Package pt.ist.phylolib.command.algorithm.goeburst

Class GoeBURST

java.lang.Object

pt.ist.phylolib.command.algorithm.Algorithm

pt.ist.phylolib.command.algorithm.goeburst.GoeBURST

All Implemented Interfaces:

ICommand<Matrix,Tree>

public class GoeBURST
extends 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, TIMING, UNUSED

Constructor Summary

Constructors

Constructor	Description
GoeBURST()

Method Summary

Modifier and Type	Method	Description
void	configureRequiredDistanceScope(Options options)	Configures a scope that depends on user input before the matrix is loaded.
void	init(Context context, Options options)	Initializes this command with the given context and options.
protected Tree	processImpl(Matrix matrix)	Processes the matrix to create a phylogenetic tree.
DistanceScope	requiredDistanceScope()	Declares the distance scope this algorithm needs.

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

process

Methods inherited from class java.lang.Object

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

Constructor Details

GoeBURST

public GoeBURST()

Method Details

requiredDistanceScope

public DistanceScope requiredDistanceScope()

Description copied from class: Algorithm

Declares the distance scope this algorithm needs. Complete is the conservative default until an algorithm proves a bounded scope.

Overrides:

requiredDistanceScope in class Algorithm

configureRequiredDistanceScope

public void configureRequiredDistanceScope(Options options)

Description copied from class: Algorithm

Configures a scope that depends on user input before the matrix is loaded. Most algorithms have a fixed requirement and do nothing here.

Overrides:

configureRequiredDistanceScope in class Algorithm

init

public void init(Context context,
 Options options)

Description copied from interface: ICommand

Initializes this command with the given context and options.

Parameters:

context - the current context of the program

options - the options for this command

processImpl

protected Tree processImpl(Matrix matrix)

Description copied from class: Algorithm

Processes the matrix to create a phylogenetic tree. Subclasses should implement their specific algorithm logic here.

Specified by:

processImpl in class Algorithm

Parameters:

matrix - the distance matrix

Returns:

the computed phylogenetic tree