Package pt.ist.phylolib.command.algorithm

Class Algorithm

java.lang.Object

pt.ist.phylolib.command.algorithm.Algorithm

All Implemented Interfaces:

ICommand<Matrix,Tree>

Direct Known Subclasses:

Edmonds, GloballyClosestPairs, GoeBURST, GoeBURSTFullMST, NeighbourJoining

public abstract class Algorithm
extends Object
implements ICommand<Matrix,Tree>

Responsible for calculating a phylogenetic tree from a distance matrix.

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
Algorithm()

Method Summary

Modifier and Type	Method	Description
void	configureRequiredDistanceScope(Options options)	Configures a scope that depends on user input before the matrix is loaded.
Tree	process(Matrix matrix)	Processes this command's input data into an output data.
protected abstract 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 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

Algorithm

public Algorithm()

Method Details

requiredDistanceScope

public DistanceScope requiredDistanceScope()

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

configureRequiredDistanceScope

public void configureRequiredDistanceScope(Options options)

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

process

public Tree process(Matrix matrix)

Description copied from interface: ICommand

Processes this command's input data into an output data.

Specified by:

process in interface ICommand<Matrix,Tree>

Parameters:

matrix - the input data of this command

Returns:

the output data resultant from processing the input data with this command

processImpl

protected abstract Tree processImpl(Matrix matrix)

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

Parameters:

matrix - the distance matrix

Returns:

the computed phylogenetic tree