Set of edges with weights between nodes represented by zero-based positive integers. More...

#include <algo/cobalt/links.hpp>

Inheritance diagram for CLinks:

Collaboration diagram for CLinks:

Classes
struct	SLink
	Single link. More...

Public Types
typedef list< SLink >::const_iterator	SLink_CI

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
	CLinks (Uint4 num_elements)
	Constructor. More...

	~CLinks ()
	Destructor. More...

void	AddLink (int first, int second, double weight)
	Add link. More...

bool	IsLink (int first, int second) const
	Check if link exists between given two nodes. More...

bool	IsLink (const vector< int > &first, const vector< int > &second, double &dist) const
	Check if links exist between all pairs of elemens from two sets. More...

bool	IsSorted (void) const
	Check whether the links are sorted according to weights. More...

void	Sort (void)
	Sort links according to weights in ascending order. More...

Uint4	GetNumElements (void) const
	Get number of nodes. More...

Uint4	GetNumLinks (void) const
	Get number of links. More...

double	GetMaxWeight (void) const
	Get maximum weight over all links. More...

SLink_CI	begin (void) const
	Get iterator pointing to the first link. More...

SLink_CI	end (void) const
	Get iterator pointing behind the last link. 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...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. 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

Protected Attributes
list< SLink >	m_Links
	Links. More...

vector< SLink * >	m_LinkPtrs
	Pointers to links in m_Links sorted according to node indexes; used for checks whether a link exists. More...

Uint4	m_NumElements
	Number of nodes. More...

Uint4	m_NumLinks
	Number of links. More...

bool	m_IsSorted
	Is list of links sorted. More...

double	m_MaxWeight
	Maximym weight in the list. More...

Private Member Functions
	CLinks (const CLinks &links)
	Forbid copy constructor. More...

CLinks &	operator= (const CLinks &links)
	Forbid assignment operator. More...

void	x_InitLinkPtrs (void)
	Initialize secondary list of link pointers. More...

bool	x_IsLinkPtr (int first, int second) const
	Check if link exists by searching list of link pointers sorted by node indexes. More...

const CLinks::SLink *	x_GetLink (int first, int second) const
	Get link by node ids. More...

Additional Inherited Members
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 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

Set of edges with weights between nodes represented by zero-based positive integers.

Definition at line 52 of file links.hpp.

Member Typedef Documentation

◆ SLink_CI

typedef list<SLink>::const_iterator CLinks::SLink_CI

Definition at line 69 of file links.hpp.

Constructor & Destructor Documentation

◆ CLinks() [1/2]

CLinks::CLinks ( Uint4 num_elements )

inline

Constructor.

Parameters

num_elements Number of nodes (not necessary connected) [in] [in] table

Definition at line 77 of file links.hpp.

◆ ~CLinks()

CLinks::~CLinks ( )

Destructor.

Definition at line 57 of file links.cpp.

◆ CLinks() [2/2]

CLinks::CLinks ( const CLinks & links )

private

Forbid copy constructor.

Member Function Documentation

◆ AddLink()

void CLinks::AddLink	(	int	first,
		int	second,
		double	weight
	)

Add link.

Parameters

first	Node number [in]
second	Node number [in]
weight	Link weight [in]

The links are assumed to be undirected. All nodes are stored such that first < second, if the inputs are different the nodes will be swaped. The method does not check whether given link already exists. Adding two links between the same nodes may cause unexpected results.

Definition at line 60 of file links.cpp.

References first(), m_IsSorted, m_Links, m_MaxWeight, m_NumElements, m_NumLinks, NCBI_THROW, swap(), and weight.

Referenced by BOOST_AUTO_TEST_CASE(), TKmerMethods< TKmerCounts >::ComputeDistLinks(), and CMultiAligner::x_FindQueryClusters().

◆ begin()

SLink_CI CLinks::begin ( void ) const

inline

Get iterator pointing to the first link.

Returns: Link iterator

Definition at line 144 of file links.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CClusterer::ComputeClustersFromLinks().

◆ end()

SLink_CI CLinks::end ( void ) const

inline

Get iterator pointing behind the last link.

Returns: Link iterator

Definition at line 149 of file links.hpp.

Referenced by CClusterer::ComputeClustersFromLinks().

◆ GetMaxWeight()

double CLinks::GetMaxWeight ( void ) const

inline

Get maximum weight over all links.

Returns: Maxium weight

Definition at line 139 of file links.hpp.

◆ GetNumElements()

Uint4 CLinks::GetNumElements ( void ) const

inline

Get number of nodes.

Returns: Number of nodes

Definition at line 129 of file links.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CClusterer::ComputeClustersFromLinks().

◆ GetNumLinks()

Uint4 CLinks::GetNumLinks ( void ) const

inline

Get number of links.

Returns: Number of links

Definition at line 134 of file links.hpp.

◆ IsLink() [1/2]

bool CLinks::IsLink	(	const vector< int > &	first,
		const vector< int > &	second,
		double &	dist
	)		const

Check if links exist between all pairs of elemens from two sets.

