Package org.biojava.nbio.core.util

Class SingleLinkageClusterer

java.lang.Object
org.biojava.nbio.core.util.SingleLinkageClusterer
public class SingleLinkageClusterer extends Object
An implementation of a single linkage clusterer See http://en.wikipedia.org/wiki/Single-linkage_clustering
Author:
Jose Duarte

  • Constructor Details

    • SingleLinkageClusterer

      public SingleLinkageClusterer(double[][] matrix, boolean isScoreMatrix)
      Constructs a new SingleLinkageClusterer Subsequently use getDendrogram() to get the full tree or getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure. A copy must be made before by the user if needing to use the original matrix further.
      Parameters:
      matrix - the distance matrix with distance values in j>i half, all other values will be ignored
      isScoreMatrix - if false the matrix will be considered a distance matrix: lower values (distances) mean closer objects, if true the matrix will be considered a score matrix: larger values (scores) mean closer objects
      Throws:
      IllegalArgumentException - if matrix not square

  • Method Details

    • getDendrogram

      public org.biojava.nbio.core.util.SingleLinkageClusterer.LinkedPair[] getDendrogram()
      Get the full dendrogram (size n-1) result of the hierarchical clustering
      Returns:

    • getClusters

      public Map<Integer,Set<Integer>> getClusters(double cutoff)
      Get the clusters by cutting the dendrogram at given cutoff
      Parameters:
      cutoff -
      Returns:
      Map from cluster numbers to indices of the cluster members