Sufficient extra functionality is needed from CRange that it justifies extending the class. More...

#include <algo/cobalt/base.hpp>

Inheritance diagram for CLocalRange< Position >:

Collaboration diagram for CLocalRange< Position >:

Public Types
typedef CRange< Position >	TParent
	parent class More...

typedef TParent::position_type	position_type
	underlying type More...

typedef CLocalRange< Position >	TThisType
	shorthand More...

Public Types inherited from CRange< Position >
typedef COpenRange< Position >	TParent

typedef TParent::position_type	position_type

typedef CRange< Position >	TThisType

Public Types inherited from CRange_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_from , e_to }

typedef int	TFrom

typedef int	TTo

typedef Tparent::CMemberIndex< E_memberIndex, 3 >	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 Types inherited from COpenRange< Position >
typedef Position	position_type

typedef COpenRange< Position >	TThisType

Public Member Functions
	CLocalRange ()
	default constructor More...

	CLocalRange (position_type from, position_type to)
	convert offsets into a range More...

	CLocalRange (const TParent &range)
	convert parent class to a range More...

bool	Contains (const TThisType &r)
	Test whether 'this' completely envelops a given sequence range. More...

bool	StrictlyBelow (const TThisType &r)
	Test whether 'this' represents a sequence range strictly less than a given sequence range. More...

void	SetEmpty ()
	Initialize an empty range. More...

Public Member Functions inherited from CRange< Position >
	CRange (void)

	~CRange (void)

	CRange (void)

	CRange (position_type from, position_type to)

	CRange (const TParent &range)

TThisType &	operator= (const TParent &range)

Public Member Functions inherited from CRange_Base
	CRange_Base (void)

virtual	~CRange_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetFrom (void) const
	Beginning of masked range (one-offset) Check if a value has been assigned to From data member. More...

bool	CanGetFrom (void) const
	Check if it is safe to call GetFrom method. More...

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

TFrom	GetFrom (void) const
	Get the From member data. More...

void	SetFrom (TFrom value)
	Assign a value to From data member. More...

TFrom &	SetFrom (void)
	Assign a value to From data member. More...

bool	IsSetTo (void) const
	End of masked range (one-offset) Check if a value has been assigned to To data member. More...

bool	CanGetTo (void) const
	Check if it is safe to call GetTo method. More...

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

TTo	GetTo (void) const
	Get the To member data. More...

void	SetTo (TTo value)
	Assign a value to To data member. More...

TTo &	SetTo (void)
	Assign a value to To 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

Public Member Functions inherited from COpenRange< Position >
	COpenRange (void)

	COpenRange (position_type from, position_type toOpen)

position_type	GetFrom (void) const

position_type	GetToOpen (void) const

position_type	GetTo (void) const

bool	Empty (void) const

bool	NotEmpty (void) const

position_type	GetLength (void) const

TThisType &	SetFrom (position_type from)

TThisType &	SetToOpen (position_type toOpen)

TThisType &	SetTo (position_type to)

TThisType &	SetOpen (position_type from, position_type toOpen)

TThisType &	Set (position_type from, position_type to)

TThisType &	SetLength (position_type length)

TThisType &	SetLengthDown (position_type length)

bool	operator== (const TThisType &r) const

bool	operator!= (const TThisType &r) const

bool	operator< (const TThisType &r) const

bool	operator<= (const TThisType &r) const

bool	operator> (const TThisType &r) const

bool	operator>= (const TThisType &r) const

bool	IsWholeFrom (void) const

bool	IsWholeTo (void) const

bool	IsWhole (void) const

TThisType	IntersectionWith (const TThisType &r) const

TThisType &	IntersectWith (const TThisType &r)

TThisType	operator& (const TThisType &r) const

TThisType &	operator&= (const TThisType &r)

bool	IntersectingWith (const TThisType &r) const

bool	AbuttingWith (const TThisType &r) const

TThisType &	CombineWith (const TThisType &r)

TThisType	CombinationWith (const TThisType &r) const

TThisType &	operator+= (const TThisType &r)

TThisType	operator+ (const TThisType &r) const

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 Member Functions inherited from COpenRange< Position >
static position_type	GetPositionMin (void)

static position_type	GetPositionMax (void)

static position_type	GetWholeFrom (void)

static position_type	GetWholeToOpen (void)

static position_type	GetWholeTo (void)

static position_type	GetWholeLength (void)

static TThisType	GetWhole (void)

static position_type	GetEmptyFrom (void)

static position_type	GetEmptyToOpen (void)

static position_type	GetEmptyTo (void)

static position_type	GetEmptyLength (void)

static TThisType	GetEmpty (void)

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

template<class Position>
class CLocalRange< Position >

Sufficient extra functionality is needed from CRange that it justifies extending the class.

Definition at line 57 of file base.hpp.

Member Typedef Documentation

◆ position_type

template<class Position >

typedef TParent::position_type CLocalRange< Position >::position_type

underlying type

Definition at line 61 of file base.hpp.

◆ TParent

template<class Position >

typedef CRange<Position> CLocalRange< Position >::TParent

parent class

Definition at line 60 of file base.hpp.

◆ TThisType

template<class Position >

typedef CLocalRange<Position> CLocalRange< Position >::TThisType

shorthand

Definition at line 62 of file base.hpp.

Constructor & Destructor Documentation

◆ CLocalRange() [1/3]

template<class Position >

CLocalRange< Position >::CLocalRange ( )

inline

default constructor

Definition at line 65 of file base.hpp.

◆ CLocalRange() [2/3]

template<class Position >

CLocalRange< Position >::CLocalRange	(	position_type	from,
		position_type	to
	)

inline

convert offsets into a range

Parameters

from	Start offset
to	End offset

Definition at line 71 of file base.hpp.

◆ CLocalRange() [3/3]

template<class Position >

CLocalRange< Position >::CLocalRange ( const TParent & range )

inline

convert parent class to a range

Parameters

range Reference to an object of the parent class

Definition at line 77 of file base.hpp.

Member Function Documentation

◆ Contains()

template<class Position >

bool CLocalRange< Position >::Contains ( const TThisType & r )

inline

Test whether 'this' completely envelops a given sequence range.

Parameters

r	Range to test for containment

Returns: true if 'this' envelops r, false otherwise

Definition at line 85 of file base.hpp.

Referenced by CHit::GetRangeFromSeq1(), CHit::GetRangeFromSeq2(), and x_RemoveEnvelopedSubHits().

◆ SetEmpty()

template<class Position >

void CLocalRange< Position >::SetEmpty ( )

inline

Initialize an empty range.

Definition at line 107 of file base.hpp.

◆ StrictlyBelow()

template<class Position >

bool CLocalRange< Position >::StrictlyBelow ( const TThisType & r )

inline

Test whether 'this' represents a sequence range strictly less than a given sequence range.

Parameters

r	Range to test for disjointness

Returns: true if offsets of 'this' are strictly below the offsets of r, false otherwise

Definition at line 100 of file base.hpp.

Referenced by CHit::ResolveSubHitConflicts(), CMultiAligner::x_FindBestPath(), CMultiAligner::x_FindConstraints(), and x_RemoveEnvelopedSubHits().

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

include/algo/cobalt/base.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

template<class Position> class CLocalRange< Position >

Member Typedef Documentation

◆ position_type

◆ TParent

◆ TThisType

Constructor & Destructor Documentation

◆ CLocalRange() [1/3]

◆ CLocalRange() [2/3]

◆ CLocalRange() [3/3]

Member Function Documentation

◆ Contains()

◆ SetEmpty()

◆ StrictlyBelow()

template<class Position>
class CLocalRange< Position >