CAlgorithm_type Class Reference

Represents ASN.1 type Algorithm-type defined in file cdd.asn

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CAlgorithm_type –. More...

#include <objects/cdd/Algorithm_type.hpp>

Inheritance diagram for CAlgorithm_type:

Collaboration diagram for CAlgorithm_type:

Public Member Functions
	CAlgorithm_type (void)
	~CAlgorithm_type (void)
Public Member Functions inherited from CAlgorithm_type_Base
	CAlgorithm_type_Base (void)
virtual	~CAlgorithm_type_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetScoring_Scheme (void) const
	Check if a value has been assigned to Scoring_Scheme data member. More...
bool	CanGetScoring_Scheme (void) const
	Check if it is safe to call GetScoring_Scheme method. More...
void	ResetScoring_Scheme (void)
	Reset Scoring_Scheme data member. More...
TScoring_Scheme	GetScoring_Scheme (void) const
	Get the Scoring_Scheme member data. More...
void	SetScoring_Scheme (TScoring_Scheme value)
	Assign a value to Scoring_Scheme data member. More...
TScoring_Scheme &	SetScoring_Scheme (void)
	Assign a value to Scoring_Scheme data member. More...
bool	IsSetClustering_Method (void) const
	Check if a value has been assigned to Clustering_Method data member. More...
bool	CanGetClustering_Method (void) const
	Check if it is safe to call GetClustering_Method method. More...
void	ResetClustering_Method (void)
	Reset Clustering_Method data member. More...
TClustering_Method	GetClustering_Method (void) const
	Get the Clustering_Method member data. More...
void	SetClustering_Method (TClustering_Method value)
	Assign a value to Clustering_Method data member. More...
TClustering_Method &	SetClustering_Method (void)
	Assign a value to Clustering_Method data member. More...
bool	IsSetScore_Matrix (void) const
	Check if a value has been assigned to Score_Matrix data member. More...
bool	CanGetScore_Matrix (void) const
	Check if it is safe to call GetScore_Matrix method. More...
void	ResetScore_Matrix (void)
	Reset Score_Matrix data member. More...
TScore_Matrix	GetScore_Matrix (void) const
	Get the Score_Matrix member data. More...
void	SetScore_Matrix (TScore_Matrix value)
	Assign a value to Score_Matrix data member. More...
TScore_Matrix &	SetScore_Matrix (void)
	Assign a value to Score_Matrix data member. More...
bool	IsSetGapOpen (void) const
	Check if a value has been assigned to GapOpen data member. More...
bool	CanGetGapOpen (void) const
	Check if it is safe to call GetGapOpen method. More...
void	ResetGapOpen (void)
	Reset GapOpen data member. More...
TGapOpen	GetGapOpen (void) const
	Get the GapOpen member data. More...
void	SetGapOpen (TGapOpen value)
	Assign a value to GapOpen data member. More...
TGapOpen &	SetGapOpen (void)
	Assign a value to GapOpen data member. More...
bool	IsSetGapExtend (void) const
	Check if a value has been assigned to GapExtend data member. More...
bool	CanGetGapExtend (void) const
	Check if it is safe to call GetGapExtend method. More...
void	ResetGapExtend (void)
	Reset GapExtend data member. More...
TGapExtend	GetGapExtend (void) const
	Get the GapExtend member data. More...
void	SetGapExtend (TGapExtend value)
	Assign a value to GapExtend data member. More...
TGapExtend &	SetGapExtend (void)
	Assign a value to GapExtend data member. More...
bool	IsSetGapScaleFactor (void) const
	Check if a value has been assigned to GapScaleFactor data member. More...
bool	CanGetGapScaleFactor (void) const
	Check if it is safe to call GetGapScaleFactor method. More...
void	ResetGapScaleFactor (void)
	Reset GapScaleFactor data member. More...
TGapScaleFactor	GetGapScaleFactor (void) const
	Get the GapScaleFactor member data. More...
void	SetGapScaleFactor (TGapScaleFactor value)
	Assign a value to GapScaleFactor data member. More...
TGapScaleFactor &	SetGapScaleFactor (void)
	Assign a value to GapScaleFactor data member. More...
bool	IsSetNTerminalExt (void) const
	Check if a value has been assigned to NTerminalExt data member. More...
bool	CanGetNTerminalExt (void) const
	Check if it is safe to call GetNTerminalExt method. More...
void	ResetNTerminalExt (void)
	Reset NTerminalExt data member. More...
TNTerminalExt	GetNTerminalExt (void) const
	Get the NTerminalExt member data. More...
void	SetNTerminalExt (TNTerminalExt value)
	Assign a value to NTerminalExt data member. More...
TNTerminalExt &	SetNTerminalExt (void)
	Assign a value to NTerminalExt data member. More...
bool	IsSetCTerminalExt (void) const
	Check if a value has been assigned to CTerminalExt data member. More...
bool	CanGetCTerminalExt (void) const
	Check if it is safe to call GetCTerminalExt method. More...
void	ResetCTerminalExt (void)
	Reset CTerminalExt data member. More...
TCTerminalExt	GetCTerminalExt (void) const
	Get the CTerminalExt member data. More...
void	SetCTerminalExt (TCTerminalExt value)
	Assign a value to CTerminalExt data member. More...
TCTerminalExt &	SetCTerminalExt (void)
	Assign a value to CTerminalExt data member. More...
bool	IsSetTree_scope (void) const
	Check if a value has been assigned to Tree_scope data member. More...
bool	CanGetTree_scope (void) const
	Check if it is safe to call GetTree_scope method. More...
void	ResetTree_scope (void)
	Reset Tree_scope data member. More...
TTree_scope	GetTree_scope (void) const
	Get the Tree_scope member data. More...
void	SetTree_scope (TTree_scope value)
	Assign a value to Tree_scope data member. More...
TTree_scope &	SetTree_scope (void)
	Assign a value to Tree_scope data member. More...
bool	IsSetColoring_scope (void) const
	Check if a value has been assigned to Coloring_scope data member. More...
bool	CanGetColoring_scope (void) const
	Check if it is safe to call GetColoring_scope method. More...
void	ResetColoring_scope (void)
	Reset Coloring_scope data member. More...
TColoring_scope	GetColoring_scope (void) const
	Get the Coloring_scope member data. More...
void	SetColoring_scope (TColoring_scope value)
	Assign a value to Coloring_scope data member. More...
TColoring_scope &	SetColoring_scope (void)
	Assign a value to Coloring_scope data member. More...
virtual void	Reset (void)
	Reset the whole object. 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 CAlgorithm_type_Base	Tparent

