Class SuffixTreeKernel

java.lang.Object
org.biojava.stats.svm.tools.SuffixTreeKernel
All Implemented Interfaces:
Serializable, SVMKernel

public class SuffixTreeKernel extends Object implements SVMKernel, Serializable
Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.

This implementation allows you to scale the sub-space for each word length independently.

Author:
Matthew Pocock
See Also:
  • Constructor Details

  • Method Details

    • getDepthScaler

      Retrieve the current DepthScaler.
      Returns:
      the current DepthScaler
    • setDepthScaler

      public void setDepthScaler(SuffixTreeKernel.DepthScaler depthScaler)
      Change the current DepthScaler to depthScaler.
      Parameters:
      depthScaler - the new DepthScaler to use
    • evaluate

      public double evaluate(Object a, Object b)
      Calculate the dot product between the SuffixTrees a and b.

      This is the sum of the dot products of each subspace for a given word length. Each subspace is scaled using the DepthScaler returned by getDepthScaler.

      Specified by:
      evaluate in interface SVMKernel
      Parameters:
      a - the first Object
      b - the second Object
      Returns:
      a.b
    • toString

      public String toString()
      Overrides:
      toString in class Object