#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...

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 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, TTaxId >	m_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< Uint8 >	TCounter
	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
	)

Definition at line 77 of file taxid_set.cpp.

References AccessionToKey(), CSeq_id::AsFastaString(), ncbi::grid::netcache::search::fields::key, and m_TaxIdMap.

Referenced by CMakeProfileDBApp::x_MakeVol().

◆ 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

deflines Deflines 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 )

Definition at line 45 of file taxid_set.cpp.

References AccessionToKey(), map_checker< Container >::empty(), f(), NStr::fAllowLeadingSpaces, ncbi::grid::netcache::search::fields::key, kTaxIdNotSet, m_GlobalTaxId, m_Matched, m_TaxIdMap, NcbiGetlineEOL(), NStr::Split(), and NStr::TruncateSpaces().

Referenced by BOOST_AUTO_TEST_CASE(), CMakeBlastDBApp::x_BuildDatabase(), and CMakeProfileDBApp::x_InitProgramParameters().

◆ 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:

include/objtools/blast/seqdb_writer/taxid_set.hpp
src/objtools/blast/seqdb_writer/taxid_set.cpp

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CTaxIdSet()

Member Function Documentation

◆ AddTaxId()

◆ FixTaxId()

◆ HasEverFixedId()

◆ SetMappingFromFile()

◆ x_SelectBestTaxid()

Member Data Documentation

◆ kTaxIdNotSet

◆ m_GlobalTaxId

◆ m_Matched

◆ m_TaxIdMap