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

Additional Inherited Members
Public Types inherited from CAlgorithm_type_Base
enum	EScoring_Scheme {   eScoring_Scheme_unassigned = 0 , eScoring_Scheme_percent_id = 1 , eScoring_Scheme_kimura_corrected = 2 , eScoring_Scheme_aligned_score = 3 ,   eScoring_Scheme_aligned_score_ext = 4 , eScoring_Scheme_aligned_score_filled = 5 , eScoring_Scheme_blast_footprint = 6 , eScoring_Scheme_blast_full = 7 ,   eScoring_Scheme_hybrid_aligned_score = 8 , eScoring_Scheme_other = 255 }
enum	EClustering_Method {   eClustering_Method_unassigned = 0 , eClustering_Method_single_linkage = 1 , eClustering_Method_neighbor_joining = 2 , eClustering_Method_fast_minimum_evolution = 3 ,   eClustering_Method_other = 255 }
enum	EScore_Matrix {   eScore_Matrix_unassigned = 0 , eScore_Matrix_blosum45 = 1 , eScore_Matrix_blosum62 = 2 , eScore_Matrix_blosum80 = 3 ,   eScore_Matrix_pam30 = 4 , eScore_Matrix_pam70 = 5 , eScore_Matrix_pam250 = 6 , eScore_Matrix_other = 255 }
enum	ETree_scope { eTree_scope_allDescendants = 0 , eTree_scope_immediateChildrenOnly = 1 , eTree_scope_selfOnly = 2 , eTree_scope_other = 255 }
enum	EColoring_scope { eColoring_scope_allDescendants = 0 , eColoring_scope_immediateChildrenOnly = 1 , eColoring_scope_other = 255 }
enum class	E_memberIndex {   e__allMandatory = 0 , e_scoring_Scheme , e_clustering_Method , e_score_Matrix ,   e_gapOpen , e_gapExtend , e_gapScaleFactor , e_nTerminalExt ,   e_cTerminalExt , e_tree_scope , e_coloring_scope }
typedef int	TScoring_Scheme
typedef int	TClustering_Method
typedef int	TScore_Matrix
typedef int	TGapOpen
typedef int	TGapExtend
typedef int	TGapScaleFactor
typedef int	TNTerminalExt
typedef int	TCTerminalExt
typedef int	TTree_scope
typedef int	TColoring_scope
typedef Tparent::CMemberIndex< E_memberIndex, 11 >	TmemberIndex
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 CAlgorithm_type_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EScoring_Scheme (void)
	Access to EScoring_Scheme's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EClustering_Method (void)
	Access to EClustering_Method's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EScore_Matrix (void)
	Access to EScore_Matrix's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ETree_scope (void)
	Access to ETree_scope's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EColoring_scope (void)
	Access to EColoring_scope's attributes (values, names) as defined in spec. 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

CAlgorithm_type –.

Definition at line 65 of file Algorithm_type.hpp.

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

• include/objects/cdd/Algorithm_type.hpp
• src/objects/cdd/Algorithm_type.cpp