Compare >::insert(), ITERATE, and location.

◆ GetTargetSet()

CConstRef< CGC_Assembly > CGC_Assembly::GetTargetSet ( ) const

Access the top-level target set that this assemhly belongs to.

Definition at line 877 of file GC_Assembly.cpp.

References m_TargetSet.

◆ GetTaxId()

TTaxId CGC_Assembly::GetTaxId ( void ) const

Retrieve the tax-id for this assembly.

Definition at line 196 of file GC_Assembly.cpp.

References CGC_Assembly_Base::GetAssembly_set(), GetDesc(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), ITERATE, CConstRef< C, Locker >::Reset(), and ZERO_TAX_ID.

◆ GetUnitClass()

CGC_AssemblyUnit::TClass CGC_Assembly::GetUnitClass ( ) const

If this is an assembly unit, get unit class.

Definition at line 254 of file GC_Assembly.cpp.

References CGC_AssemblyUnit_Base::eClass_other, CGC_AssemblyUnit_Base::GetClass(), CGC_Assembly_Base::GetUnit(), and CGC_Assembly_Base::IsUnit().

◆ IsGenBank()

bool CGC_Assembly::IsGenBank ( ) const

Is this assembly a GenBank assembly?

Definition at line 234 of file GC_Assembly.cpp.

References CGC_AssemblyDesc_Base::eRelease_type_genbank, CGC_Assembly_Base::GetAssembly_set(), GetDesc(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), and CConstRef< C, Locker >::Reset().

Referenced by CVcfLoadingJob::x_FindSynonyms().

◆ IsOrganelle()

bool CGC_Assembly::IsOrganelle ( ) const

Is this a non-nuclear assembly unit?

Definition at line 249 of file GC_Assembly.cpp.

References GetName().

◆ IsRefSeq()

bool CGC_Assembly::IsRefSeq ( ) const

Is this assembly a RefSeq assembly?

Definition at line 218 of file GC_Assembly.cpp.

References CGC_AssemblyDesc_Base::eRelease_type_refseq, CGC_Assembly_Base::GetAssembly_set(), GetDesc(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), and CConstRef< C, Locker >::Reset().

Referenced by CTableAnnotDataSource::AddSeqLoc(), CIdMapperNumAssembly::CIdMapperNumAssembly(), CTableAnnotDataSource::CreateFeature(), CAssemblyObjectLoader::Execute(), CGencollIdMapperAdapter::GetIdMapper(), s_GCSeqsToSeqLocs(), and CMappingObjectLoader::x_CreateMapper().

◆ IsTargetSetReference()

bool CGC_Assembly::IsTargetSetReference ( ) const

Is this assembly the reference assembly of the target set, or part of it?

Definition at line 882 of file GC_Assembly.cpp.

References CGC_AssemblySet_Base::eSet_type_assembly_set, eUnknown, CGC_Assembly_Base::GetAssembly_set(), CGC_AssemblyUnit::GetFullAssembly(), CGC_AssemblySet_Base::GetPrimary_assembly(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), IsTargetSetReference(), CGC_Assembly_Base::IsUnit(), m_TargetSet, and NCBI_THROW.

Referenced by IsTargetSetReference().

◆ operator=()

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

private

◆ PostRead()

void CGC_Assembly::PostRead ( )

Definition at line 454 of file GC_Assembly.cpp.

References CreateHierarchy().

◆ PreWrite()

void CGC_Assembly::PreWrite ( ) const

PreWrite() / PostRead() handle events for indexing of local structures.

Definition at line 450 of file GC_Assembly.cpp.

◆ x_GetId()

const list< CRef< CDbtag > > & CGC_Assembly::x_GetId ( ) const

private

Definition at line 77 of file GC_Assembly.cpp.

References eUnknown, CGC_Assembly_Base::GetAssembly_set(), CGC_AssemblySet_Base::GetId(), CGC_AssemblyUnit_Base::GetId(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), and NCBI_THROW.

Referenced by GetAccession(), GetReleaseId(), and x_GetSubmitterId().

◆ x_GetSubmitterId()

string CGC_Assembly::x_GetSubmitterId ( ) const

private

Definition at line 119 of file GC_Assembly.cpp.

References ITERATE, and x_GetId().

Referenced by GetBestIdentifier().

◆ x_Index() [1/8]

void CGC_Assembly::x_Index	(	CGC_Assembly &	assm,
		CGC_Replicon &	replicon
	)

private

indexing infrastructure

Definition at line 605 of file GC_Assembly.cpp.

References CGC_Replicon_Base::GetSequence(), CGC_Replicon_Base::C_Sequence::IsSingle(), CGC_Replicon::m_Assembly, NON_CONST_ITERATE, and CGC_Replicon_Base::SetSequence().

Referenced by CreateHierarchy(), and x_Index().

◆ x_Index() [2/8]

void CGC_Assembly::x_Index	(	CGC_Assembly &	assm,
		CGC_Sequence &	seq
	)

private

Definition at line 623 of file GC_Assembly.cpp.

References i, CGC_Sequence_Base::IsSetSequences(), CGC_Sequence::m_Assembly, NON_CONST_ITERATE, CGC_Sequence_Base::SetSequences(), and x_Index().

