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Interface Summary | |
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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 | |
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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. |
MCLEfficiencyCalculator | 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 ). |
MCLParameters | Represents a set of parameters for MCL clustering . |
Enum Summary | |
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HierarchicalLinkage | Linkage methods for hierarchical agglomerative clustering |
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