CBlast4_value Class Reference

Search Toolkit Book for CBlast4_value

CBlast4_value –. More...

#include <objects/blast/Blast4_value.hpp>

Inheritance diagram for CBlast4_value:

Collaboration diagram for CBlast4_value:

Public Member Functions
	CBlast4_value (void)
	~CBlast4_value (void)
Public Member Functions inherited from CBlast4_value_Base
	CBlast4_value_Base (void)
virtual	~CBlast4_value_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
virtual void	Reset (void)
	Reset the whole object. More...
virtual void	ResetSelection (void)
	Reset the selection (set it to e_not_set). More...
E_Choice	Which (void) const
	Which variant is currently selected. More...
void	CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...
void	ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...
void	Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...
void	Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...
bool	IsBig_integer (void) const
	Check if variant Big_integer is selected. More...
TBig_integer	GetBig_integer (void) const
	Get the variant data. More...
TBig_integer &	SetBig_integer (void)
	Select the variant. More...
void	SetBig_integer (TBig_integer value)
	Select the variant and set its data. More...
bool	IsBioseq (void) const
	Check if variant Bioseq is selected. More...
const TBioseq &	GetBioseq (void) const
	Get the variant data. More...
TBioseq &	SetBioseq (void)
	Select the variant. More...
void	SetBioseq (TBioseq &value)
	Select the variant and set its data. More...
bool	IsBoolean (void) const
	Check if variant Boolean is selected. More...
TBoolean	GetBoolean (void) const
	Get the variant data. More...
TBoolean &	SetBoolean (void)
	Select the variant. More...
void	SetBoolean (TBoolean value)
	Select the variant and set its data. More...
bool	IsCutoff (void) const
	Check if variant Cutoff is selected. More...
const TCutoff &	GetCutoff (void) const
	Get the variant data. More...
TCutoff &	SetCutoff (void)
	Select the variant. More...
void	SetCutoff (TCutoff &value)
	Select the variant and set its data. More...
bool	IsInteger (void) const
	Check if variant Integer is selected. More...
TInteger	GetInteger (void) const
	Get the variant data. More...
TInteger &	SetInteger (void)
	Select the variant. More...
void	SetInteger (TInteger value)
	Select the variant and set its data. More...
bool	IsMatrix (void) const
	Check if variant Matrix is selected. More...
const TMatrix &	GetMatrix (void) const
	Get the variant data. More...
TMatrix &	SetMatrix (void)
	Select the variant. More...
void	SetMatrix (TMatrix &value)
	Select the variant and set its data. More...
bool	IsReal (void) const
	Check if variant Real is selected. More...
TReal	GetReal (void) const
	Get the variant data. More...
TReal &	SetReal (void)
	Select the variant. More...
void	SetReal (TReal value)
	Select the variant and set its data. More...
bool	IsSeq_align (void) const
	Check if variant Seq_align is selected. More...
const TSeq_align &	GetSeq_align (void) const
	Get the variant data. More...
TSeq_align &	SetSeq_align (void)
	Select the variant. More...
void	SetSeq_align (TSeq_align &value)
	Select the variant and set its data. More...
bool	IsSeq_id (void) const
	Check if variant Seq_id is selected. More...
const TSeq_id &	GetSeq_id (void) const
	Get the variant data. More...
TSeq_id &	SetSeq_id (void)
	Select the variant. More...
void	SetSeq_id (TSeq_id &value)
	Select the variant and set its data. More...
bool	IsSeq_loc (void) const
	Check if variant Seq_loc is selected. More...
const TSeq_loc &	GetSeq_loc (void) const
	Get the variant data. More...
TSeq_loc &	SetSeq_loc (void)
	Select the variant. More...
void	SetSeq_loc (TSeq_loc &value)
	Select the variant and set its data. More...
bool	IsStrand_type (void) const
	Check if variant Strand_type is selected. More...
TStrand_type	GetStrand_type (void) const
	Get the variant data. More...
TStrand_type &	SetStrand_type (void)
	Select the variant. More...
void	SetStrand_type (TStrand_type value)
	Select the variant and set its data. More...
bool	IsString (void) const
	Check if variant String is selected. More...
const TString &	GetString (void) const
	Get the variant data. More...
TString &	SetString (void)
	Select the variant. More...
void	SetString (const TString &value)
	Select the variant and set its data. More...
bool	IsBig_integer_list (void) const
	Check if variant Big_integer_list is selected. More...
const TBig_integer_list &	GetBig_integer_list (void) const
	Get the variant data. More...
TBig_integer_list &	SetBig_integer_list (void)
	Select the variant. More...
bool	IsBioseq_list (void) const
	Check if variant Bioseq_list is selected. More...
const TBioseq_list &	GetBioseq_list (void) const
	Get the variant data. More...
TBioseq_list &	SetBioseq_list (void)
	Select the variant. More...
bool	IsBoolean_list (void) const
	Check if variant Boolean_list is selected. More...
const TBoolean_list &	GetBoolean_list (void) const
	Get the variant data. More...
TBoolean_list &	SetBoolean_list (void)
	Select the variant. More...
bool	IsCutoff_list (void) const
	Check if variant Cutoff_list is selected. More...
const TCutoff_list &	GetCutoff_list (void) const
	Get the variant data. More...
TCutoff_list &	SetCutoff_list (void)
	Select the variant. More...
bool	IsInteger_list (void) const
	Check if variant Integer_list is selected. More...
const TInteger_list &	GetInteger_list (void) const
	Get the variant data. More...
TInteger_list &	SetInteger_list (void)
	Select the variant. More...
bool	IsMatrix_list (void) const
	Check if variant Matrix_list is selected. More...
const TMatrix_list &	GetMatrix_list (void) const
	Get the variant data. More...
TMatrix_list &	SetMatrix_list (void)
	Select the variant. More...
bool	IsReal_list (void) const
	Check if variant Real_list is selected. More...
const TReal_list &	GetReal_list (void) const
	Get the variant data. More...
TReal_list &	SetReal_list (void)
	Select the variant. More...
bool	IsSeq_align_list (void) const
	Check if variant Seq_align_list is selected. More...
const TSeq_align_list &	GetSeq_align_list (void) const
	Get the variant data. More...
TSeq_align_list &	SetSeq_align_list (void)
	Select the variant. More...
bool	IsSeq_id_list (void) const
	Check if variant Seq_id_list is selected. More...
const TSeq_id_list &	GetSeq_id_list (void) const
	Get the variant data. More...
TSeq_id_list &	SetSeq_id_list (void)
	Select the variant. More...
bool	IsSeq_loc_list (void) const
	Check if variant Seq_loc_list is selected. More...
const TSeq_loc_list &	GetSeq_loc_list (void) const
	Get the variant data. More...
TSeq_loc_list &	SetSeq_loc_list (void)
	Select the variant. More...
bool	IsStrand_type_list (void) const
	Check if variant Strand_type_list is selected. More...
const TStrand_type_list &	GetStrand_type_list (void) const
	Get the variant data. More...
TStrand_type_list &	SetStrand_type_list (void)
	Select the variant. More...
bool	IsString_list (void) const
	Check if variant String_list is selected. More...
const TString_list &	GetString_list (void) const
	Get the variant data. More...
TString_list &	SetString_list (void)
	Select the variant. More...
bool	IsBioseq_set (void) const
	Check if variant Bioseq_set is selected. More...
const TBioseq_set &	GetBioseq_set (void) const
	Get the variant data. More...
TBioseq_set &	SetBioseq_set (void)
	Select the variant. More...
void	SetBioseq_set (TBioseq_set &value)
	Select the variant and set its data. More...
bool	IsSeq_align_set (void) const
	Check if variant Seq_align_set is selected. More...
const TSeq_align_set &	GetSeq_align_set (void) const
	Get the variant data. More...
TSeq_align_set &	SetSeq_align_set (void)
	Select the variant. More...
void	SetSeq_align_set (TSeq_align_set &value)
	Select the variant and set its data. More...
bool	IsQuery_mask (void) const
	Check if variant Query_mask is selected. More...
const TQuery_mask &	GetQuery_mask (void) const
	Get the variant data. More...
TQuery_mask &	SetQuery_mask (void)
	Select the variant. More...
void	SetQuery_mask (TQuery_mask &value)
	Select the variant and set its data. 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_value_Base	Tparent

