Search Toolkit Book for CClusterer::CSingleCluster

Single cluster. More...

#include <algo/cobalt/clusterer.hpp>

Inheritance diagram for CClusterer::CSingleCluster:

Collaboration diagram for CClusterer::CSingleCluster:

Public Types
typedef vector< int >::const_iterator	const_iterator

typedef vector< int >::iterator	iterator

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
	CSingleCluster (void)
	Create empty cluster. More...

void	AddElement (int el)
	Add element to the cluster. More...

void	clear (void)
	Removes all elements from the cluster. More...

void	SetPrototype (int el)
	Set cluster prototype. More...

int	GetPrototype (void) const
	Get cluster prototype. More...

void	SetMaxDistance (double dist)
	Set maximum distance in cluster. More...

double	GetMaxDistance (void) const
	Get maximum distance in cluster. More...

size_t	size (void) const
	Get cluster size. More...

int	FindCenterElement (const TDistMatrix &dmatrix) const
	Find element that is closest to the center of the cluster. More...

const vector< int > &	GetElements (void) const
	Get list of cluster elements. More...

int	operator[] (size_t index) const
	Get element. More...

const_iterator	begin (void) const

const_iterator	end (void) const

iterator	begin (void)

iterator	end (void)

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

Public Attributes
TPhyTreeNode *	m_Tree
	Cluster tree root. More...

vector< double >	m_DistToRoot
	Distances between cluster elements and tree root. More...

Protected Attributes
int	m_Prototype
	Index of cluster representative element. More...

double	m_Diameter
	Max distance between elements. More...

vector< int >	m_Elements
	List of indeces of cluster elements. 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

Single cluster.

Definition at line 74 of file clusterer.hpp.

Member Typedef Documentation

◆ const_iterator

typedef vector<int>::const_iterator CClusterer::CSingleCluster::const_iterator

Definition at line 77 of file clusterer.hpp.

◆ iterator

typedef vector<int>::iterator CClusterer::CSingleCluster::iterator

Definition at line 78 of file clusterer.hpp.

Constructor & Destructor Documentation

◆ CSingleCluster()

CClusterer::CSingleCluster::CSingleCluster ( void )

inline

Create empty cluster.

Definition at line 83 of file clusterer.hpp.

Member Function Documentation

◆ AddElement()

void CClusterer::CSingleCluster::AddElement ( int el )

inline

Add element to the cluster.

Parameters

el	Index of an element

Definition at line 88 of file clusterer.hpp.

Referenced by CClusterer::ComputeClusters(), CClusterer::x_CreateCluster(), CClusterer::x_JoinClusters(), and CClusterer::x_JoinElements().

◆ begin() [1/2]

iterator CClusterer::CSingleCluster::begin ( void )

inline

Definition at line 142 of file clusterer.hpp.

◆ begin() [2/2]

const_iterator CClusterer::CSingleCluster::begin ( void ) const

inline

Definition at line 140 of file clusterer.hpp.

◆ clear()

void CClusterer::CSingleCluster::clear ( void )

inline

Removes all elements from the cluster.

Definition at line 92 of file clusterer.hpp.

Referenced by CClusterer::x_JoinClusters().

◆ end() [1/2]

iterator CClusterer::CSingleCluster::end ( void )

inline

Definition at line 143 of file clusterer.hpp.

◆ end() [2/2]

const_iterator CClusterer::CSingleCluster::end ( void ) const

inline

Definition at line 141 of file clusterer.hpp.

◆ FindCenterElement()

int CClusterer::CSingleCluster::FindCenterElement ( const TDistMatrix & dmatrix ) const

Find element that is closest to the center of the cluster.

Parameters

dmatrix Full distance matrix used to cluster data

Returns: Index of element that has smallest distance to all other elements

Definition at line 1184 of file clusterer.cpp.

References i, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE().

◆ GetElements()

const vector<int>& CClusterer::CSingleCluster::GetElements ( void ) const

inline

Get list of cluster elements.

