| OpenMS 2.5.0

Classes | Functions
Clustering
Analysis

This class contains SpectraClustering classes These classes are components for clustering all kinds of data for which a distance relation, normalizable in the range of [0,1], is available. Mainly this will be data for which there is a corresponding CompareFunctor given (e.g. PeakSpectrum) that is yielding the similarity normalized in the range of [0,1] of such two elements, so it can easily converted to the needed distances. More...

## Classes

class | AverageLinkage
| AverageLinkage ClusterMethod. More...
class | ClusterAnalyzer
| Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) More...
class | ClusterFunctor
| Base class for cluster functors. More...
class | ClusterHierarchical
| Hierarchical clustering with generic clustering functions. More...
class | CompleteLinkage
| CompleteLinkage ClusterMethod. More...
class | SingleLinkage
| SingleLinkage ClusterMethod. More...

## Functions

void | cluster (std::vector< PeakSpectrum > &data, const BinnedSpectrumCompareFunctor &comparator, double sz, UInt sp, float offset, const ClusterFunctor &clusterer, std::vector< BinaryTreeNode > &cluster_tree, DistanceMatrix< float > &original_distance)
| clustering function for binned PeakSpectrum More...

## Detailed Description

This class contains SpectraClustering classes These classes are components for clustering all kinds of data for which a distance relation, normalizable in the range of [0,1], is available. Mainly this will be data for which there is a corresponding CompareFunctor given (e.g. PeakSpectrum) that is yielding the similarity normalized in the range of [0,1] of such two elements, so it can easily converted to the needed distances.

See also
  PeakSpectrumCompareFunctor.

## Function Documentation

## ◆ cluster()

void cluster | ( | std::vector< PeakSpectrum > & | data,
|  | const BinnedSpectrumCompareFunctor & | comparator,
|  | double | sz,
|  | UInt | sp,
|  | float | offset,
|  | const ClusterFunctor & | clusterer,
|  | std::vector< BinaryTreeNode > & | cluster_tree,
|  | DistanceMatrix< float > & | original_distance
| ) |  |

inline

clustering function for binned PeakSpectrum

A version of the clustering function for PeakSpectra employing binned similarity methods. From the given PeakSpectrum BinnedSpectrum are generated, so the similarity functor

See also
  BinnedSpectrumCompareFunctor can be applied.

Parameters

  data | vector of PeakSpectrum s to be clustered
  comparator | a BinnedSpectrumCompareFunctor
  sz | the desired binsize for the BinnedSpectrum s
  sp | the desired binspread for the BinnedSpectrum s
  offset | the desired bins offset for the BinnedSpectrum s
  clusterer | a clustermethod implementation, base class ClusterFunctor
  cluster_tree | the vector that will hold the BinaryTreeNodes representing the clustering (for further investigation with the ClusterAnalyzer methods)
  original_distance | the DistanceMatrix holding the pairwise distances of the elements in `data`, will be made newly if given size does not fit to the number of elements given in `data`

See also
  ClusterFunctor, BinaryTreeNode, ClusterAnalyzer, BinnedSpectrum, BinnedSpectrumCompareFunctor

References DistanceMatrix< Value >::clear(), DistanceMatrix< Value >::resize(), and DistanceMatrix< Value >::setValue().