Private Member Functions
	CBlast4_value (const CBlast4_value &value)
CBlast4_value &	operator= (const CBlast4_value &value)

Additional Inherited Members
Public Types inherited from CBlast4_value_Base
enum	E_Choice {   e_not_set = 0 , e_Big_integer , e_Bioseq , e_Boolean ,   e_Cutoff , e_Integer , e_Matrix , e_Real ,   e_Seq_align , e_Seq_id , e_Seq_loc , e_Strand_type ,   e_String , e_Big_integer_list , e_Bioseq_list , e_Boolean_list ,   e_Cutoff_list , e_Integer_list , e_Matrix_list , e_Real_list ,   e_Seq_align_list , e_Seq_id_list , e_Seq_loc_list , e_Strand_type_list ,   e_String_list , e_Bioseq_set , e_Seq_align_set , e_Query_mask }
	Choice variants. More...
enum	E_ChoiceStopper { e_MaxChoice = 28 }
	Maximum+1 value of the choice variant enumerator. More...
typedef Int8	TBig_integer
typedef CBioseq	TBioseq
typedef bool	TBoolean
typedef CBlast4_cutoff	TCutoff
typedef int	TInteger
typedef CPssmWithParameters	TMatrix
typedef double	TReal
typedef CSeq_align	TSeq_align
typedef CSeq_id	TSeq_id
typedef CSeq_loc	TSeq_loc
typedef EBlast4_strand_type	TStrand_type
typedef string	TString
typedef list< Int8 >	TBig_integer_list
typedef list< CRef< CBioseq > >	TBioseq_list
typedef list< bool >	TBoolean_list
typedef list< CRef< CBlast4_cutoff > >	TCutoff_list
typedef list< int >	TInteger_list
typedef list< CRef< CPssmWithParameters > >	TMatrix_list
typedef list< double >	TReal_list
typedef list< CRef< CSeq_align > >	TSeq_align_list
typedef list< CRef< CSeq_id > >	TSeq_id_list
typedef list< CRef< CSeq_loc > >	TSeq_loc_list
typedef list< EBlast4_strand_type >	TStrand_type_list
typedef list< string >	TString_list
typedef CBioseq_set	TBioseq_set
typedef CSeq_align_set	TSeq_align_set
typedef CBlast4_mask	TQuery_mask
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 CBlast4_value_Base
static string	SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). 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

CBlast4_value –.

Definition at line 65 of file Blast4_value.hpp.

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

• include/objects/blast/Blast4_value.hpp
• src/objects/blast/Blast4_value.cpp