NCBI C++ ToolKit
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CTaxIdSet Class Reference

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#include <objtools/blast/seqdb_writer/taxid_set.hpp>

+ Inheritance diagram for CTaxIdSet:
+ Collaboration diagram for CTaxIdSet:

Public Member Functions

 CTaxIdSet (TTaxId global_taxid=kTaxIdNotSet)
 
void SetMappingFromFile (CNcbiIstream &f)
 
void FixTaxId (CRef< objects::CBlast_def_line_set > deflines)
 Check that each defline has the specified taxid; if not, replace the defline and set the taxid. More...
 
bool HasEverFixedId () const
 
void AddTaxId (const objects::CSeq_id &seqid, const TTaxId &taxid)
 
- 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 Attributes

static const TTaxId kTaxIdNotSet = ZERO_TAX_ID
 
- 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...
 

Private Member Functions

TTaxId x_SelectBestTaxid (const objects::CBlast_def_line &defline)
 Selects the most suitable tax id for the input passed in, checking the global taxid first, then the mapping provided by an input file, and finally what's found in the defline argument. More...
 

Private Attributes

TTaxId m_GlobalTaxId
 
map< string, TTaxIdm_TaxIdMap
 
bool m_Matched
 

Additional Inherited Members

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

Detailed Description

Definition at line 47 of file taxid_set.hpp.

Constructor & Destructor Documentation

◆ CTaxIdSet()

CTaxIdSet::CTaxIdSet ( TTaxId  global_taxid = kTaxIdNotSet)
inline

Definition at line 51 of file taxid_set.hpp.

Member Function Documentation

◆ AddTaxId()

void CTaxIdSet::AddTaxId ( const objects::CSeq_id &  seqid,
const TTaxId taxid 
)

◆ FixTaxId()

void CTaxIdSet::FixTaxId ( CRef< objects::CBlast_def_line_set >  deflines)

Check that each defline has the specified taxid; if not, replace the defline and set the taxid.

Parameters
deflinesDeflines to fix taxIDs [in|out]

Definition at line 131 of file taxid_set.cpp.

References NON_CONST_ITERATE, and x_SelectBestTaxid().

Referenced by BOOST_AUTO_TEST_CASE(), CBuildDatabase::x_DupLocal(), CBuildDatabase::x_EditHeaders(), and CMakeProfileDBApp::x_MakeVol().

◆ HasEverFixedId()

bool CTaxIdSet::HasEverFixedId ( ) const
inline

Definition at line 62 of file taxid_set.hpp.

References m_Matched.

Referenced by CBuildDatabase::~CBuildDatabase().

◆ SetMappingFromFile()

void CTaxIdSet::SetMappingFromFile ( CNcbiIstream f)

◆ x_SelectBestTaxid()

TTaxId CTaxIdSet::x_SelectBestTaxid ( const objects::CBlast_def_line &  defline)
private

Selects the most suitable tax id for the input passed in, checking the global taxid first, then the mapping provided by an input file, and finally what's found in the defline argument.

Definition at line 84 of file taxid_set.cpp.

References map_checker< Container >::empty(), map_checker< Container >::end(), map_checker< Container >::find(), GetDeflineKeys(), ITERATE, ncbi::grid::netcache::search::fields::key, kTaxIdNotSet, m_GlobalTaxId, m_Matched, m_TaxIdMap, NStr::SplitInTwo(), and version.

Referenced by FixTaxId().

Member Data Documentation

◆ kTaxIdNotSet

const TTaxId CTaxIdSet::kTaxIdNotSet = ZERO_TAX_ID
static

Definition at line 49 of file taxid_set.hpp.

Referenced by SetMappingFromFile(), and x_SelectBestTaxid().

◆ m_GlobalTaxId

TTaxId CTaxIdSet::m_GlobalTaxId
private

Definition at line 67 of file taxid_set.hpp.

Referenced by SetMappingFromFile(), and x_SelectBestTaxid().

◆ m_Matched

bool CTaxIdSet::m_Matched
private

Definition at line 69 of file taxid_set.hpp.

Referenced by HasEverFixedId(), SetMappingFromFile(), and x_SelectBestTaxid().

◆ m_TaxIdMap

map< string, TTaxId > CTaxIdSet::m_TaxIdMap
private

Definition at line 68 of file taxid_set.hpp.

Referenced by AddTaxId(), SetMappingFromFile(), and x_SelectBestTaxid().


The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:08:10 2024 by modify_doxy.py rev. 669887