SaitouNei

java.lang.Object

pt.ist.phylolib.command.algorithm.Algorithm

pt.ist.phylolib.command.algorithm.nj.NeighbourJoining

pt.ist.phylolib.command.algorithm.nj.SaitouNei

All Implemented Interfaces:: ICommand<Matrix,Tree>

public final class SaitouNei
extends NeighbourJoining

Responsible for calculating a phylogenetic tree from a distance matrix using the Neighbour Joining algorithm by Saitou and Nei.

Nested Class Summary

Nested classes/interfaces inherited from class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining
NeighbourJoining.Cluster

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

SaitouNei()

Method Summary

Modifier and Type	Method	Description
`protected double`	`lambda(NeighbourJoining.Cluster ci, NeighbourJoining.Cluster cj)`	Gets the proportion of a given cluster according to another.
`protected double`	`length(double distance)`	Gets the length corresponding to the given distance.
`protected int`	`weight(NeighbourJoining.Cluster i)`	Gets the weight of a given cluster.

Methods inherited from class pt.ist.phylolib.command.algorithm.nj.NeighbourJoining

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
- SaitouNei
  
  public SaitouNei()
Method Details
- weight
  
  protected int weight(NeighbourJoining.Cluster i)
  
  Description copied from class: NeighbourJoining
  
  Gets the weight of a given cluster.
  
  Specified by:
  
  weight in class NeighbourJoining
  
  Parameters:
  
  i - the cluster to get the weight from
  
  Returns:
  
  the weight of the cluster
- lambda
  
  protected double lambda(NeighbourJoining.Cluster ci, NeighbourJoining.Cluster cj)
  
  Description copied from class: NeighbourJoining
  
  Gets the proportion of a given cluster according to another.
  
  Specified by:
  
  lambda in class NeighbourJoining
  
  Parameters:
  
  ci - the cluster to get the proportion of
  
  cj - the cluster to take into account in the proportion
  
  Returns:
  
  the proportion of the cluster according to the other
- length
  
  protected double length(double distance)
  
  Description copied from class: NeighbourJoining
  
  Gets the length corresponding to the given distance.
  
  Specified by:
  
  length in class NeighbourJoining
  
  Parameters:
  
  distance - the distance to get the length of
  
  Returns:
  
  the length corresponding to the distance