Returns: Cluster elements

Definition at line 130 of file clusterer.hpp.

◆ GetMaxDistance()

double CClusterer::CSingleCluster::GetMaxDistance ( void ) const

inline

Get maximum distance in cluster.

Returns: Maximum distance in cluster

Definition at line 113 of file clusterer.hpp.

◆ GetPrototype()

int CClusterer::CSingleCluster::GetPrototype ( void ) const

inline

Get cluster prototype.

Returns: Index of element used as cluster prototype

Definition at line 103 of file clusterer.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CMultiAligner::x_AddRpsFreqsToCluster(), CMultiAligner::x_AlignInClusters(), CMultiAligner::x_BuildFullTree(), x_GetClusterGapLocations(), and CMultiAligner::x_MakeClusterResidueFrequencies().

◆ operator[]()

int CClusterer::CSingleCluster::operator[] ( size_t index ) const

Get element.

Parameters

index Element index

Returns: Element

Definition at line 1173 of file clusterer.cpp.

References m_Elements, and NCBI_THROW.

◆ SetMaxDistance()

void CClusterer::CSingleCluster::SetMaxDistance ( double dist )

inline

Set maximum distance in cluster.

Parameters

dist	Maximum distance

Definition at line 108 of file clusterer.hpp.

Referenced by CClusterer::x_JoinElements().

◆ SetPrototype()

void CClusterer::CSingleCluster::SetPrototype ( int el )

inline

Set cluster prototype.

Parameters

el	Index of element to be used as cluster prototype

Prototype does not have to belong to the cluster

Definition at line 98 of file clusterer.hpp.

◆ size()

size_t CClusterer::CSingleCluster::size ( void ) const

inline

Get cluster size.

Returns: Number of elements in the cluster

Definition at line 118 of file clusterer.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CClusterer::ComputeClustersFromLinks(), CClusterer::GetClusterDistMatrix(), s_FindDistAsMax(), s_FindDistAsMean(), s_FindMaxDistFromElem(), s_FindSumDistFromElem(), s_MakeTwoLeafTree(), s_SetLeafIds(), s_TestClusterTree(), CMultiAligner::x_ComputeClusterTrees(), CMultiAligner::x_FindQueryClusters(), CClusterer::x_JoinClusters(), and CMultiAligner::x_MakeClusterResidueFrequencies().

Member Data Documentation

◆ m_Diameter

double CClusterer::CSingleCluster::m_Diameter

protected

Max distance between elements.

Definition at line 147 of file clusterer.hpp.

◆ m_DistToRoot

vector<double> CClusterer::CSingleCluster::m_DistToRoot

Distances between cluster elements and tree root.

Definition at line 156 of file clusterer.hpp.

Referenced by CClusterer::x_JoinClusters().

◆ m_Elements

vector<int> CClusterer::CSingleCluster::m_Elements

protected

List of indeces of cluster elements.

Definition at line 148 of file clusterer.hpp.

Referenced by operator[]().

◆ m_Prototype

int CClusterer::CSingleCluster::m_Prototype

protected

Index of cluster representative element.

Definition at line 146 of file clusterer.hpp.

◆ m_Tree

TPhyTreeNode* CClusterer::CSingleCluster::m_Tree

Cluster tree root.

Definition at line 153 of file clusterer.hpp.

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

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

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

Public Types

Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ iterator

Constructor & Destructor Documentation

◆ CSingleCluster()

Member Function Documentation

◆ AddElement()

◆ begin() [1/2]

◆ begin() [2/2]

◆ clear()

◆ end() [1/2]

◆ end() [2/2]

◆ FindCenterElement()

◆ GetElements()

◆ GetMaxDistance()

◆ GetPrototype()

◆ operator[]()

◆ SetMaxDistance()

◆ SetPrototype()

◆ size()

Member Data Documentation

◆ m_Diameter

◆ m_DistToRoot

◆ m_Elements

◆ m_Prototype

◆ m_Tree