Package pt.ist.phylolib.command.algorithm.gcp

Class CL

java.lang.Object
pt.ist.phylolib.command.algorithm.Algorithm
pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs
pt.ist.phylolib.command.algorithm.gcp.CL
All Implemented Interfaces:
ICommand<Matrix,​Tree>
public final class CL
extends GloballyClosestPairs
Responsible for calculating a phylogenetic tree from a distance matrix using the Complete-Linkage algorithm.

  • Nested Class Summary

    Nested classes/interfaces inherited from interface pt.ist.phylolib.command.ICommand

    ICommand.IGetter<T>

  • Field Summary

    Fields inherited from interface pt.ist.phylolib.command.ICommand

    COMMAND, FINISHED, STARTED, UNUSED

  • Constructor Summary

    Constructors 
    Constructor Description
    CL()  

  • Method Summary

    Modifier and Type Method Description
    protected double dissimilarity​(double ij, double ik, double jk, int ci, int cj)
    Calculates the dissimilarity between a given previously existing node and a given node created by joining two existing nodes.

    Methods inherited from class pt.ist.phylolib.command.algorithm.gcp.GloballyClosestPairs

    process

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface pt.ist.phylolib.command.ICommand

    init

  • Constructor Details

    • CL

      public CL()

  • Method Details

    • dissimilarity

      protected double dissimilarity​(double ij, double ik, double jk, int ci, int cj)
      Description copied from class: GloballyClosestPairs
      Calculates the dissimilarity between a given previously existing node and a given node created by joining two existing nodes.
      Specified by:
      dissimilarity in class GloballyClosestPairs
      Parameters:
      ij - the distance between the two existing nodes that were joined
      ik - the distance between one of the nodes that was joined and the previously existing node
      jk - the distance between another of the nodes that was joined and the previously existing node
      ci - the number of elements in the cluster of one of the nodes that were joined
      cj - the number of elements in the cluster of another of the nodes that were joined
      Returns:
      the dissimilarity between the previously existing node and the created node