Existence of links whithin the sets is not checked.

Parameters

first	List of elements for the first set [in]
second	List of elements for the second set [in]
dist	Average distance between elements of the two sets [out]

Returns: true if links between all pairs exist, false otherwise

The existance of a link is checked by doing binary search in sorted list of links

Definition at line 99 of file links.cpp.

References ITERATE, m_IsSorted, NCBI_THROW, CLinks::SLink::weight, and x_GetLink().

◆ IsLink() [2/2]

bool CLinks::IsLink	(	int	first,
		int	second
	)		const

Check if link exists between given two nodes.

Parameters

first	Node number [in]
second	Node number [in]

Returns: True if link exists, false otherwise

The link is checked by doing binary search in sorted list of links

Definition at line 81 of file links.cpp.

References first(), m_IsSorted, m_NumElements, NCBI_THROW, swap(), and x_IsLinkPtr().

Referenced by BOOST_AUTO_TEST_CASE(), CClusterer::x_CanAddElem(), and CClusterer::x_CanJoinClusters().

◆ IsSorted()

bool CLinks::IsSorted ( void ) const

inline

Check whether the links are sorted according to weights.

Returns: True if links are sorted, false otherwise

Definition at line 120 of file links.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CClusterer::ComputeClustersFromLinks().

◆ operator=()

CLinks& CLinks::operator= ( const CLinks & links )

private

Forbid assignment operator.

◆ Sort()

void CLinks::Sort ( void )

Sort links according to weights in ascending order.

Definition at line 124 of file links.cpp.

References m_IsSorted, m_Links, and x_InitLinkPtrs().

Referenced by BOOST_AUTO_TEST_CASE(), CClusterer::ComputeClustersFromLinks(), and CMultiAligner::x_FindQueryClusters().

◆ x_GetLink()

const CLinks::SLink * CLinks::x_GetLink	(	int	first,
		int	second
	)		const

private

Get link by node ids.

Parameters

first	First node
second	Second node

Returns: Pointer to the link or NULL if link does not exist

Definition at line 158 of file links.cpp.

References _ASSERT, compare_links_by_nodes(), first(), m_LinkPtrs, NULL, and swap().

Referenced by IsLink().

◆ x_InitLinkPtrs()

void CLinks::x_InitLinkPtrs ( void )

private

Initialize secondary list of link pointers.

Definition at line 135 of file links.cpp.

References compare_links_by_nodes(), m_LinkPtrs, m_Links, NON_CONST_ITERATE, and ct::sort().

Referenced by Sort().

◆ x_IsLinkPtr()

bool CLinks::x_IsLinkPtr	(	int	first,
		int	second
	)		const

private

Check if link exists by searching list of link pointers sorted by node indexes.

Parameters

first	Node number [in]
second	Node number [in]

Returns: True if link exists, false otherwise

Definition at line 148 of file links.cpp.

References _ASSERT, compare_links_by_nodes(), first(), and m_LinkPtrs.

Referenced by IsLink().

Member Data Documentation

◆ m_IsSorted

bool CLinks::m_IsSorted

protected

Is list of links sorted.

Definition at line 190 of file links.hpp.

Referenced by AddLink(), IsLink(), and Sort().

◆ m_LinkPtrs

vector<SLink*> CLinks::m_LinkPtrs

protected

Pointers to links in m_Links sorted according to node indexes; used for checks whether a link exists.

Definition at line 181 of file links.hpp.

Referenced by x_GetLink(), x_InitLinkPtrs(), and x_IsLinkPtr().

◆ m_Links

list<SLink> CLinks::m_Links

protected

Links.

Definition at line 177 of file links.hpp.

Referenced by AddLink(), Sort(), and x_InitLinkPtrs().

◆ m_MaxWeight

double CLinks::m_MaxWeight

protected

Maximym weight in the list.

Definition at line 193 of file links.hpp.

Referenced by AddLink().

◆ m_NumElements

Uint4 CLinks::m_NumElements

protected

Number of nodes.

Definition at line 184 of file links.hpp.

Referenced by AddLink(), and IsLink().

◆ m_NumLinks

Uint4 CLinks::m_NumLinks

protected

Number of links.

Definition at line 187 of file links.hpp.

Referenced by AddLink().

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

include/algo/cobalt/links.hpp
src/algo/cobalt/links.cpp

Classes

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SLink_CI

Constructor & Destructor Documentation

◆ CLinks() [1/2]

◆ ~CLinks()

◆ CLinks() [2/2]

Member Function Documentation

◆ AddLink()

◆ begin()

◆ end()

◆ GetMaxWeight()

◆ GetNumElements()

◆ GetNumLinks()

◆ IsLink() [1/2]

◆ IsLink() [2/2]

◆ IsSorted()

◆ operator=()

◆ Sort()

◆ x_GetLink()

◆ x_InitLinkPtrs()

◆ x_IsLinkPtr()

Member Data Documentation

◆ m_IsSorted

◆ m_LinkPtrs

◆ m_Links

◆ m_MaxWeight

◆ m_NumElements

◆ m_NumLinks