#include <objtools/cleanup/influenza_set.hpp>

Inheritance diagram for CInfluenzaSet:

Collaboration diagram for CInfluenzaSet:

Public Types
enum	EInfluenzaType { eNotInfluenza = 0 , eInfluenzaA , eInfluenzaB , eInfluenzaC , eInfluenzaD }

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
	CInfluenzaSet (const string &key)

	~CInfluenzaSet ()

bool	OkToMakeSet () const

void	MakeSet ()

void	AddBioseq (CBioseq_Handle bsh)

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...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. 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 string	GetKey (const COrg_ref &org)

static EInfluenzaType	GetInfluenzaType (const string &taxname)

static size_t	GetNumRequired (EInfluenzaType fluType)

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)

Protected Types
typedef vector< CBioseq_Handle >	TMembers

Protected Attributes
TMembers	m_Members

const string	m_Key

EInfluenzaType	m_FluType

size_t	m_Required

Additional Inherited Members
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 42 of file influenza_set.hpp.

Member Typedef Documentation

◆ TMembers

typedef vector<CBioseq_Handle> CInfluenzaSet::TMembers

protected

Definition at line 65 of file influenza_set.hpp.

Member Enumeration Documentation

◆ EInfluenzaType

enum CInfluenzaSet::EInfluenzaType

Enumerator
eNotInfluenza
eInfluenzaA
eInfluenzaB
eInfluenzaC
eInfluenzaD

Definition at line 51 of file influenza_set.hpp.

Constructor & Destructor Documentation

◆ CInfluenzaSet()

CInfluenzaSet::CInfluenzaSet ( const string & key )

Definition at line 64 of file influenza_set.cpp.

References ncbi::grid::netcache::search::fields::key.

◆ ~CInfluenzaSet()

CInfluenzaSet::~CInfluenzaSet ( )

inline

Definition at line 45 of file influenza_set.hpp.

Member Function Documentation

◆ AddBioseq()

void CInfluenzaSet::AddBioseq ( CBioseq_Handle bsh )

Definition at line 133 of file influenza_set.cpp.

References m_Members.

◆ GetInfluenzaType()

CInfluenzaSet::EInfluenzaType CInfluenzaSet::GetInfluenzaType ( const string & taxname )

static

Definition at line 80 of file influenza_set.cpp.

References eInfluenzaA, eInfluenzaB, eInfluenzaC, eInfluenzaD, NStr::eNocase, eNotInfluenza, and NStr::StartsWith().

Referenced by GetKey(), s_CheckForSegments(), and CCleanupHugeAsnReader::x_PruneIfSegsMissing().

◆ GetKey()

string CInfluenzaSet::GetKey ( const COrg_ref & org )

static

Definition at line 95 of file influenza_set.cpp.

References eInfluenzaA, eNotInfluenza, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_strain, GetInfluenzaType(), COrgName_Base::GetMod(), COrg_ref_Base::GetOrgname(), COrg_ref_Base::GetTaxname(), NStr::IsBlank(), COrgName_Base::IsSetMod(), COrg_ref_Base::IsSetOrgname(), COrg_ref_Base::IsSetTaxname(), and kEmptyStr.

Referenced by CCleanup::MakeSmallGenomeSet(), and s_GetInfluenzaLabel().

◆ GetNumRequired()

size_t CInfluenzaSet::GetNumRequired ( EInfluenzaType fluType )

static

Definition at line 71 of file influenza_set.cpp.

References eInfluenzaA, and eInfluenzaB.

Referenced by s_CheckForSegments(), and CCleanupHugeAsnReader::x_PruneIfSegsMissing().

◆ MakeSet()

void CInfluenzaSet::MakeSet ( )

Definition at line 192 of file influenza_set.cpp.

References CBioseq_set_EditHandle::AttachEntry(), CSeq_entry_EditHandle::AttachEntry(), CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_small_genome_set, CBioseq_set_Handle::GetClass(), CBioseq_set_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CBioseq_set_Handle::IsSetClass(), ITERATE, m_Members, CSeq_entry_EditHandle::Remove(), CBioseq_set_Base::SetClass(), and CSeq_entry_Base::SetSet().

◆ OkToMakeSet()

bool CInfluenzaSet::OkToMakeSet ( ) const

Definition at line 161 of file influenza_set.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqdesc_Base::e_Source, eExtreme_Biological, f(), g_FindSegs(), CSeqdesc_Base::GetSource(), SAnnotSelector::IncludeFeatType(), m_Members, m_Required, and set< Key, Compare >::size().

Member Data Documentation

◆ m_FluType

EInfluenzaType CInfluenzaSet::m_FluType

protected

Definition at line 68 of file influenza_set.hpp.

◆ m_Key

const string CInfluenzaSet::m_Key

protected

Definition at line 67 of file influenza_set.hpp.

◆ m_Members

TMembers CInfluenzaSet::m_Members

protected

Definition at line 66 of file influenza_set.hpp.

Referenced by AddBioseq(), MakeSet(), and OkToMakeSet().

◆ m_Required

size_t CInfluenzaSet::m_Required

protected

Definition at line 69 of file influenza_set.hpp.

Referenced by OkToMakeSet().

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

include/objtools/cleanup/influenza_set.hpp
src/objtools/cleanup/influenza_set.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TMembers

Member Enumeration Documentation

◆ EInfluenzaType

Constructor & Destructor Documentation

◆ CInfluenzaSet()

◆ ~CInfluenzaSet()

Member Function Documentation

◆ AddBioseq()

◆ GetInfluenzaType()

◆ GetKey()

◆ GetNumRequired()

◆ MakeSet()

◆ OkToMakeSet()

Member Data Documentation

◆ m_FluType

◆ m_Key

◆ m_Members

◆ m_Required