NCBI C++ ToolKit
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CInfluenzaSet Class Reference

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#include <objtools/cleanup/influenza_set.hpp>

+ Inheritance diagram for CInfluenzaSet:
+ Collaboration diagram for CInfluenzaSet:

Public Types

enum  EInfluenzaType {
  eNotInfluenza = 0 , eInfluenzaA , eInfluenzaB , eInfluenzaC ,
- 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< Uint8TCounter
 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...
CObjectoperator= (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_HandleTMembers

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

Definition at line 65 of file influenza_set.hpp.

Member Enumeration Documentation

◆ EInfluenzaType


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 ( )

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)

◆ GetKey()

string CInfluenzaSet::GetKey ( const COrg_ref org)

◆ GetNumRequired()

size_t CInfluenzaSet::GetNumRequired ( EInfluenzaType  fluType)

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 ( )

◆ OkToMakeSet()

bool CInfluenzaSet::OkToMakeSet ( ) const

Member Data Documentation

◆ m_FluType

EInfluenzaType CInfluenzaSet::m_FluType

Definition at line 68 of file influenza_set.hpp.

◆ m_Key

const string CInfluenzaSet::m_Key

Definition at line 67 of file influenza_set.hpp.

◆ m_Members

TMembers CInfluenzaSet::m_Members

Definition at line 66 of file influenza_set.hpp.

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

◆ m_Required

size_t CInfluenzaSet::m_Required

Definition at line 69 of file influenza_set.hpp.

Referenced by OkToMakeSet().

The documentation for this class was generated from the following files:
Modified on Tue May 21 10:59:46 2024 by rev. 669887