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AverageLinkage Class Reference
[Clustering]

AverageLinkage ClusterMethod. More...

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

Inheritance diagram for AverageLinkage:
ClusterFunctor ProgressLogger

List of all members.

Public Member Functions

 AverageLinkage ()
 default constructor
 AverageLinkage (const AverageLinkage &source)
 copy constructor
virtual ~AverageLinkage ()
 destructor
AverageLinkage & operator= (const AverageLinkage &source)
 assignment operator
void operator() (DistanceMatrix< Real > &original_distance, std::vector< BinaryTreeNode > &cluster_tree, const Real threshold=1) const
 clusters the indices according to their respective element distances

Static Public Member Functions

static ClusterFunctor * create ()
 creates a new instance of a AverageLinkage object
static const String getProductName ()
 get the identifier for this object

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 (  ) 

default constructor

AverageLinkage ( const AverageLinkage &  source  ) 

copy constructor

virtual ~AverageLinkage (  )  [virtual]

destructor

Member Function Documentation

static ClusterFunctor* create (  )  [inline, static]

creates a new instance of a AverageLinkage object

static const String getProductName (  )  [inline, static]

get the identifier for this object

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

clusters the indices according to their respective element distances

Parameters:
original_distance DistanceMatrix<Real> 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 Real 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 theshold is exceeded, cluster_tree is filled with dummy clusteringsteps (children: (0,1), distance: -1) to the root.
See also:
ClusterFunctor , BinaryTreeNode
AverageLinkage& operator= ( const AverageLinkage &  source  ) 

assignment operator

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1