Package methods.clustering

Interface Summary
Clusterer Common interface implemented by clustering methods which take a ProteinNetwork as input and return a set of clusters calculated on that similarity network.
 

Class Summary
HierarchicalClusterer Wrapper for HierarchicalClusteringTrees which implements the Clusterer interface.
HierarchicalClusteringTrees Implements hierarchical agglomerative clustering in O(n2) time and space complexity.
HierarchicalTreeNode Represents one node of the tree generated by hierarchical agglomerative clustering.
MarkovClusterer Performs clustering using the Markov Cluster Algorithm as proposed in the PhD thesis Graph Clustering by Flow Simulation by Stijn van Dongen.
MCLParameters Represents a set of parameters for MCL clustering.
MCLPerfomanceCalculator Calculates the quality of a clustering using a given scores network according to the method proposed in the PhD of Stijn van Dongen (for a reference see: MarkovClusterer).
 

Enum Summary
HierarchicalLinkage Linkage methods for hierarchical agglomerative clustering