◆ x_Index() [3/8]

void CGC_Assembly::x_Index ( CGC_Assembly & root )

private

Definition at line 567 of file GC_Assembly.cpp.

References CGC_Assembly_Base::GetUnit(), i, CGC_Assembly_Base::IsAssembly_set(), CGC_Assembly_Base::IsUnit(), CGC_AssemblyUnit::m_Assembly, NON_CONST_ITERATE, CGC_Assembly_Base::SetAssembly_set(), CGC_Assembly_Base::SetUnit(), and x_Index().

◆ x_Index() [4/8]

void CGC_Assembly::x_Index	(	CGC_AssemblyUnit &	unit,
		CGC_Replicon &	replicon
	)

private

Definition at line 638 of file GC_Assembly.cpp.

References CGC_TaggedSequences_Base::eState_placed, CGC_Replicon_Base::GetSequence(), CGC_Replicon_Base::C_Sequence::IsSingle(), CGC_Replicon::m_AssemblyUnit, CGC_Sequence::m_ParentRel, NON_CONST_ITERATE, CGC_Replicon_Base::SetSequence(), and x_Index().

◆ x_Index() [5/8]

void CGC_Assembly::x_Index	(	CGC_AssemblyUnit &	unit,
		CGC_Sequence &	seq
	)

private

Definition at line 662 of file GC_Assembly.cpp.

References i, CGC_Sequence_Base::IsSetSequences(), CGC_Sequence::m_AssemblyUnit, NON_CONST_ITERATE, CGC_Sequence_Base::SetSequences(), and x_Index().

◆ x_Index() [6/8]

void CGC_Assembly::x_Index	(	CGC_Replicon &	replicon,
		CGC_Sequence &	seq
	)

private

Definition at line 678 of file GC_Assembly.cpp.

References i, CGC_Sequence_Base::IsSetSequences(), CGC_Sequence::m_Replicon, NON_CONST_ITERATE, CGC_Sequence_Base::SetSequences(), and x_Index().

◆ x_Index() [7/8]

void CGC_Assembly::x_Index	(	CGC_Sequence &	parent,
		CGC_Sequence &	seq,
		CGC_TaggedSequences::TState	relation
	)

private

Definition at line 693 of file GC_Assembly.cpp.

References i, CGC_Sequence_Base::IsSetSequences(), CGC_Sequence::m_ParentRel, CGC_Sequence::m_ParentSequence, NON_CONST_ITERATE, CGC_Sequence_Base::SetSequences(), and x_Index().

◆ x_Index() [8/8]

void CGC_Assembly::x_Index	(	CGC_Sequence &	seq,
		CGC_TaggedSequences::TState	relation
	)

private

Definition at line 709 of file GC_Assembly.cpp.

References i, CGC_Sequence_Base::IsSetSequences(), CGC_Sequence::m_ParentRel, CGC_Sequence::m_ParentSequence, NON_CONST_ITERATE, NULL, CGC_Sequence_Base::SetSequences(), and x_Index().

Member Data Documentation

◆ m_Mutex

CMutex CGC_Assembly::m_Mutex

private

Definition at line 193 of file GC_Assembly.hpp.

Referenced by CreateIndex().

◆ m_SequenceMap

TSequenceIndex CGC_Assembly::m_SequenceMap

private

Definition at line 195 of file GC_Assembly.hpp.

Referenced by CreateIndex(), and Find().

◆ m_TargetSet

CGC_Assembly* CGC_Assembly::m_TargetSet

private

Definition at line 197 of file GC_Assembly.hpp.

Referenced by CreateHierarchy(), GetTargetSet(), and IsTargetSetReference().

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

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

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAssemblyUnits

◆ TFullAssemblies

◆ Tparent

◆ TSequenceIndex

◆ TSequenceList

Member Enumeration Documentation

◆ EFindSeqOption

◆ ESubset

Constructor & Destructor Documentation

◆ CGC_Assembly() [1/2]

◆ ~CGC_Assembly()

◆ CGC_Assembly() [2/2]

Member Function Documentation

◆ CreateHierarchy()

◆ CreateIndex()

◆ Find() [1/2]

◆ Find() [2/2]

◆ GetAccession()

◆ GetAssemblyUnits()

◆ GetBestIdentifier()

◆ GetDesc()

◆ GetDisplayName()

◆ GetFileSafeDisplayName()

◆ GetFileSafeName()

◆ GetFullAssemblies()

◆ GetMolecules()

◆ GetMoleculesByUnit()

◆ GetName()

◆ GetReleaseId()

◆ GetRepliconTypeLocRole()

◆ GetTargetSet()

◆ GetTaxId()

◆ GetUnitClass()

◆ IsGenBank()

◆ IsOrganelle()

◆ IsRefSeq()

◆ IsTargetSetReference()

◆ operator=()

◆ PostRead()

◆ PreWrite()

◆ x_GetId()

◆ x_GetSubmitterId()

◆ x_Index() [1/8]

◆ x_Index() [2/8]

◆ x_Index() [3/8]

◆ x_Index() [4/8]

◆ x_Index() [5/8]

◆ x_Index() [6/8]

◆ x_Index() [7/8]

◆ x_Index() [8/8]

Member Data Documentation

◆ m_Mutex

◆ m_SequenceMap

◆ m_TargetSet