Package org.forester.development

Class DevelopmentTools

  • public final class DevelopmentTools
extends java.lang.Object

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Phylogeny createBalancedPhylogeny​(int levels, int children_per_node)
      Creates a completely balanced rooted phylogeny with a given number of levels and children per node.
      static void intervalNumberSpecies​(Phylogeny t, int i)
      Sets the species name of the external Nodes of Phylogeny t to 1, 1+i, 2, 2+i, 3, 3+i, ....
      static void numberSpeciesInDescOrder​(Phylogeny t)
      Sets the species namea of the external Nodes of Phylogeny t to descending integers, ending with 1.
      static void numberSpeciesInOrder​(Phylogeny t)
      Sets the species namea of the external Nodes of Phylogeny t to ascending integers, starting with 1.
      static void randomizeSpecies​(int min, int max, Phylogeny t)
      Sets the species names of the external Nodes of Phylogeny t to a random positive integer number between (and including) min and max.

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • createBalancedPhylogeny

        public static Phylogeny createBalancedPhylogeny​(int levels,
                                                int children_per_node)
        Creates a completely balanced rooted phylogeny with a given number of levels and children per node.
        Parameters:
        levels -
        children_per_node -
        Returns:
        a completely balanced rooted phylogeny

      • intervalNumberSpecies

        public static void intervalNumberSpecies​(Phylogeny t,
                                         int i)
        Sets the species name of the external Nodes of Phylogeny t to 1, 1+i, 2, 2+i, 3, 3+i, .... Examples: i=2: 1, 3, 2, 4 i=4: 1, 5, 2, 6, 3, 7, 4, 8 i=8: 1, 9, 2, 10, 3, 11, 4, 12, ...

      • numberSpeciesInDescOrder

        public static void numberSpeciesInDescOrder​(Phylogeny t)
        Sets the species namea of the external Nodes of Phylogeny t to descending integers, ending with 1.

      • numberSpeciesInOrder

        public static void numberSpeciesInOrder​(Phylogeny t)
        Sets the species namea of the external Nodes of Phylogeny t to ascending integers, starting with 1.

      • randomizeSpecies

        public static void randomizeSpecies​(int min,
                                    int max,
                                    Phylogeny t)
        Sets the species names of the external Nodes of Phylogeny t to a random positive integer number between (and including) min and max.
        Parameters:
        t - whose external species names are to be randomized
        min - minimal value for random numbers
        max - maximum value for random numbers