Package org.biojava.nbio.alignment.template

Interface HierarchicalClusterer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,​C extends org.biojava.nbio.core.sequence.template.Compound>

  • Type Parameters:
    S - each Sequence in the tree is of type S
    C - each element of a Sequence is a Compound of type C
    public interface HierarchicalClusterer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,​C extends org.biojava.nbio.core.sequence.template.Compound>
    Defines a clustering algorithm that converts a distance matrix into a tree.
    Author:
    Mark Chapman

    • Method Detail

      • getDistanceMatrix

        float[][] getDistanceMatrix()
        Returns the distance matrix used in clustering. May be calculated from another original source.
        Returns:
        the distance matrix input to clustering

      • getRoot

        GuideTreeNode<S,​C> getRoot()
        Returns the root node of the tree resulting from this clustering algorithm.
        Returns:
        the resulting tree output from clustering