Package pal.tree

Class 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
    • 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