Package pal.tree

Class SimulatedAlignment.Factory

java.lang.Object
pal.tree.SimulatedAlignment.Factory
Enclosing class:
SimulatedAlignment

public static final class SimulatedAlignment.Factory extends Object
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model
  • Constructor Details

  • Method Details

    • generateAlignment

      public final SimulatedAlignment generateAlignment(Tree tree)
      Generate a simulated alignment based on input tree
      Parameters:
      tree - The tree, with branchlengths set appropriately.
      Throws:
      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:
      IllegalArgumentException - if trees units are not EXPECTED SUBSTITUTIONS, or UNKNOWN