pal.tree

Class SimulatedAlignment.Factory

java.lang.Object

pal.tree.SimulatedAlignment.Factory

Enclosing class:

SimulatedAlignment

public static final class SimulatedAlignment.Factory
extends java.lang.Object

A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model

Constructor Summary

Constructors

Constructor and Description
SimulatedAlignment.Factory(int sequenceLength, SubstitutionModel model)

Method Summary

Methods

Modifier and Type	Method and Description
SimulatedAlignment	generateAlignment(Tree tree) Generate a simulated alignment based on input tree
SimulatedAlignment[]	generateAlignments(Tree[] trees, AlgorithmCallback callback) Generate an array of simulated alignments based on an array of input trees

Methods inherited from class java.lang.Object

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

Constructor Detail

SimulatedAlignment.Factory

public SimulatedAlignment.Factory(int sequenceLength,
                          SubstitutionModel model)

Method Detail

generateAlignment

public final SimulatedAlignment generateAlignment(Tree tree)

Generate a simulated alignment based on input tree

Parameters:

tree - The tree, with branchlengths set appropriately.

Throws:

java.lang.IllegalArgumentException - if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN

generateAlignments

public final SimulatedAlignment[] generateAlignments(Tree[] trees,
                                      AlgorithmCallback callback)

Generate an array of simulated alignments based on an array of input trees

Parameters:

trees - The tree, with branchlengths set appropriately.

callback - An AlgorithmCallback for monitoring progress and premature stopping

Throws:

java.lang.IllegalArgumentException - if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN