Search Toolkit Book for CBlast4_parameters

#include <objects/blast/Blast4_parameters.hpp>

Inheritance diagram for CBlast4_parameters:

Collaboration diagram for CBlast4_parameters:

Public Member Functions
	CBlast4_parameters (void)
	constructor More...

	~CBlast4_parameters (void)
	destructor More...

CRef< CBlast4_parameter >	Add (const string name, const int &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	Add (const string name, const string &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	Add (const string name, const bool &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	Add (const string name, const double &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	Add (const string name, const Int8 &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	Add (const string name, const EBlast4_strand_type &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	Add (const string name, const CBlast4_cutoff &value)
	Append Blast4_parameter. More...

CRef< CBlast4_parameter >	GetParamByName (const string name) const
	Returns Blast4_parameter with specified name. More...

Public Member Functions inherited from CBlast4_parameters_Base
	CBlast4_parameters_Base (void)

virtual	~CBlast4_parameters_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSet (void) const
	Check if a value has been assigned to data member. More...

bool	CanGet (void) const
	Check if it is safe to call Get method. More...

void	Reset (void)
	Reset data member. More...

const Tdata &	Get (void) const
	Get the member data. More...

Tdata &	Set (void)
	Assign a value to data member. More...

	operator const Tdata & (void) const
	Conversion operator to 'const Tdata' type. More...

	operator Tdata & (void)
	Conversion operator to 'Tdata' type. 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 CBlast4_parameters_Base	Tparent

Private Member Functions
	CBlast4_parameters (const CBlast4_parameters &value)

CBlast4_parameters &	operator= (const CBlast4_parameters &value)

Additional Inherited Members
Public Types inherited from CBlast4_parameters_Base
typedef list< CRef< CBlast4_parameter > >	Tdata

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 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 55 of file Blast4_parameters.hpp.

Member Typedef Documentation

◆ Tparent

typedef CBlast4_parameters_Base CBlast4_parameters::Tparent

private

Definition at line 57 of file Blast4_parameters.hpp.

Constructor & Destructor Documentation

◆ CBlast4_parameters() [1/2]

CBlast4_parameters::CBlast4_parameters ( void )

inline

constructor

Definition at line 170 of file Blast4_parameters.hpp.

◆ ~CBlast4_parameters()

CBlast4_parameters::~CBlast4_parameters ( void )

destructor

Definition at line 50 of file Blast4_parameters.cpp.

◆ CBlast4_parameters() [2/2]

CBlast4_parameters::CBlast4_parameters ( const CBlast4_parameters & value )

private

Member Function Documentation

◆ Add() [1/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const bool &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	A boolean containing Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 93 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetBoolean(), and rapidjson::value.

◆ Add() [2/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const CBlast4_cutoff &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	A CBlast4_cutoff containing Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 166 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CRef< C, Locker >::Reset(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetCutoff(), and rapidjson::value.

◆ Add() [3/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const double &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	A double containing Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 111 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetReal(), and rapidjson::value.

◆ Add() [4/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const EBlast4_strand_type &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	A EBlast4_strand_type containing Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 148 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetStrand_type(), and rapidjson::value.

◆ Add() [5/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const int &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	An int conatinig Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 54 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CRef< C, Locker >::Reset(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetInteger(), and rapidjson::value.

Referenced by CRemoteBlast::x_SetAlgoOpts().

◆ Add() [6/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const Int8 &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	A Int8 containing Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 130 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetBig_integer(), and rapidjson::value.

◆ Add() [7/7]

CRef< CBlast4_parameter > CBlast4_parameters::Add	(	const string	name,
		const string &	value
	)

Append Blast4_parameter.

If node with the specified name exists, the value is substituted

Parameters

name	A string containing Blast4_parameter node name
value	A string conatinig Blast4_parameter value

Returns: CRef to created Blast4_parameter

Definition at line 73 of file Blast4_parameters.cpp.

References CRef< C, Locker >::Empty(), GetParamByName(), CRef< C, Locker >::Reset(), CBlast4_parameters_Base::Set(), CBlast4_value_Base::SetString(), and rapidjson::value.

◆ GetParamByName()

CRef< CBlast4_parameter > CBlast4_parameters::GetParamByName ( const string name ) const

Returns Blast4_parameter with specified name.

Parameters

name	A string containg Blast4_parameter node name

Returns: CRef to CBlast4_parameter list node or empty reference if name does not exist

Definition at line 187 of file Blast4_parameters.cpp.

References CBlast4_parameters_Base::Get(), and ITERATE.

Referenced by Add(), BOOST_AUTO_TEST_CASE(), CImportStrategy::FetchData(), CRemoteBlast::x_GetStringFromSearchInfoReply(), and CRemoteBlast::x_GetSubjects().

◆ operator=()

CBlast4_parameters& CBlast4_parameters::operator= ( const CBlast4_parameters & value )

private

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

include/objects/blast/Blast4_parameters.hpp
src/objects/blast/Blast4_parameters.cpp

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CBlast4_parameters() [1/2]

◆ ~CBlast4_parameters()

◆ CBlast4_parameters() [2/2]

Member Function Documentation

◆ Add() [1/7]

◆ Add() [2/7]

◆ Add() [3/7]

◆ Add() [4/7]

◆ Add() [5/7]

◆ Add() [6/7]

◆ Add() [7/7]

◆ GetParamByName()

◆ operator=()