CMarkov_chain_array_Base Class Reference

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CMarkov_chain_array_Base –. More...

#include <algo/gnomon/Markov_chain_array_.hpp>

Inheritance diagram for CMarkov_chain_array_Base:

Collaboration diagram for CMarkov_chain_array_Base:

Public Types
enum class	E_memberIndex { e__allMandatory = 0 , e_in_exon , e_in_intron , e_matrix }
typedef int	TIn_exon
typedef int	TIn_intron
typedef list< CRef< CMarkov_chain_params > >	TMatrix
typedef Tparent::CMemberIndex< E_memberIndex, 4 >	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...

Public Member Functions
	CMarkov_chain_array_Base (void)
virtual	~CMarkov_chain_array_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetIn_exon (void) const
	Check if a value has been assigned to In_exon data member. More...
bool	CanGetIn_exon (void) const
	Check if it is safe to call GetIn_exon method. More...
void	ResetIn_exon (void)
	Reset In_exon data member. More...
TIn_exon	GetIn_exon (void) const
	Get the In_exon member data. More...
void	SetIn_exon (TIn_exon value)
	Assign a value to In_exon data member. More...
TIn_exon &	SetIn_exon (void)
	Assign a value to In_exon data member. More...
bool	IsSetIn_intron (void) const
	Check if a value has been assigned to In_intron data member. More...
bool	CanGetIn_intron (void) const
	Check if it is safe to call GetIn_intron method. More...
void	ResetIn_intron (void)
	Reset In_intron data member. More...
TIn_intron	GetIn_intron (void) const
	Get the In_intron member data. More...
void	SetIn_intron (TIn_intron value)
	Assign a value to In_intron data member. More...
TIn_intron &	SetIn_intron (void)
	Assign a value to In_intron data member. More...
bool	IsSetMatrix (void) const
	in-exon+in-intron elements Check if a value has been assigned to Matrix data member. More...
bool	CanGetMatrix (void) const
	Check if it is safe to call GetMatrix method. More...
void	ResetMatrix (void)
	Reset Matrix data member. More...
const TMatrix &	GetMatrix (void) const
	Get the Matrix member data. More...
TMatrix &	SetMatrix (void)
	Assign a value to Matrix 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 CSerialObject	Tparent

Private Member Functions
	CMarkov_chain_array_Base (const CMarkov_chain_array_Base &)
CMarkov_chain_array_Base &	operator= (const CMarkov_chain_array_Base &)

Private Attributes
Uint4	m_set_State [1]
int	m_In_exon
int	m_In_intron
list< CRef< CMarkov_chain_params > >	m_Matrix

Additional Inherited Members
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

CMarkov_chain_array_Base –.

Definition at line 76 of file Markov_chain_array_.hpp.

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

• include/algo/gnomon/Markov_chain_array_.hpp
• src/algo/gnomon/Markov_chain_array_.cpp