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

Inheritance diagram for SingleLinkage:

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

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

virtual	~SingleLinkage ()
	destructor More...

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

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

	~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 () const
	Ends the progress display. More...

Static Public Member Functions
static ClusterFunctor *	create ()
	creates a new instance of a SingleLinkage 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

SingleLinkage ClusterMethod.

The details of the method can be found in: SLINK: An optimally efficient algorithm for the single-link cluster method, The Computer Journal 1973 16(1):30-34; doi:10.1093/comjnl/16.1.30

See also: ClusterFunctor() base class.

Constructor & Destructor Documentation

◆ SingleLinkage() [1/2]

SingleLinkage ( )

default constructor

◆ SingleLinkage() [2/2]

SingleLinkage ( const SingleLinkage & source )

copy constructor

◆ ~SingleLinkage()

virtual ~SingleLinkage ( )

virtual

destructor

Member Function Documentation

◆ create()

static ClusterFunctor* create ( )

static

creates a new instance of a SingleLinkage 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

virtual

clusters the indices according to their respective element distances

Parameters

original_distance	DistanceMatrix<float> containing the distances of the elements to be clustered
cluster_tree	vector< BinaryTreeNode >, represents the clustering, each node contains the next two clusters merged and their distance, strict order is kept: left_child < right_child
threshold	float value to meet Base class interface, will not be used because algorithm used is considerably fast and does not work by growing distances

Exceptions

ClusterFunctor::InsufficientInput thrown if input is <2 The clustering method is single linkage, where the updated distances after merging two clusters are each the minimal distance between the elements of their clusters.

See also: ClusterFunctor , BinaryTreeNode

Implements ClusterFunctor.

◆ operator=()

SingleLinkage& operator= ( const SingleLinkage & source )

assignment operator

Public Member Functions

Static Public Member Functions

Additional Inherited Members