Package pt.ist.phylolib.command.algorithm.nj

Class 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, TIMING, 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

processImpl

Methods inherited from class pt.ist.phylolib.command.algorithm.Algorithm

configureRequiredDistanceScope, process, requiredDistanceScope

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