#include <OpenMS/COMPARISON/CLUSTERING/AverageLinkage.h>

Inheritance diagram for AverageLinkage:

Collaboration diagram for AverageLinkage:

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

	AverageLinkage (const AverageLinkage &source)
	copy constructor More...

	~AverageLinkage () override
	destructor More...

AverageLinkage &	operator= (const AverageLinkage &source)
	assignment operator More...

void	operator() (DistanceMatrix< float > &original_distance, std::vector< BinaryTreeNode > &cluster_tree, const float threshold=1) const override
	clusters the indices according to their respective element distances More...

Public Member Functions inherited from ClusterFunctor
	ClusterFunctor ()
	default constructor More...

	ClusterFunctor (const ClusterFunctor &source)
	copy constructor More...

virtual	~ClusterFunctor ()
	destructor More...

ClusterFunctor &	operator= (const ClusterFunctor &source)
	assignment operator More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Member Functions
static ClusterFunctor *	create ()
	creates a new instance of a AverageLinkage object More...

static const String	getProductName ()
	get the identifier for this object More...

Static Public Member Functions inherited from ClusterFunctor
static void	registerChildren ()
	registers all derived products More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

AverageLinkage ClusterMethod.

The details of the method can be found in: Backhaus, Erichson, Plinke, Weiber Multivariate Analysemethoden, Springer 2000 and Ellen M. Voorhees: Implementing agglomerative hierarchic clustering algorithms for use in document retrieval. Inf. Process. Manage. 22(6): 465-476 (1986)

See also: ClusterFunctor

Constructor & Destructor Documentation

◆ AverageLinkage() [1/2]

AverageLinkage ( )

default constructor

◆ AverageLinkage() [2/2]

AverageLinkage ( const AverageLinkage & source )

copy constructor

◆ ~AverageLinkage()

~AverageLinkage ( )

override

destructor

Member Function Documentation

◆ create()

static ClusterFunctor* create ( )

static

creates a new instance of a AverageLinkage object

◆ getProductName()

static const String getProductName ( )

static

get the identifier for this object

◆ operator()()

void operator()	(	DistanceMatrix< float > &	original_distance,
		std::vector< BinaryTreeNode > &	cluster_tree,
		const float	threshold = `1`
	)		const

overridevirtual

clusters the indices according to their respective element distances

Parameters

original_distance	DistanceMatrix<float> containing the distances of the elements to be clustered, will be changed during clustering process, make sure to have a copy or be able to redo
cluster_tree	vector< BinaryTreeNode >, represents the clustering, each node contains the next merged clusters (not element indices) and their distance, strict order is kept: left_child < right_child
threshold	float value, the minimal distance from which on cluster merging is considered unrealistic. By default set to 1, i.e. complete clustering until only one cluster remains

Exceptions

ClusterFunctor::InsufficientInput thrown if input is <2 The clustering method is average linkage, where the updated distances after merging two clusters are each the average distances between the elements of their clusters. After threshold is exceeded, cluster_tree is filled with dummy clusteringsteps (children: (0,1), distance: -1) to the root.

See also: ClusterFunctor , BinaryTreeNode

Implements ClusterFunctor.

◆ operator=()

AverageLinkage& operator= ( const AverageLinkage & source )

assignment operator

Public Member Functions

Static Public Member Functions

Additional Inherited Members